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VNMR 6.1C User Programming

1. short word status word short word short word long word spare for block header spare spare spare 2D f 2 left phase 2D f2 right float word float word Main data block header mode bits 0 15 Bits 0 3 bit 3 is currently unused 0 __PHMODE 0x1 P_AVMODE 0x2 2 P_PWRMODE 0x4 Bits 4 7 bit 7 is currently unused 4 _PHMODE 0x10 F_AVMODE 0x20 _PWRMODE 0x40 Bits 8 11 bit 11 is currently unused I_PHMODE 0x100 I_AVMODE 0x200 10 I_PWRMODE 0x400 Bits 12 15 bit 15 is currently unused 12 12_PHMODE 0x8 13 I2_AVMODE 0x100 14 I2_PWRMODE 0x2000 phase spare spare 1 ph mode 1 av mode 1 pwr mode 1 ph mode 1 av mode 1 pwr mode 1 ph mode 1 av mode 1 pwr mode 1 ph mode 1 av mode 1 pwr mode Usage bits for additional block headers hypercmplxbhead status U_HYP ERCOMP LEX 0x2 1 hypercomplex block structure The actual FID data is typically stored as pairs of integers in either 16 bit format or 32 bit format The first integer represents the real part of a complex pair or the X channel from the perspective of quadrature detection the second integer represents the imaginary component or the Y channel In phase sensitive 2D experiments X and Y 01 999165 00 A0800 VNMR 6 1C User Programming 287 Chapter 5 Parameters and Data experiments are si
2. Patterns are read in scaled according to their respective amplitudes rotated into x y and z patterns rescaled converted to DAC values and written out to temporary files shapedgradient_x shapedgradient_y and shapedgradient_z in the users shapelib directory and set with their corresponding shapedgradient statements If an axis does not have a pattern use empty quotes to indicate a null pattern The patterns must have the same number of points or an integral multiple number of points The pulse sequence generation aborts if the DACs on a particular gradient are overrun after the angles and amplitude have been resolved patil pat2 pat 3 are names of gradient shapes Note that the VNMR 5 1 and 5 2 software releases used only one pattern in the argument list width is the length of the gradient in seconds lv11 1v12 1v13 are gradient values in gauss cm psi is an Euler angle in degrees with a range of 90 to 90 phi is an Euler angle in degrees with the range 180 to 180 theta is an Euler angle in degrees with the range 90 to 90 loops is the number of times from 1 to 255 to loop the waveform wait is a keyword either WAIT or NOWAIT that selects whether or not a delay is inserted to stop until the gradient has completed before executing the next statement WAIT or NOWAIT adds extra pulse sequence programming flexibility for imaging experiments It allows performing other pulse s
3. The decstepsize dec2stepsize dec3stepsize and obsstepsize statements are similar to the stepsize statement but have the channel selection fixed Each of the following pairs of statements are functionally the same e obsstepsize base and stepsize base OBSch e decstepsize base and stepsize base DECch e dec2stepsize base and stepsize base DEC2ch e dec3stepsize base and stepsize base DEC3ch On systems with Output boards only see page 72 for the types of boards if the product of the base and multiplier is greater than 90 the sub 90 part is set by the 01 999165 00 A0800 VNMR 6 1C User Programming 87 Chapter 2 Pulse Sequence Programming 88 xmtrphase dcplrphase dcplr2phase or dcplr3phase statements Carryovers that are multiples of 90 are automatically saved and added in at the time of the next 90 phase selection e g at the time of the next pulse or decpulse This is true even if stepsize has not been used and base is at its default value of 90 The following example may help you to understand this question of carryovers obsstepsize 60 0 set 60 step size for obs xmtr initval 6 0 vl modn ct vl v2 v2 012345012345 xmtrphase v2 phase 0 60 120 180 240 300 small angle part 0 60 30 0 60 30 carry over 0 0 90 180 180 270 mod4 ct v3 pulse pw v3 specified phase 0 90 180 270 90 phase shift actually used 0
4. VNMR User Programming 0800 ave VARIAN VNMR User Programming VNMR 6 1C Software Pub No 01 999165 00 Rev A0800 Revision history A0500 Initial release for VNMR 6 1C Applicability of manual UNITYTNOVA MERCURY VxWorks Powered shortened to MERCURY VX throughout this manual MERCURY UNITYplus GEMINI 2000 UNITY and VXR S NMR spectrometer systems with VNMR 6 1C software installed Technical contributors Dan Iverson Frits Vosman Matt Howitt Greg Brissey Hung Lin Debbie Mattiello Evan Williams Technical writers Michael Carlisle Dan Steele Mike Miller Technical editor Dan Steele Copyright 2000 by Varian Inc 3120 Hansen Way Palo Alto California 94304 http www varianinc com All rights reserved Printed in the United States The information in this document has been carefully checked and is believed to be entirely reliable However no responsibility is assumed for inaccuracies Statements in this document are not intended to create any warranty expressed or implied Specifications and performance characteristics of the software described in this manual may be changed at any time without notice Varian reserves the right to make changes in any products herein to improve reliability function or design Varian does not assume any liability arising out of the application or use of any product or circuit described herein neither does it convey any license under its patent rights nor the rights of
5. 01 999165 00 A0800 VNMR 6 1C User Programming 233 Chapter 3 Pulse Sequence Statement Reference CAUTION On systems with linear amplifiers be careful when using values of power greater than 49 about 2 watts Performing continuous decoupling or long pulses at power levels greater than this can result in damage to the probe Use config to set a safety maximum for the tpwr dpwr dpwr2 and dpwr3 parameters Examples pulsesequence double newpwr newpwr getval newpwr initval newpwr v2 power v2 OBSch Related decpower Change first decoupler power linear amplifier systems dec2power Change second decoupler power linear amplifier systems dec3power Change third decoupler power linear amplifier systems initval Initialize a real time variable to a specified value obspower Change observe transmitter power linear amplifier systems pwrf Change transmitter or decoupler fine power rlpower Change transmitter or decoupler power linear amplifier rlpwrf Set transmitter or decoupler fine power pulse Pulse observe transmitter with amplifier gating Syntax pulse width phase double width pulse length in sec codeint phase real time variable for phase Description Turns on a pulse the same as the rgpulse width phase RG1 RG2 statement but with RG1 and RG2 set to the parameters rof1 and rof2 respectively Thus pulse is a special case of rgpulse where the hidden parameters rof1 and rof2 rem
6. decpwrf Set first decoupler fine power dec2pwrf Set second decoupler fine power dec3pwrf Set third decoupler fine power ipwrf Change transmitter or decoupler fine power with IPA ipwrm Change transmitter or decoupler linear modulator power obspwrf Set observe transmitter fine power rlpwrm Set transmitter or decoupler linear modulator power R revrofft Syntax Turn off receiver gate and amplifier blanking gate revroff 01 999165 00 A0800 VNMR 6 1C User Programming 235 Chapter 3 Pulse Sequence Statement Reference Description Related revron Syntax Description Related readuserap Applicability Syntax Description On UN TYINOVA and GEMINI 2000 systems the receiver is normally off during the pulse sequence and iis turned on only during acquisition On other systems rcvroff provides explicit receiver gating in the pulse sequence The rcvroff statement also unblanks or enables the observe transmitter Receiver gating is normally controlled automatically by decpulse decrgpulse dec2rgpulse dec3rgpulse obspulse pulse and rgpulse At the end of each of these statements the receiver is automatically turned back on if and only if the receiver has not been previously turned off explicitly bya rcvroff statement In all cases the receiver is implicitly turned back on immediately prior to data acquisition revron Turn on receiver gate and amplifier blanking gate recoff Turn off rece
7. Functions the same as the decpulse statement but generates interactive parameter adjustment IPA information when gf or go acqi is typed idecpulse is the same as decpulse if go is typed width is the duration in seconds of the pulse phase is the phase of the pulse It must be a real time variable v1 to v14 oph etc or a real time constant zero one etc label1 is the short character string to be given to the slider when displayed in the Acquisition window acqi program idecpulse pp vl decpul idecpulse pp v2 pp decpulse Pulse the decoupler transmitter 01 999165 00 A0800 VNMR 6 1C User Programming 201 Chapter 3 Pulse Sequence Statement Reference idecrgpulse Applicability Syntax Description Arguments Examples Related idelay Applicability Syntax Description Arguments Examples Related ifzero Syntax Description Pulse first decoupler with amplifier gating and IPA All systems except MERCURY VX MERCURY and GEMINI 2000 idecrgpulse width phase RG1 RG2 label double width pulse width in sec codeint phase real time variable for phase double RG1 gating delay before pulse in sec double RG2 gating delay after pulse in sec char label slider label in acqi Works similar to the decrgpulse statement but generates interactive parameter adjustment IPA information when gf or go acqi is typed idecrgpulse
8. delay time Delay specified time hsdelay time Delay specified time with possible hs pulse idelay time string Delay specified time with IPA incdelay count index Set real time incremental delay initdelay time_increment index Initialize incremental delay vdelay timebase count Set delay with fixed timebase and real time count The main statement to create a delay in a pulse sequence for a specified time is the statement delay time where time is a real number e g delay d1 The hsdelay and idelay statements are variations of delay e To add a possible homospoil pulse to the delay use hsdelay time If the homospoil parameter hs is set to y then at the beginning of the delay hsdelay inserts a homospoil pulse of length hst seconds Although homospoil is not available 01 999165 00 A0800 VNMR 6 1C User Programming 79 Chapter 2 Pulse Sequence Programming 80 on the GEMINI 2000 the hsde lay statement can still be used for a delay on GEMINI 2000 systems e To cause interactive parameter adjustment IPA information to be generated when gf or go acqi is entered use idelay time string where string is the label used in acqi If go is entered idelay is the same as delay See Using Interactive Parameter Adjustment page 120 for details on IPA IPA and idelay are not available on the MERCURY VX MERCURY and GEMINI 2000 To set a delay to the product of a fixed timebase and a real time count
9. For the amplifiers associated with the first second and third decouplers decblank and decunblank dec2blank and dec2unblank and dec3blank and dec3unblank respectively These statements replace blankon and blankoff no longer in VNMR e On MERCURY VX and MERCURY the receiver and amplifier are linked At the end of each pulse statement the receiver is automatically turned back on and the amplifier blanked Immediately prior to data acquisition the receiver is implicitly turned back on e On UNITYplus the receiver is linked to the observe amplifier The statements to blank and unblank amplifiers on the Y TYINOVA also apply to the UNITYplus e On UNITY and VXR S the receiver is linked to both amplifiers At the end of each pulse statement if and only if the receiver has not been previously turned off explicitly by a rcvroff statement the receiver is automatically turned back on and the amplifier blanked Immediately prior to data acquisition the receiver is implicitly turned back 96 VNMR 6 1C User Programming 01 999165 00 A0800 2 3 Spectrometer Control on and the amplifier off UNITY and VXR S systems use the obsunblank and decunblank statements to unblank the amplifiers e On GEMINI 2000 the receiver and amplifier are not linked The receiver is turned on just before the acquisition and turned off during the rest of the pulse sequence however the blankingon andblankingoff statements blank
10. Related rotorperiod Applicability obspower Change observe transmitter power linear amplifier systems power Change transmitter or decoupler power linear amp sys rlpwrf Set transmitter or decoupler fine power Set transmitter or decoupler fine power Systems with fine power control Not available on MERCURY VX MERCURY and GEMINI 2000 systems This statement is due to be eliminated in future versions of VNMR software Although it is still functional you should not write any new pulse sequences using it and should replace it in existing sequences with obspwrf decpwrf dec2pwrf or dec3pwrf as appropriate rlpwrf power device double power new level for fine power int device OBSch DECch DEC2ch or DEC3ch Changes transmitter or decoupler fine power the same as the pwrf statement except rlpwrf uses a real number variable for the power level desired instead of consuming a real time variable for the level power is the fine power desired device is OBSch observe transmitter or DECch first decoupler For the UNITYINOVA and UNITYplus only device can also be DEC2ch second decoupler or DEC3ch third decoupler rlpwrf 4 0 OBSch decpwrf Set first decoupler fine power dec2pwrf Set second decoupler fine power dec3pwrf Set third decoupler fine power ipwrf Change transmitter or decoupler fine power with IPA obspwrf Set observe transmitter fine power power Change transmitter or
11. getarray Retrieves all values of an arrayed parameter poffset_list Set frequency from position list position_offset Set frequency based on position Change power level linear amplifier systems Systems with linear amplifiers Not available on GEMINI 2000 systems Use of statements obspower decpower dec2power or dec3power as appropriate is preferred power power device int power new value for coarse power control int device OBSch DECch DEC2ch or DEC3ch Changes transmitter or decoupler power by assuming values of 0 minimum power to 63 maximum power on channels with a 63 dB attenuator or 16 minimum power to 63 maximum power on channels with a 79 dB attenuator On systems with an Output board by default power statements are preceded internally by a 0 2 us delay see the apovrride statement for more details power is the power desired It must be stored in a real time variable v1 v14 etc which means it cannot be placed directly in the power statement This allows the power to be changed in real time or from pulse to pulse Setting the power argument is most commonly done using initval see example below To avoid consuming a real time variable use the rlpower statement instead of the power statement device is OBSch observe transmitter or DECch first decoupler For the UNITYTNOVA and UNITYplus only device can also be DEC2ch second decoupler or DEC3ch third decoupler
12. set addExp id addExp set addExp label Add Entry set addExp rtoutput write alpha loc Sloc val set addExp rtoutput2 write alpha info written to file filenan If any variables are included in the value of the attribute the value must be enclosed in braces Adding a Control Button that Sends a Command to VNMR A control button can be made that sends a command to VNMR when the button is selected For example to add a he11o button to the bottom of the Sample Entry Form window add hello button to the cnt rls line and then define the button in the enter conf file The control buttons have access a variable filename that is the name of the file where the output from the enter program will be written set cntrls addExp saveAndExit quit hello set hello id vnmrexec set hello label hello set hello rtoutput banner hello The id attribute must be vnmrexec and the rtoutput attribute will be sent to VNMR If any variables are included in the value of the attribute the value must be enclosed in braces Using radio and check with set_rtoutout and unset_rtoutput Attributes Selections of type radio and check have optional attributes set_rtoutput and unset_rtoutput These attributes are magical commands that will be sent to VNMR when the button is selected and deselected respectively The value of the attribute can include any other attribute from that group VNMR 6 1C User
13. Description Unblanks or enables both amplifier channels Related blankingon Blank amplifier channels and turn amplifiers off blankingon Blank amplifier channels and turn amplifiers off Applicability MERCURY VX MERCURY and GEMINI 2000 systems only Syntax blankingon Description Blanks or disables both amplifier channels Related blankingoff Unblank amplifier channels and turn amplifiers on blankoff Stop blanking observe or decoupler amplifier obsolete Description No longer in VNMR The blankoff statement is replaced by the statements obsunblank decunblank dec2unblank and dec3unblank Related decunblank Unblank amplifier associated with first decoupler dec2unblank Unblank amplifier associated with second decoupler dec3unblank Unblank amplifier associated with third decoupler obsunblank Unblank amplifier associated with observe transmitter 164 VNMR6 1C User Programming 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference blankon Start blanking observe or decoupler amplifier obsolete Description No longer in VNMR The blankon statement is replaced by the statements obsblank decblank dec2blank and dec3blank Related decblank Blank amplifier associated with first decoupler dec2blank Blank amplifier associated with second decoupler dec3blank Blank amplifier associated with third decoupler obsblank Blank amplifier associated with observe transmitter clearapdatatable Zero all data in acquisitio
14. Pulse decoupler transmitter with amp gating Pulse first decoupler with amplifier gating Pulse second decoupler with amplifier gating Pulse third decoupler with amplifier gating Pulse deuterium decoupler with amplifier gating Pulse first decoupler transmitter with IPA Pulse first decoupler with amplifier gating and IPA Use decpulse width phase to pulse the decoupler in the pulse sequence at its current power level width is the time of the pulse in seconds and phase is a real time variable for the phase of the pulse e g decpulse pp v3 The amplifier is gated on during decoupler pulses as it is during observe pulses The amplifier gating times see RG1 and RG2 for decrgpulse below are internally set to zero The decoupler modulation mode parameter dmm should be c during any period of time in which decoupler pulses occur To pulse the decoupler at its current power level and have user settable amplifier gating times use decrgpulse width phase RG1 RG2 where width and phase are the same as used with decpulse and RG1 and RG2 are the same as used with the rgpulse statement for observe transmitter pulses In fact decrgpulse is syntactically equivalent to rgpulse and functionally equivalent with two exceptions e The decoupler is pulsed at its current power level instead of the transmitter e If homo n the slow gate 100 ns switching time on N YINOVA or UNITYplus 1 to 3 us switching time on other systems on
15. Pulse sequences can be written that require the user to recognize this difference or more elegantly a mathematical transformation within the pulse sequence can allow the user to enter normal values that are then reversed by the pulse sequence The transformation approach is recommended for writing pulse sequences For example assume that you want to have a parameter shapepwr that sets the overall power of the shaped pulse with the third attenuator while using the standard attenuator to apply the shape The relevant part of the pulse sequence might look like this double shapepwr shapepwr 63 getval shapepwr initval shapepwr v1l0 pwrf v10 O0BSch This method allows the user to enter 0 to get minimum power and 63 to get maximum power just as with tpwr and dpwr and reverses the sense of the parameter within the pulse sequence where the user need not be concerned with it Notice that the only thing different about this sequence is the 63 added before the get val everything else in this example would be required in any case 2 12 Internal Hardware Delays 142 Many pulse sequence statements result in hidden delays These delays are not intrinsic to pulse sequence generation PSG software but are rather internal to the hardware Each AP bus instruction is considered a FIFO event and incurs the following delay which is the time it takes to set the hardware on the AP bus e On UNTYINOVA 0
16. Related create_delay_list Create table of delays create_freq_list Create table of frequencies getarray Retrieves all values of an arrayed parameter delay Delay for a specified time voffset Select frequency offset from table D dbl Double an integer value Syntax dbl vi vj codeint vi variable for starting value codeint vj variable for twice starting value Description Sets vj equal to twice the integer value of vi Arguments vi and vj are real time variables v1 to v14 oph etc Examples dbl v1 v2 Related add Add integer values assign Assign integer values decr Decrement an integer value divn Divide integer values hiy Half the value of an integer incr Increment an integer value mod2 Find integer value modulo 2 mod4 Find integer value modulo 4 modn Find integer value modulo n mult Multiply integer values sub Subtract integer values dcphase Set decoupler phase obsolete Description No longer supported Replace dcphase statements with the decphase statement Related decphase Set phase of first decoupler 168 VNMR 6 1C User Programming 01 999165 00 A0800 dcplrphase Applicability Syntax Description Arguments Examples Related dcplr2phase Applicability Syntax Description Chapter 3 Pulse Sequence Statement Reference Set small angle phase of 1st decoupler rf type C or D Systems using a first decoupler with rf type C or D and MERCURY VX and MERCU
17. channel loops wait char pattern name of shape text file double width length of pulse double amp amplitude of pulse char channel gradient channel x y or z int loops number of loops int wait WAIT or NOWAIT Syntax 12 dps_show Sshaped2Dgradient pattern width amp channel loops wait tag char pattern name of shape text file double width length of pulse double amp amplitude of pulses char channel gradient channel x y or z int loops number of loops int wait WAIT or NOWAIT int tag unique number for gradient element Description Draws for dps graphical display the pulses lines and labels related to the statement if it exists given as the first argument e Syntax 1 draws a line to represent a delay e Syntax 2 draws a pulse picture and display a label underneath the picture e Syntax 3 draws the picture of a shaped pulse and displays a label underneath the picture e Syntax 4 draws observe and decoupler pulses at the same time e Syntax 5 draws a shaped pulse for observe and decoupler channels at the same time e Syntax 6 draws observe decoupler and second decoupler pulses at the same time e Syntax 7 draws a shaped pulse for observe decoupler and the second decoupler channels at the same time e Syntax 8 draws a pulse on the z channel e Syntax 9 draws a pulse on the specified channel
18. delta_t dwell time user written part The variable wt pnt r is a pointer and must be dealt with differently than an ordinary variable such as delta_t wtpntr contains the address in memory of the first element of the user calculated weighting vector wtpntr_ is the value of that first element The statement wt pnt r x implies that wtpnt r is set equal to x and the pointer wtpntr is subsequently incremented to the address of the next element in the weighting vector The following examples show using the filename program set by wt file filename e Source file filename c inauser s vnmrsys wt1lib directory include weight h wtcalc wtpntr npoints delta_t int npoints number of complex data points float wtpntr pointer to weighting vector delta_t dwell time 308 VNMR 6 1C User Programming 01 999165 00 A0800 5 6 User Written Weighting Functions int i for i 0 i lt npoints i wtpntr float exp delta_t i wtconst 0 wtconst 0 to wtconst 9 are 10 internal weighting parameters with default values of 1 and type float e Optional parameter file filename wtp in the current experiment directory 0 35 value placed in wtconst 0 2 4 value placed in wtconst 1 etc e Text file filename in the current experiment directory 0 9879 value of first weighting vector element 0 8876 value of second weighting vector element 0
19. griserate trise gradstepsz 3 2 PARAMETER READ IN FROM EXPERIMENT Initialize a real time variable to specified value initval number vi double number value to use for initialization codeint vi variable to be initialized Initializes a real time variable with a real number The real number input is rounded off and placed in the variable vi Unlike add sub etc initval is executed once and only once at the start of a non arrayed 1D experiment or at the start of each increment in an n dimensional or an arrayed experiment not at the start of each transient this must be taken into account in pulse sequence programming as seen in the example below number is the real number from 32768 0 to 32767 0 to be placed in the real time variable Entering a value less than 32768 0 after rounding off results in using 32768 and entering a value greater than 32767 0 after rounding off results in using 32767 vi is the real time variable v1 to v14 etc to be initialized 1 initval nt v8 2 ifzero ct assign v8 v7 j elsenz ct decr v7 endif ct elsenz Execute succeeding statements if argument is nonzero ifzero Execute succeeding statements if argument is zero loop Start loop Pulse observe transmitter with IPA All systems except MERCURY VX MERCURY and GEMINI 2000 iobspulse label char label slider label in acqi Functions the same as obspulse except iob
20. int mode SLI_SET SLI_OR SLI_AND SLI_XOR unsigned value bit pattern Sets lines on the SLI board It has no return value The board contains 32 TTL compatible logic signals that can be set by these functions Each line has an LED indicator and a 100 ohm series resistor for circuit protection The lines are accessible through the 50 pin ribbon connector J4 on the front edge of the SLI board The pin assignments are as follows e Pins 1 and 49 area 5 V supply through 100 ohm series resistor enabled by installing jumper J3L e Pins 3 to 10 control bits 0 to 7 e Pins 12 to 19 control bits 8 to 15 e Pins 21 to 28 control bits 16 to 23 e Pins 41 to 48 control bits 24 to 31 e Pins 2 11 20 29 40 and 50 are ground sli has a pre execution delay of 10 950 us but no post execution delay The delay is composed of a 200 ns startup delay with 5 AP bus cycles 1 AP bus cycle 2 150 us The logic levels on the SLI lines are not all set simultaneously The four bytes of the 32 bit word are set consecutively the low order byte first The delay between setting of consecutive bytes is 1 AP bus cycle 100 ns This 100 ns timing jitter is non cumulative 01 999165 00 A0800 VNMR 6 1C User Programming 255 Chapter 3 Pulse Sequence Statement Reference Arguments Examples Related sp off Applicability Syntax Description The error message Illegal mode nis caused by the mode argument not being one of SLI_
21. 126 127 set autoSample id autoSample 128 set autoSample label Add Sample 129 130 set autoSampleNoExit id autoSampleNoExit 131 set autoSampleNoExit label Add Sample 132 133 set priortySample id priortySample 134 set priortySample label Priority Sample 135 set priortySample passwd 136 137 set quit id quit 138 set quit label Quit 139 140 list of files from which excluded locations are taken 141 the files names are relative to the directory of the enter file 142 set exList 143 set locList 144 145 show and edit can be yes or no 146 content can be all or new 147 num sets the number of entries to be shown in the scrolling window 148 col sets the width of the scrolling window in characters 149 set results show no 150 set results edit no 151 set results content all 152 set results num 3 153 set results col 60 Setting Which Selections Are Displayed On line 6 the infields parameter specifies which selections are displayed by enter and in what order The default requests five selections named loc user solvent exp and text field Most of the names chosen are arbitrary but as you will see subsequent definitions depend on the names set here Also while names such as x j and k1d could also work their meaning is not obvious You might however want to add a name such as notebook We use notebook as an example later in this chapter Note
22. After each button action is complete the Pulse Sequences Entry Main Menu page 66 is displayed Button PW Pl 2PW 2P1 Other Return Description Add a pulse pw at this point in the sequence Add a pulse p1 at this point in the sequence Add a pulse 2 pw at this point in the sequence Add a pulse 2 p1 at this point in the sequence Show prompt Input Name of Pulse and add name you enter as a pulse at this point in the sequence Display Pulse Sequence Entry Main Menu page 66 without adding a pulse at this point in the sequence Pulse Sequence Entry Decoupler Pulses Menu The Pulse Sequence Entry Decoupler Menu is typically entered by selecting DecPulse in the Pulse Sequence Entry Main Menu or by menu psg_decpulse After each button action is complete the Pulse Sequences Entry Main Menu page 66 is displayed Button PP 2PP Other Return Description Add a decoupler pulse pp at this point in the sequence Add a decoupler pulse 2 pp at this point in the sequence Show prompt Input Name of Pulse and add the name you enter as a decoupler pulse at this point in the sequence Display Pulse Sequence Entry Main Menu page 66 without adding a decoupler pulse at this point in the sequence Pulse Sequence Entry Status Menu The Pulse Sequence Entry Status Menu is typically entered by selecting Status in the Pulse Sequence Entry Main Menu or by entering menu psg_status After each
23. Arguments Examples Related vscan Applicability Syntax Description Arguments Examples dps_show Draw delay or pulses in a sequence for graphical display getorientation Read image plane orientation rgradient Set gradient to specified level shapedgradient Provide shaped gradient pulse to gradient channel shaped2Dgradient Generate arrayed shaped gradient pulse shapedvgradient Generate dynamic variable shaped gradient pulse zgradpulse Create a gradient pulse on the z channel Select frequency offset from table Not applicable on MERCURY VX MERCURY and GEMINI 2000 voffset list_number vindex int list_number number of list codeint vindex real time or AP table variable Provides a means of indexing into previously created frequency offset lists using a real time variable or an AP table The indexing into the list is from 0 to N 1 where N is the number of items in the list The offset table has to have been created with the create_offset_list statement It has no return value list _number is the number between 0 and 255 for each list This number must match the 1ist_number used when creating the table vindex is a real time variable v1 to v14 or an AP table t1 to t 60 See the example for the vdelay statement reate offset list Create table of frequency offsets vdelay Select delay from table vfreq Select frequency from table Provide dynamic variable scan Systems with imaging capabilit
24. Create gradient pattern file init_gradpattern pattern_name gradpat_struct nsteps name of GID pattern file pointer to struct Gpattern number of steps in pattern amplitude of pattern step pattern step length in sec Creates and defines gradient patterns within a pulse sequence The patterns can be created by any algorithm as long as each pattern step is correctly put into the gradpat_struct argument The number of steps in the pattern also has to be furnished as an argument init_gradpattern saves the created pattern as a pattern file with a GRD suffix is appended to the name in the user s shapelib directory This statement has no return value pattern is the name of the pattern file without the GRD suffix gradpat_struct is the gradient structure that contains the pattern See the example for the init_rfpattern statement Pulse observe transmitter with amplifier gating Perform shaped pulse on observe transmitter Pulse observe and decouple channels simultaneously Perform simultaneous two pulse shaped pulse Applicability Syntax char pattern Gpattern gradpat_struct int nsteps typedef struct _Gpattern double amp double time Gpattern Description Arguments nsteps is the number of steps in the pattern Examples Related pulse shaped_pulse simpulse simshaped_pulse 206 VNMR 6 1C User Programming 01 999165 00 A0800 init_vscan Applicability Syntax Descript
25. In Listing 3 strings 1 through 6 contain a single command If one of these buttons is selected the command is executed and the same menu is reactivated String 7 however issues a page command and then a second command that changes to the display_1D menu The assumption here is that several of the choices through 6 may be made on a single plot but that once choice 7 is made the user is finished with this menu and wants to revert back to the parent menu Note the reverse quotation marks C in strings 7 and 8 which are converted to regular quotation marks when the string is executed The sample menu in Listing 4 illustrates additional features of menus Notice the new features in this menu e The clear command appears near the start of the file Executing clear 2 clears the graphics window Because this command is in the menu itself and not in any particular string it is executed each time the menu is activated e A number of comments are included in addition to the title these are perfectly permissible and are encouraged to make the statement action clearer 56 VNMR 6 1C User Programming 01 999165 00 A0800 1 5 Customizing the Menu System Listing 4 Typical Menu with Additional Features mlabel mstring clear 2 clear any spectrum from screen mlabel 1 No WT mstring 1 sb n sbs n lb n gf n gfs n awc n mlabel 2 Resolve mstring 2 resolv 0 1 0 3 noft gt ml
26. The pulse sequence generation aborts if the DACs on a particular gradient are overrun after the angles and amplitude have been resolved levell level2 level3 are gradient values in gauss cm obl_gradient 0 0 0 0 gss obl_gradient gro 0 0 0 0 oblique_gradient Execute an oblique gradient 01 999165 00 A0800 VNMR 6 1C User Programming 217 Chapter 3 Pulse Sequence Statement Reference oblique_gradientExecute an oblique gradient Applicability Syntax Description Arguments Examples Related Not applicable on MERCURY VX MERCURY and GEMINI 2000 oblique_gradient levell level2 level3 psi phi theta double levell level2 level3 gradient values in G cm double psi phi theta Euler angles in degrees Defines an oblique gradient with respect to the magnet reference frame It has no return value The gradient amplitudes level1 level2 level3 are put through a coordinate transformation matrix using psi phi and theta to determine the actual x y and z gradient levels These are then converted into DAC values and set with their corresponding gradient statements For more coordinate system information refer to the manual User Guide Imaging The pulse sequence generation aborts if the DACs on a particular gradient are overrun after the angles and amplitude have been resolved levell level2 level3 are gradient values in gauss cm psi is an Euler angle
27. decprgoff Applicability Syntax Description Related 176 VNMR 6 1C User Programming power Sets the power level by assuming values from 0 minimum power to 63 maximum power on channels with a 63 dB attenuator or from 16 minimum power to 63 maximum power on channels with a 79 dB attenuator decpower Change first decoupler power linear amplifier systems dec3power Change third decoupler power linear amplifier systems obspower Change observe transmitter power linear amplifier systems rlpower Change power level linear amplifier systems Change third decoupler power level linear amp systems UNITYTNOVA and UNITYplus systems with a third decoupler dec3power power double power new power level for DO3DEV Changes the third decoupler power It is functionally the same as rlpower value DO3DEV power Sets the power level by assuming values from 0 minimum power to 63 maximum power on channels with a 63 dB attenuator or from 16 minimum power to 63 maximum power on channels with a 79 dB attenuator decpower Change first decoupler power linear amplifier systems dec2power Change second decoupler power linear amplifier systems obspower Change observe transmitter power linear amplifier systems rlpower Change power level linear amplifier systems Change fourth decoupler power level linear amp systems UNITYTNOVA systems with a deuterium decoupler channel as the fourth decoupler
28. frequency For the observe channel this means that the phase of the transmitter and the receiver are linked That is a 60 phase shift of the observe transmitter during the course of the pulse sequence will also shift the receiver by 60 If this is not desirable it would again be possible simply to shift the phase by 60 after the last pulse but before the start of the acquisition A third point about phaseshift is the time factor The phase shift is created by shifting the frequency by a fixed amount for a variable time However the introduction of a time delay into a pulse sequence whose length would be variable depending upon the phase shift chosen would be in most cases undesirable Thus what we have done is to shift the frequency for a variable time then shift the frequency back followed by waiting for another variable time at the original frequency such that the total time of this combined operation is a constant This time has been chosen to be 30 us Thus whenever the pulse sequence statement phaseshift is encountered in a pulse sequence an implicit delay of 30 us occurs In many pulse sequences this has little consequence In cases involving spin echoes however it will be important to correct for this time The final point to understand is the step size Because of limitations on the timing in the system 25 ns for systems with the Acquisition Controller board or Pulse Sequence Controller board 0 1 us time resolution for sy
29. setdivnfactor t7 4 getelem Retrieve an element from an AP table loadtable Load AP table elements from table text file setautoincrement Set autoincrement attribute for an AP table setreceiver Associate the receiver phase cycle with an AP table settable Store an array of integers in a real time AP table Associate the receiver phase cycle with an AP table All systems except the GEMINI 2000 setreceiver table codeint table real time table variable Assigns the ct th element of a table to the receiver variable oph If multiple setreceiver statements are used in a pulse sequence or if the value of oph is changed by real time math statements such as assign add etc the last value of oph prior to the acquisition of data determines the value of the receiver phase table specifies the name of the table t 1 to t 60 setreceiver t18 getelem Retrieve an element from an AP table loadtable Load AP table elements from table text file setautoincrement Set autoincrement attribute for an AP table setdivnfactor Set divn return attribute and divn factor for AP table settable Store an array of integers in a real time AP table Set status of observe transmitter or decoupler transmitter All systems except MERCURY VX MERCURY and GEMINI 2000 setstatus channel on mode sync mod_freq int channel OBSch DECch DEC2ch or DEC3ch int on TRUE on or FALSE off char mode tata w
30. text label selected by user double width_of_obs pulse length in sec char label_of_dec text label selected by user double width_of_dec pulse length in sec char label_of_dec2 text label selected by user double width_of_dec2 pulse length in sec 7 dps_show sim3shaped_pulse label_of_obs width_of_obs label_of_dec width_of_dec label_of_dec2 width_of_dec2 char label_of_obs text label selected by user double width_of_obs pulse length in sec 01 999165 00 A0800 VNMR 6 1C User Programming 191 Chapter 3 Pulse Sequence Statement Reference char label_of_dec text label selected by user double width_of_dec pulse length in sec char label_of_dec2 text label selected by user double width_of_dec2 pulse length in sec Syntax 8 dps_show zgradpulse value delay double value amplitude of gradient on z channel double delay length of gradient in sec Syntax 9 dps_show rgradient channel value char channel fe UK Tey AL ty tat On Ve double value amplitude of gradient amplifier Syntax 10 dps_show vgradient channel intercept slope mult char channel gradient channel x y or Zt int intercept initial gradient level int slope gradient increment codeint mult real time variable Syntax 11 dps_show shapedgradient pattern width amp
31. 0 00 100 0 1 0 0 00 20 0 1 0 will result in an actual shape of 0 00 1023 0 10 0 100 0 1 0 0 00 102 30 L0 0 00 1023 0 100 0 100 0 1 0 or 0 00 1023 0 1 0 0 00 1023 0 20 0 100 0 1 0 0 00 204 60 dL 50 A shape with elements 0 00 1023 0 0 0 0 00 10 0 1 0 0 00 100 0 1 0 0 00 20 0 1 0 will result in an actual shape of 0 00 1023 0 10 0 1023 0 1 0 0 00 10 0 1 0 0 00 1023 0 100 0 1023 0 1 0 or 0 00 100 0 1 0 0 00 1023 0 20 0 1023 0 1 0 0 00 20 0 10 Decoupler Patterns Column Description Limits Default 1 Tip angle per element in degrees 0 to 500 1 resolution Required Phase limits No limit on magnitude 2 RF phase in degrees 0 5 resolution Required Amplitude 0 to scalable max max 4 Transmitter gate 0 1 0 gate off For example the first 8 elements after the comment lines of the file walt z16 DEC 270 0 180 0 360 0 0 0 180 0 180 0 270 0 0 0 90 0 180 0 180 0 0 0 360 0 180 0 180 0 0 0 In using the gate field in DEC patterns note the following e The waveform generator gate is OR ed with the output board gate This means that any time the output board gate is on the transmitter is on irrespective of any waveform generator gate 01 999165 00 A0800 VNMR 6 1C User Programming 133 Chapter 2 Pulse Sequence Programming e Ifa decoupler pattern is activated under status control using dmm p an implicit output board gate statement is added In this situation any Os or Is in the gate field of the
32. 1 second FT S_TRANSF 0x200 0 regular 1 transposed 11 S_NP 0x800 1 np dimension is active 12 S_NF 0x 1000 1 nf dimension is active 13 S_NI 0x2000 1 ni dimension is active 14 S_NI2 0x4000 1 ni2 dimension is active Block headers are defined by the following C specifications struct datablockhead Bach file block contains the following header short scale scaling factor short status status of data in block short index block index short mode mode of data in block long ctcount ct value for FID float lpval 2 2D f1 left phase in phasefile float rpval 2 2D f1 right phase in phasefile float Ivi level drift correction float tlt tilt drift correction 286 VNMR 6 1C User Programming 01 999165 00 A0800 5 1 VNMR Data Files status is bits 0 6 defined the same as for file header status Bits 7 11 are defined below all other bits must be zero 10 11 MOR E_BLOCKS NP_CMPLX NF_CMPLX NI_CMPLX NI2_CMPLX 0x80 0x100 0x200 0x400 0x800 0 absent 1 present 0 real 1 complex 0 real 1 complex 0 real 1 complex 0 real 1 complex Additional data block header for hypercomplex 2D data struct hypercmplxbhead shor short shor shor long floa floa float floa s_sparel status s_spare2 s_spare3 l_sparel lpvall rpvall f_sparel f_spare2
33. 19 21 sample changer errors 75 Sample Entry Form window 311 Sample Location buttons 316 sample location exclusion 321 Sample Number 315 saveAndExit selection 319 VNMR 6 1C User Programming 357 Index saved display file 284 saveExp button 319 scale fields 327 scalelimits macro 42 scalesw parameter 46 scaling factors for axis 46 scroll fields 327 scrolling list of experiments 324 SCSI errors 77 searching a text file 41 searching files for a pattern UNIX 279 second decoupler blank associated amplifier 170 fine power 180 fine power adjustment 92 gating 95 homodecoupler gating 84 offset frequency 90 91 172 phase control 87 power adjustment 92 power level 175 programmable decoupling 177 pulse shaping via AP bus 162 pulse with receiver gating 182 quadrature phase 174 shaped pulse 184 simultaneous pulses 84 small angle phase 169 spin lock waveform control 187 step size 188 turn off 172 turn on 173 unblank decoupler 189 select command 39 semicolon notation 73 semicolon notation UNIX 278 SEMS pulse sequence 96 send mail to other users UNIX 279 send2Vnmr command UNIX 47 separators 31 seqcon parameter 157 216 seqgen command 70 71 101 seqgen command UNIX 70 seqlib directory 70 101 set command 315 set2d macro 148 set3dproc command 284 setautoincrement statement 107 241 setdgroup command 301 setdivnfactor statement 108 242 setenumeral command
34. 289 2D plane of a 3D data set 39 2D plane selection without display 39 2D pulse sequence in standard form creating 148 2D 3D and 4D data sets 148 3D coefficient text file 284 3D parameter set 284 3D pulse sequence in standard form creating 148 3D spectral data default directory 284 4D pulse sequence in standard form creating 148 63 dB attenuator 92 138 79 dB attenuator 92 139 01 999165 00 A0800 Index A abort command 37 abort current process UNIX 280 abortoff command 37 aborton command 37 abs command 43 abs macro 37 A codes 102 acos command 43 acq_errors file 74 acqi command 46 120 124 Acqstat command 46 acqstatus parameter 74 acquire data explicitly 159 acquire data points 129 acquire statement 128 129 144 159 acquisition bus trap 77 Acquisition codes 102 acquisition controller board types 72 Acquisition Controller boards 72 73 126 160 acquisition CPU 146 acquisition phase AP tables See AP table acquisition processor memory 165 acquisition statements 74 acquisition status codes 74 acquisition time 117 Acquisition window 120 124 active menu 55 active parameter test 48 ADC overflow warning 75 add AP table to second AP table 263 add integer to AP table 261 add integer values 160 add statement 99 160 addExp selection 319 addSaveAndExit button 319 alfa parameter 74 alias UNIX 278 ampersand amp character 280 amplifier blanking gate 235
35. 73 97 160 257 Pulse Sequence Entry Decoupler Menu 68 Pulse Sequence Entry Decoupler Pulses Menu 65 Pulse Sequence Entry Delay Menu 66 Pulse Sequence Entry Main Menu 66 70 Pulse Sequence Entry Phases Menu 67 Pulse Sequence Entry Pulses Menu 65 67 Pulse Sequence Entry Status Menu 68 pulse sequence gated from external event 275 pulse sequence generation PSG 63 71 directory 69 statement categories 79 pulse sequence programming menus 65 pulse sequences compiling 70 execution control 98 files 69 general form 73 graphical display 70 104 imaging 152 internal hardware delays 142 object code 72 object file 157 parameter set up 41 programming 69 synchronization 131 pulse shape definitions 132 pulse shaping through AP bus 135 pulse shaping via AP bus 141 162 163 pulse statement 81 122 128 147 234 pulse transmitter with IPA 208 209 210 pulse transmitter with receiver gating 222 234 238 pulse width array 33 Pulsed Field Gradient module 150 pulsed field gradient module 153 pulseinfo macro 138 pulses entry 68 pulsesequence function 73 102 pulsesequence o file 157 pulse type parameter 299 pulsing channels simultaneously 84 pulsing the decoupler transmitter 82 purge command 29 45 pw parameter 76 82 pwd command 279 pwrf statement 92 128 140 142 144 234 pwrm statement 92 140 142 235 pwsadj macro 137 01 999165 00 A0800 Q quadrature detection 287
36. A return status of returned or aborted can help track down which macro or command failed If VNMR is started when the user logs in or if it started from a drop down menu or the CDE tool the output goes to a Console window If no Console window is present the output goes into a file in the var tmp directory This last option is not recommended 1 3 Relevant VNMR Commands Many VNMR commands are particularly well suited for use with MAGICAL programming This section lists some of those commands with their syntax if the command uses arguments and a short summary taken from the VVMR Command and Parameter Reference Refer to that publication for more information Remember that string arguments must be enclosed in single quotes Spectral Analysis Tools dres Syntax Description dsn Syntax Description dsnmax Syntax Description get11 Syntax Description getreg Syntax Description 38 VNMR 6 1C User Programming Measure linewidth and digital resolution dres lt lt frequency lt fractional_height gt gt gt linewidth resolution Analyzes line defined by current cursor position cr for linewidth and digital resolution frequency overrides cr as the line frequency fractional_height specifies the height at which linewidth is measured Measure signal to noise dsnx low_field high_field gt signal_to_noise noise Measures signal to noise of a spectrum Noise regi
37. DEC pattern are irrelevant because they are overridden as indicated above If a decoupler pattern is activated by the decprgon statement the waveform generator gate is the controlling factor If this gate is specified as Os or 1s in the D F EC file that gating will occur If there is no gate field in the DEC file the default occurs the gate is set to 0 and the decoupler is off An alternate is to follow the decprgon statement with some kind of gate statement e g decon to turn on the output board gate overriding the default of the gate set to 0 from the waveform generator and to proceed the decprgoff statement with a statement to turn the gate off for example decoff Gradient Patterns Column Description Limits Default 1 Output amplitude 32767 to 32767 1 unit resolution Required 2 Relative duration 1 to 255 1 For example the first 8 elements after the comment lines of the file trap GRD 1024 2048 3072 4096 5120 6144 7168 8192 1 Performing Shaped Pulses Statements to perform shaped pulses on YN TYTNOVA UNITY plus and UNITY systems with optional waveform generators are decshaped_pulse dec2shaped_pulse dec3shaped_pulse shaped_pulse simshaped_pulse and sim3shaped_pulse Table 27 provides a summary of these statements Table 27 Shaped Pulse Statements decshaped_pulse Perform shaped pulse on first decoupler dec2shaped_pulse Perform shaped pulse on second d
38. E echo command 40 echo command UNIX 40 ed command UNIX 279 280 edit command 280 editing configuration files 328 macros 28 45 parameter attributes 300 text files 279 effective transient counter 149 elsenz statement 101 193 194 Emacs editor 29 end hardware loop 194 end ifzero statement 194 end loop started by loop 194 end of file UNIX 280 endhardloop statement 126 194 endif statement 101 105 194 endloop statement 100 101 125 194 195 endmsloop statement 195 endpeloop statement 195 ENI 5100 class A amplifier 83 enter program 311 enter conf file 311 enter conf file listing 312 enterlcnmr conf file 311 enterQ file 315 319 322 entervast conf file 311 entry field 326 VNMR 6 1C User Programming 349 Index enumeral values of a parameter 303 env command UNIX 28 52 errmsg text file 71 error codes 74 75 error during acquisition 75 error macro 36 errormess attribute 318 Euler angles 155 event in a hardware loop 127 evolution time 64 exec command 36 46 executable pulse sequence code 70 execute statements conditionally 101 execute statements repeatedly 100 execute succeeding statements if argument nonzero 193 if argument zero 202 executing a VNMR command 46 execution of macros and commands 27 exists command 46 60 exList field 321 exp command 43 experiment files 110 experiment increment pointers 99 Experiment Specific configuration files 331 experime
39. G_Delay DELAY_TIME d2 equals delay d2 0 required terminating zero IPA allows one slider to control more than one delay or pulse The maximum number of delays or pulses a slider can control is 32 This multiple control is obtained whenever multiple calls to G_Pulse or G_Delay have the same value for the SLIDER_LABEL attribute The first call to G_Pulse in a pulse sequence sets the initial value the maximum and minimum of the slider and the scale Later calls to G_Pulse within that pulse sequence do not alter these The SLIDER_UNITS attribute are unique to each call to G_Pulse This allows changing the value seen by a particular event by some multiplication factor For example the following two statements create a single slider in the Acquisition window opened by the acqi command labeled PW that will control two separate pulses G_ Pulse PULSE_DEVICE TODEV PULSE_WIDTH pw SLIDER_LABEL PW SLIDER_SCALE y SLIDER_MAX 1000 SLIDER_MIN 0 SLIDER_UNITS 1 0e 6 0 G_Pulse PULSE_DEVICE TODEV PULSE_WIDTH pw 2 0 SLIDER_LABEL PW SLIDER_UNITS 2 0e 6 0 The width of the first pulse will initially be pw as set by the PULSE_WIDTH attribute for the first G_Pulse call The width of the second pulse will initially be pw 2 0 as set by the PULSE_WIDTH attribute for the second G_Pulse call When the sl
40. Pulse Sequence Statement Reference Arguments Examples Related xmt rphase should be distinguished from t xphase xmt rphase is needed any time the transmitter phase shift is to be set to a value that is not a multiple of 90 txphase is optional and rarely is needed multiplier is a small angle phaseshift multiplier and must be an AP variable xmtrphase vl dcplrphase Set small angle phase of first decoupler rf type C or D dcplr2phase_ Set small angle phase of second decoupler rf type C or D dcplr3phase_ Set small angle phase of third decoupler rf type C or D stepsize Set small angle phase step size rf type C or D Z zero_all_ gradients Zero all gradients Syntax Description Examples Related zgradpulse Applicability Syntax Description Arguments Examples Related zero_all_gradients Sets the gradients in the x y and z axes to zero vagradient 3 0 54 7 0 0 delay 0 001 zero_all_gradients vagradient Variable angle gradient vagradpulse Variable angle gradient pulse vashapedgradient Variable angle shaped gradient vashapedgradpulse Variable angle shaped gradient pulse Create a gradient pulse on the z channel Systems with imaging or PFG module zgradpulse value delay double value amplitude of gradient on z channel double delay length of gradient in sec Creates a gradient pulse on the z channel with amplitude and duration given by the ar
41. Syntax Description Chapter 3 Pulse Sequence Statement Reference mashapedgradpulse is used if there are no other actions required when the gradients are on mashapedgradient is used if there are actions to be performed while the gradients are on pattern is the name of a text file describing the shape of the gradient The text file is located in Svnmrsystem shapelib or in the user directory Svnmruser shapelib gradlv1 is the gradient amplitude in gauss cm gradtime is the gradient application time in seconds theta defines the angle in degrees from the z axis phi defines the angle of rotation in degrees about the xy plane mashapedgradpulse hsine 3 0 0 001 magradient Simultaneous gradient at the magic angle magradpulse Simultaneous gradient pulse at the magic angle mashapedgradient Simultaneous shaped gradient at the magic angle vagradient Variable angle gradient vagradpulse Variable angle gradient pulse vashapedgradient Variable angle shaped gradient vashapedgradpulse Variable angle shaped gradient pulse zero_all_gradients Zero all gradients Find integer value modulo 2 mod2 vi vj codeint vi variable for starting value codeint vj variable for result Sets the value of vj equal to vi modulo 2 vi is the starting integer value and vj is the value of vi modulo 2 the remainder after vi is divided by 2 Both arguments must be real time variables v1 to v14 etc mod2 v3 v5 add A
42. The done code is set in acqstatus 1 and the error code is set in acqstatus 2 Macros can take different actions depending on the acquisition condition The done codes and error codes are listed in Table 5 and in the file acq_errors in vnmr manual For example a werr command could specify special processing if the maximum number of transients is accumulated The appropriate test would be the following if acqstatus 2 200 then do special processing e g dp y au endif a These codes apply to all systems except codes marked with an asterisk are not used on MERCURY and GEMINI 2000 systems Codes marked with a double asterisk apply only to YTYINOVA Whole Body Imaging systems VNMR 6 1C User Programming 01 999165 00 A0800 2 2 Overview of Pulse Sequence Programming Table 5 Acquisition Status Codes Done 11 FID complete codes 12 Block size complete error code indicates bs number completed 13 Soft error 14 Warning 15 Hard error 16 Experiment aborted 17 Setup completed error code indicates type of setup completed 101 Experiment complete 102 Experiment started Error Warnings codes 101 Low noise signal 102 High noise signal 103 ADC overflow occurred 104 Receiver overflow occurred Soft errors 200 Maximum transient completed for single precision data 201 Lost lock during experiment LOCKLOST 300 Spinner errors 301 Sample fails to spin after 3 attempts to reposition BUMPFAIL 302 S
43. The highlighted characters can be deleted as a group or changed as a group by typing new characters e Triple clicking highlights the entire entry This spans multiple words The action on deletion or overtyping is the same as the double click highlight Types of Fields Many types of fields are available titles labels entries tabs menus buttons check boxes and more Each type of field available is described in this section Titles Titles are inactive but identify groups of elements normally below the title Labels A label consists of two components a character string and its current value A label is noninteractive An example of a label is Completed transients 423 Entries An entry consists of three components a character string label its current value and its units The value field is interactive and is editable using the previous rules The unit field may be absent may be fixed or may be selectable If selectable the selection is through a menu that is accessed by holding down the left mouse button on the field and then moving it to the desired new value before releasing it Unit changes are local they require no action from within VNMR Tabs Each pane of dg has a tab associated with it These tabs are normally on the right edge of the window The currently displayed pane has its tab raised to the front You can go to any other pane simply by clicking on its tab The tab labeled Spare typically
44. e Syntax 10 draws a gradient picture e Syntax 11 draws a shaped pulse on a specified channel 192 VNMR 6 1C User Programming 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference e Syntax 12 draws a shaped pulse on a specified channel For an explanation of the arguments delay shapedpulse etc see the corresponding entry in this reference Examples dps_show delay d1l dps_show pulse obs obspulse pl dps_show pulse dec pw pw dps_show shaped_pulse obs shaped p1 2 dps_show shaped_pulse dec2 gauss pw dps_show simpulse obs_pulse pl dec_pulse p2 dps_show simshaped_pulse gauss pl1l gauss p2 dps_show sim3pulse p1 pl1 p2 p2 p1 2 pl1 2 dps_show zgradpulse 123 0 d1 dps_show rgradient x 1234 0 dps_show vgradient x 0 2000 v10 dps_show shapedgradient sinc 1000 0 3000 0 y 1 NOWAIT dps_show shaped2Dgradient square 1000 0 3000 0 y 0 NOWAIT 1 Related delay Delay for a specified time dps_off Turn off graphical display of statements dps_on Turn on graphical display of statements dps_skip Skip graphical display of next statement pulse Pulse observe transmitter with amplifier gating rgradient Set gradient to specified level shaped_pulse Perform shaped pulse on observe transmitter shapedgradient Generate shaped gradient pulse shaped2Dgradient Generate arrayed shaped gradient pulse simpulse Pulse
45. lice nter o E i F X AXIS a134 A Cosines orientation Figure 6 Magnet Coordinates as Related to User Coordinates 292 VNMR 6 1C User Programming 01 999165 00 A0800 5 2 FDF Flexible Data Format Files orientation specifies the orientation of the user reference frame x y z with respect to the magnet frame X Y Z orientation is given as a set of nine direction cosines in the order di1 di2 di3 doy dy doz d31 d32 d33 where x d X d Y d 3Z y d X d Y d 3Z z d3 X dz Y d33Z and X dix d y d3 Z Y dyoX dy d33Z Z di3X d33y d33z The value is written as nine floating point values grouped as three triads e g float orientation 0 0 0 0 1 0 1 0 0 0 0 0 0 0 1 0 0 0 e location is the position of the center of the acquired data volume relative to the center of the magnet in the user s coordinate system The position is given in centimeters as a triple three floating point values of x y z distances e g float location 10 0 15 0 0 208 e roiis the size of the acquired data volume three floating point values in centimeters in the user s coordinate frame not the magnet frame e g float roi J 10 0 15 0 0 208 Donotconfuse this roi with ROIs that might be specified inside the data set Data Axes The data axes entries specify the user coordinates of data points These axes do not tell how to orient the display of the data but
46. mouse enters and then leaves the area of the screen covered by the dg window the value of geometry in the configuration window is updated Once the desired geometry is set the value displayed in the configuration window should be copied into the proper line in the dg conf file The dg pane is broken up into a grid of rectangles as represented by the matrix window The size of the grid in terms of the number of rows and columns is controlled by the Rows and Columns menus in the configuration window The Rows represents how many items can be placed in a column It basically defines the height of the dg window There are different choices that can be made when deciding the number of rows and columns This will be discussed after all the customizable elements are described Below the Rows and Columns menus is a label that identifies which element of the matrix window is selected Below that is the Type of Element menu This menu provides a list of all the different types of interaction items that can be placed at the current location If a pink highlighted button is selected from the matrix window this menu displays the current item at that location The next two rows are Row Extent and Column Extent menus Interaction items can be defined to be larger than a single grid rectangle Increasing the Row Extent of an item causes it to occupy a corresponding number of grid rectangles below the currently selected rectangle Increasing the Column extent of
47. notation 55 backward single quote C 30 bandinfo macro 138 banner command 40 beeper sound 46 beepoff command 46 beepon command 46 binary files 283 binary information file 284 blanking amplifiers 96 164 170 220 blankingoff statement 97 164 blankingon statement 97 164 blankoff statement 96 164 blankon statement 96 165 block size complete 75 block size counter 99 block size variable 102 Boolean expressions 35 Boolean operations 31 bootup macro 27 46 47 box mode 39 Breakout panel 97 236 bs parameter 75 99 102 bsctr real time variable 99 102 bsval real time variable 99 102 buffering in memory 284 button definition file 53 button field 327 button labels 56 C C loop 141 C programming language 69 C programming language framework 72 cat command 59 cat command UNIX 279 cautions defined 19 01 999165 00 A0800 cd command UNIX 279 cf parameter 130 change bar 24 change current directory 279 channel control 146 channel identifiers 146 channel selection 82 char type variables 73 74 check box field 327 check style 316 checkpw macro 36 checksum of FDF file data 294 chemical shift 48 chmod command UNIX 279 clear command 40 56 clearapdatatable statement 129 165 clearing a window 40 cmp command UNIX 279 cntrls parameter 319 324 coarse attenuators 92 code table 102 codeint type variables 73 coef file 284 coherence transfer s
48. power VNMR 6 1C User Programming 91 Chapter 2 Pulse Sequence Programming 92 Coarse Attenuator Control On UNTYTNOVA UNITY plus and UNITY systems with linear amplifiers the statement power value device changes transmitter or decoupler power by adjusting the coarse attenuators from 0 minimum power to 63 maximum power on channels with a 63 dB attenuator or from 16 minimum power to 63 maximum power on channels with a 79 dB attenuator e value must be stored in a real time variable such as v2 the actual value cannot be placed directly in the power statement This allows the attenuators to be changed in real time or from pulse to pulse e device is OBSch to change the transmitter power DECch to change the first decoupler power DEC2ch to change the second decoupler power or DEC3ch to change the third decoupler power e g power v2 OBSch To avoid using a real time variable the fixed channel statements obspower value decpower value dec2power value and dec3power value can be used in place of the power statement for example obspower 63 0 For all of these statements value is either a real number or a variable The power and associated fixed channel statements allow configurations such as the use of the transmitter at a low power level for presaturation followed by a higher power for uniform excitation The phase of the transmitter is specified as being constant to within 5 over the whole ran
49. stop status D 1 0 1 25 4 3 10 75 4 6 5 75 dmm from f to w UNTYINOVA and UNITYplus synchronize dmm2 from c to p status E 1 75 0 5 15 05 4 3 8 0542 3 dmm from w to p c and start WFG dmm2 from p to c only stop WFG status A is the initial state To keep the status timing constant use the statusdelay statement This statement allows the user to specify a defined period of time for the status statement to execute For example if statusdelay B 2 0e 5 is used as long as the time it takes to execute status for state B is less than 20 microseconds the statement will always take 20 microseconds If the time to execute state B is greater than 20 microseconds the statement still executes but a warning message is generated Waveform Generator High Speed Line Trigger Along with the AP bus overhead delay the waveform generator has an offset delay as a result of high speed line WFG propagation delay This shifts the rf pattern beyond the AP bus delay Figure 5 illustrates the delay for YNITYZNOVA The time overhead for the AP bus is 1 25 us this includes a 0 5 us AP bus delay and a 0 75 us board delay The offset delay is an additional 0 45 us for a total delay of 1 70 us The YNTYZNOVA WFG also has a post pulse overhead delay 1 25 us 0 45 us Ut lt p RF out oi RF gt 40 45 us XMTR j 1 25 us gt HS line WFG HS line Figure 5 Waveform
50. t1 rof1 rof2 performs an observe transmitter pulse whose phase is specified by a particular statement in the real time AP table t 1 whereas rgpulse pw vl rofl rof2 performs the same pulse whose phase is specified by the real time variable v1 The real time math functions add assign etc listed in Table 17 cannot be used with tables t1 t 60 The appropriate functions to use are given in Table 20 Statements using a table can occur anywhere in a pulse sequence except in the statements enclosed by an ifzero endif pair Loading AP Table Statements from UNIX Text Files Table statements can be loaded from an external UNIX text file with the loadtable statement or can be set directly within the pulse sequence with the sett able statement The values stored must be integral and must lie within the 16 bit integer range of 32768 to 32767 The AP table file must be placed in the user s private directory tablib which might be for example home vnmr1 vnmrsys tab1ib or in the system directory for table files vnmr tab1lib The software looks first in the user s personal t abl ib directory for a table of the specified name then in the system directory The format for the table file is quite flexible comments are allowed and several special notations are available Table Names and Statements Entries in the table file are referred to as table names Each table name must come from the set t1 to t 60 e g t 14 is a table name A t
51. v3 endloop vl setuserap Set user AP register vsetuserap Set user AP register using real time variable Turn off receiver gate only UNITYINOVA systems recoff On UN TYINOVA systems receiver gating has been decoupled from amplifier blanking The recoff statement is similar to the rcvroff statement in that it defaults the receiver off throughout the pulse sequence however unlike rcevroff the recoff statement only affects the receiver gate and does not affect the amplifier blanking gate In all cases the receiver is turned off when applying pulses and turned on during acquisition The default state of the receiver is off for YNITYZNOVA systems except for whole body systems and for imaging pulses sequences that have the initparms_sis statement at the beginning initparms_sis Initialize parameters for spectroscopy imaging sequences revroff Turn off receiver gate and amplifier blanking gate revron Turn on receiver gate and amplifier blanking gate recon Turn on receiver gate only Turn on receiver gate only UNITYTNOVA systems recon On UN TYINOVA systems receiver gating has been decoupled from amplifier blanking The recoff statement is similar to the rcvron statement in that it defaults the receiver on throughout the pulse sequence however unlike rcvron the recon statement only affects the receiver gate and does not affect the amplifier blanking gate In all cases the receiver is turned off when applying pulses a
52. vmult3 char pattern name of gradient shape file double width width of gradient in sec double statl stat2 stat3 static gradient components double stepl step2 step3 var gradient components codeint vmultl vmult2 vmult3 real time variables Sets three oblique phase encode shaped gradients This statement is the same as the statement phase_encode3_shapedgradient except the Euler angles are read from the default set for imaging The lim1 lim2 and lim3 arguments in phase_encode3_shapedgradient are set to nv 2 nv2 2 and nv3 2 respectively Pulse sequence generation aborts if the DACs on a particular gradient are overrun after the angles and amplitude have been resolved 226 VNMR 6 1C User Programming 01 999165 00 A0800 Arguments Related peloop Applicability Syntax Description Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference pattern is the name of a gradient shape file width is the length in seconds of the gradient statl stat2 stat3 are values in gauss cm of the components for the static portion of the gradient in the logical reference frame stepl step2 step3 are values in gauss cm of the components for the step size change in the variable portion of the gradient vmult1 vmult2 vmult3 are real time math variables v1 to v14 ct zero one two three or references to AP tables t1 to t 60 whose associated values v
53. 00 A0800 1 3 Relevant VNMR Commands Modifies an existing user macro or creates a new macro To edit a system macro copy it to a personal macro directory first Load a macro into memory macrold file lt dummy gt Loads a macro user or system into memory If macro already exists in memory it is overwritten by the new macro Including a return value suppresses the message on line 3 that the macro is loaded Remove a user macro macrorm file Removes a user macro from the user macro directory Display a system macro on the text window macrosyscat filel lt file2 gt lt gt Displays one or more system macro files where filel names of macros in the system macro directory file2 are Copy a system macro to become a user macro macrosyscp from_file to_file Makes a copy of an existing system macro List system macros Lists names of system macros Remove a system macro macrosysrm file Removes a system macro from the macro directory Edit a user macro with vi text editor macrovi file Modifies an existing user macro or creates a new macro using the vi text editor To edit a system macro copy it to a personal macro directory first Display memory usage statistics mstat lt program_id gt Displays memory usage statistics on macros loaded into memory Remove a macro from memory purge lt file gt 45 VNMR 6 1C User Programming Chapter 1 MAGICAL II Programming Description re
54. 13 This file exists in the user_templates dg default directory of the system directory Listing 16 shows a default version of dg conf the lines are numbered for reference Alternatively if a user has a private copy of dg conf in the user s directory vnmrsys templates dg default that copy is used The dg conf file specifies the tabs the associated label and the configuration file for each window pane If this file specifies only a single tab then the actual tabs are not displayed and the specified configuration file is used for the single pane One special configuration file dg info is present that mimics the behavior of the old dg window The dghocal output number forthe dg info pane must be set to 1 The dgLocal output number for all other panes must be set to 0 Two other parameters in the dg conf control the layout of the tabs and the overall geometry of the window The dg conf file must be edited by hand if you wish to make changes Three parameters control the background color of entry elements if the parameter being displayed is arrayed is set to Not Active or does not exist Another parameter specifies whether the dg template configuration tool is available The window configuration files are checked for in the following order of priority 1 Inthe user s vnmrsys templates dg directory if an Experiment Specific configuration file exists in a directory named after the value of seqfil 2 Inth
55. 132 phase calculation 98 phase carryover 88 phase control 99 phase cycle 64 phase cycle length 66 phase cycle storage 104 phase cycling 109 phase encode loops 157 phase file in the current experiment 290 phase parameter 148 phase step size 260 phase_encode_gradient statement 155 228 phase_encode_shapedgradient statement 229 phase_encode3_gradient statement 228 phase_encode3_shapedgradient statement 230 phasel integer 149 phasel variable 71 phase2 parameter 148 phase3 parameter 148 phased 2D data storage 289 phased spectral information 284 phased spectrum 288 phase encode loop 195 227 phasefile file 284 288 289 phase pulse technique 88 89 231 phase related statements 85 phases entry 67 VNMR 6 1C User Programming 355 Index phase sensitive 2D NMR 148 287 phaseshift statement 89 231 phi angle 154 phi parameter 155 218 pipe 279 plotif macro 37 plotting curves 42 pmode parameter 284 poffset statement 157 231 poffset_list statement 157 232 pointer to memory 98 pointers to constants 99 poly0 command 42 polynomial curves 42 position list 232 position statements 157 position_offset statement 157 232 position_offset_list statement 157 233 position based frequency 231 232 power control statements 91 power level of shaped pulse 139 power statement 92 128 140 142 143 144 233 pplvl parameter 93 ppm of solvent resonances 48 preacquisition and acquisition steps
56. 170 dec2off statement 95 172 dec2offset statement 91 172 dec2on statement 95 173 dec2phase statement 128 174 dec2power statement 92 128 144 175 dec2prgoff statement 137 144 177 dec2prgon statement 95 137 144 177 dec2pwrf statement 92 128 144 180 dec2rgpulse statement 84 128 182 dec2shaped_pulse statement 135 141 144 184 dec2spinlock statement 138 144 187 dec2stepsize statement 87 188 dec2unblank statement 96 189 dec3blank statement 96 171 dec3off statement 95 172 dec3offset statement 91 173 dec3on statement 95 174 dec3phase statement 86 128 174 dec3power power 144 dec3power statement 92 128 176 dec3prgoff statement 137 144 177 dec3prgon program 137 dec3prgon statement 95 144 178 dec3pwrf statement 128 144 180 dec3rgpulse statement 84 128 182 dec3shaped_pulse statement 135 144 185 dec3spinlock statement 138 144 187 dec3stepsize statement 87 189 dec3unblank statement 96 189 dec4offset statement 173 dec4phase statement 175 dec4power statement 176 dec4rgpulse statement 183 decblank statement 96 170 DECch DEC2ch DEC3ch devices 167 168 declaring variables 33 73 declvlflag variable 93 96 declvloff statement 93 95 128 171 declvlon statement 93 95 128 171 decoff statement 95 172 decoffset statement 91 172 decon statement 95 173 decoupler blank associated amplifier 96 170 fine power 179 234 240 fine power adjustment 92 fine power w
57. 1C User Programming 01 999165 00 A0800 2 9 Pulse Sequence Synchronization 2 9 Pulse Sequence Synchronization If broken down to its fundamental elements a pulse sequence is just a set of accurately timed delays in which the appropriate hardware is turned on or off External Time Base For purposes of synchronization an external timebase halts the pulse sequence until the number of external events in the count field have occurred The source of events or ticks of this external timebase is up to the user See your system technical reference for specifics This feature is not available on MERCURY VX MERCURY or GEMINI 2000 systems Controlling Rotor Synchronization Statements for rotor control on systems with solids rotor synchronization hardware are rotorperiod rotorsync and xgate Table 26 summarizes these statements Table 26 Rotor Synchronization Control Statements rotorperiod period Obtain rotor period of high speed rotor rotorsync rotations Gated pulse sequence delay from MAS rotor position xgate events Gate pulse sequence from an external event e To obtain the rotor period use rotorperiod period where period is a real time variable into which is the rotor period is placed e g rotorperiod v5 The period is placed into the referenced variable as an integer in units of 100 ns To insert a variable length delay use rotorsync rotations where rotations isa real time variable that points to the
58. 234 238 pulse related statements 80 quadrature phase 265 set status 242 shaped pulse 135 244 simultaneous pulses 84 small angle phase 275 small angle phase step size 260 spin lock control 137 257 step size 222 temporary frequency shifting 88 unblank 223 troubleshooting acquisition status codes 74 troubleshooting a new sequence 71 TRUE Boolean value 35 trunc operator 30 truncate real number 30 tsadd statement 108 261 tsdiv statement 108 262 tsmult statement 108 262 tssub statement 108 263 ttadd statement 108 109 263 ttdiv statement 108 263 ttmult statement 108 264 ttsub statement 108 264 two attenuators system 141 two periods notation UNIX 278 two pointer 99 two pulse pulse 85 two pulse sequence T2PUL 108 two pulse shaped pulse 135 253 254 txphase statement 85 88 128 265 type A or B rf 88 type of parameter 300 typeof operator 31 35 types of parameters 298 302 U U H1 Only label 146 uname command UNIX 279 unblank amplifier 96 189 underline prefix 27 uniform excitation 92 uninitialized variable 71 unit command 49 units command UNIX 279 UNIX commands 278 file names 278 manuals 277 operating system 277 shell 280 shell programming 282 shell startup 48 text commands 279 text editor 280 tools 277 updtgcoil macro 153 upper barrel warning 20 01 999165 00 A0800 usenextloc attribute 319 user AP lines 97 user AP
59. 298 301 setgroup command 301 setlimit command 32 300 setprotect command 300 setreceiver statement 99 108 130 242 setstatus statement 94 95 143 242 settable statement 105 107 243 settcldefault macro 305 settype command 300 setuserap statement 97 setuserpsg shell script 157 158 setvalue command 300 310 sh2pul macro 132 shaped gradient 268 358 VNMR 6 1C User Programming pulse generation 245 246 249 variable angle 266 shaped oblique gradient 218 219 shaped pulse decoupler 183 delays 146 information 138 on transmitter 244 simultaneous three pulse 254 simultaneous two pulse 253 time truncation error 137 using attenuators 138 waveform generator control 135 shaped two pulse experiment 132 shaped_pulse statement 135 141 144 244 shaped2Dgradient statement 246 shapedgradient statement 151 155 245 shapedincgradient statement 155 248 shapedvgradient statement 155 249 shapelib directory 132 161 245 shell command 48 281 shell command UNIX 280 shell scripts 282 shelli command 280 shimming errors 76 short type variables 74 showfields parameter 324 signal to noise measurement 38 sim3pulse statement 84 128 251 sim3shaped_pulse statement 136 144 254 sim4pulse statement 85 252 simpulse statement 84 128 251 simshaped_pulse statement 135 144 253 simultaneous gradient 212 simultaneous pulses 84 85 simultaneous shaped gradient 213 simultaneous shaped gradient p
60. 31 56 notation pulse shaping file 132 dollar sign notation 29 33 special input argument 35 0 special input argument 35 1 2 input arguments 35 amp ampersand notation UNIX 280 single quotes notation 27 30 parentheses notation 34 notation AP table file 106 asterisk notation display template 307 addition operator 31 notation AP table file 106 single period notation UNIX 278 double period notation UNIX 278 c file extension 69 fdf file extension 290 fid file extension 283 notation UNIX 278 colon notation 28 semicolon notation 73 semicolon notation UNIX 278 lt notation UNIX 279 lt gt angled brackets notation 27 gt notation UNIX 279 gt gt notation UNIX 279 question mark notation UNIX 279 notation display template file 307 notation square brackets 33 notation AP table file 106 backslash notation 30 backslash single quote notation 55 _ x macro name 27 reverse single quotes notation 55 56 curly braces notation 35 73 notation AP table file 106 vertical bar notation UNIX 279 tilde notation UNIX 278 Numerics 1D data file 285 1D display 288 1D Fourier transform 288 2D data file 289 2D FID display 289 2D FID storage 289 2D hypercomplex data 285 2D phased data storage
61. 4 dg info set dgLocal output 4 1 set dgLocal title 5 Spare set dgLocal file 5 dg spare set dgLocal output 5 0 set dgLocal title 6 Spare set dgLocal file 6 dg spare set dgLocal output 6 0 Color for Arrayed entries set dgLocal ac pink Color for Not Active entries set dgLocal off gray80 Color for Not defined entries set dgLocal nc gray70 set edit to yes or no to toggle configuration access set dgLocal edit yes set dgLocal side vert Uncomment the following line to have the tabs appear across the top set dgLocal side horiz wm geometry 925x350 0 0 window is used to select items and rearrange items Each button in the matrix window represents a corresponding grid element in the dg pane The buttons highlighted in pink indicate that some interaction item is present at that grid location The first four characters of the label of the interaction are displayed To move items within the pane hold the left mouse button down over one of the highlighted grid buttons drag the mouse arrow with the button still down to a non highlighted grid item and then release the mouse button The change is immediately shown in the dg pane To select grid items click the left mouse button over one of the grid items in the matrix window The currently selected item will blink in the matrix window By selecting a grid item you can either define or redefine the contents of that grid item The second
62. 90 270 450 180 360 specified carry over On systems with Acquisition Controller boards or Pulse Sequence Controller boards the 90 multiples are set by the call to xmt rphase dcplrphase dcplr2phase and dcplr3phase If xmt rphase dcplrphase dcplr2phase or dcplr3phase is used to set the phase for some pulses in a pulse sequence it is often necessary to use xmtrphase zero dcplrphase zero dcplr2phase zero or dcplr3phase zero preceding other pulses to ensure that the phase specified by a previous xmt rphase dcplrphase dcplr2phase or dcplr3phase does not carry over into an unwanted pulse or decpulse statement Phases specified in txphase pulse rgpulse decphase decpulse decrgpulse dec2phase dec2rgpulse dec3rgpulse and dec4rgpulse statements change the 90 portion of the phase shift only This feature provides a separation between the small angle phase shift and the 90 phase shifts and facilitates programming phase cycles or additional coherence transfer selective phase cycling on top of small angle phase shifts Be sure to distinguish xmt rphase from txphase txphase is optional and rarely needed xmt rphase is needed any time the transmitter phase shift is to be set to a value not a multiple of 90 The same distinction can be made between dcplrphase and decphase dcplr2phase and dec2phase and dcplr3phase and dec3phase Phase Pulse Technique The third method is a phase shifting te
63. Acquisition Controller Acquisition Controller and Pulse Sequence Controller boards no such restrictions exist The acquire number_points sampling_interval statement explicitly acquires data points at the specified sampling interval where the sequence of events is acquire a pair of points for 200 ns delay for sampling_interval less 200 ns then repeat number_points 2 times For example acquiring an FID would use acquire np 1 0 sw Both arguments to the acquire statement must be real numbers or variables If an acquire statement occurs outside a hardware loop the number of complex points to be acquired must be a multiple of 2 for Data Acquisition Controller Acquisition Controller and Pulse Sequence Controller boards or a multiple of 32 for Output boards Inside a hardware loop Data Acquisition Controller and Pulse Sequence Controller boards can accept a maximum of 2048 complex points Acquisition Controller boards can accept a maximum of 1024 complex points and Output boards can accept a maximum of 63 complex points number_points must be a multiple of 2 because only pairs of points can be acquired note that this is a different definition than was used on VXR style systems UNITYINOVA systems include small overhead delays before and after the acquire statement The pre acqui re delay takes into account setting the receiver phase oph and enabling data overflow detection Disabling data overflow detection creates a post acquire del
64. Arguments can be variables which requires appropriate get val and get str statements to permit changes via parameters see second example below pattern isthe name of the text file without the DEC file suffix in the shapelib directory that stores the decoupling pattern 221 VNMR 6 1C User Programming Chapter 3 Pulse Sequence Statement Reference Examples Related obspulse Syntax Description Related obspwrf Applicability Syntax Description Arguments Examples Related obsstepsize Applicability Syntax Description Arguments 222 VNMR 6 1C User Programming 90_pulselength is the pulse duration in seconds for a 90 tip angle on the observe transmitter tipangle_resoln is the resolution in tip angle degrees to which the decoupling pattern is stored in the waveform generator obsprgon waltz16 pw90 90 0 obsprgon modulation pp90 dres decprgon Start programmable decoupling on first decoupler dec2prgon Start programmable decoupling on second decoupler obsprgoff End programmable control of observe transmitter Pulse observe transmitter with amplifier gating obspulse A special case of the rgpulse width phase RG1 RG2 statement in which width is preset to pw and phase is preset to oph Thus obspulse is exactly equivalent to rgoulse pw oph rofl rof2 Note that obspulse has nothing whatsoever to do with data acquisition despite its name Exc
65. Menu page 66 without adding a delay at this point in the sequence 66 VNMR 6 1C User Programming 01 999165 00 A0800 2 1 Programming Pulse Sequences from Menus Pulse Sequence Entry Phases Menu The Pulse Sequence Entry Phases Menu is typically entered by selecting Pulse or DecPulse in the Pulse Sequence Entry Main Menu by selecting Set Revr Phase in the Pulse Sequence Entry Status Menu or by entering menu psg_phase For buttons 1 to 7 the Pulse Sequence Entry Pulses Menu page 67 the Pulse Sequence Entry Decoupler Pulses Menu page 68 or the Pulse Sequences Entry Main Menu is displayed page 66 as appropriate Button Description SELECT PHASE Use Previous Use the phase of the previous pulse for this pulse as well X Use a phase of X which will have additional phase cycling automatically added to it For example if the phase cycle length has been set to be 2 the additional phase cycle will be 00112233 or 0 0 90 90 180 180 270 270 and an X pulse will have the same phase 00112233 This choice will be common if this menu is used to set receiver phase Y Use a phase of Y see description of X X Use a phase of X see description of X Y Use a phase of Y see description of X Fixed 0 Use a fixed phase of 0 that is not phase cycled Use phase alternation for this pulse Phase cycling will be automatically added the minimum phase cycle length that should have been selected for thi
66. Only or the system is a GEMINI 2000 tn is set to H1 and dn is not set to H1 If this is the case the parameters and pulse statements for rf channels and 2 are exchanged automatically MERCURY VX MERCURY and GEMINI 2000 support automatic channel swapping as well VNMR 6 1C User Programming 01 999165 00 A0800 2 13 Indirect Detection on Fixed Frequency Channel UNITY and VXR S Systems UNITY and VXR S fixed frequency systems present special pulse sequence programming and hardware considerations The hardware issues are discussed in the operation manuals In this section we discuss pulse sequence programming of these systems Pulse sequences written to perform indirect detection experiments must use decpulse and related statements to pulse the 1H channel and pulse statements to pulse the X channel Having done this and having set tn C13 and dn H1 the software would normally set Channel A the high frequency channel of the pulse amplifier into a CW mode as appropriate for decoupling and Channel B the low frequency channel of the amplifier into a pulse mode Proper operation of the pulse sequence requires that these modes be switched the low frequency channel in CW mode and the high frequency channel in pulse mode To accomplish this the C source file revmode c is provided and must be included in any pulse sequence to be run in the reversed configuration as shown here s2pulr reverse mode s2pul i
67. PFG module shapedincgradient channel pattern width a0 al a2 a3 x1 x2 x3 loops wait char channel gradient channel x y or z char pattern name of pulse shape text file double width length of pulse double a0 al a2 a3 coefficients to determine level codeint x1 x2 x3 variables to determine level int loops number of loops int wait WAIT or NOWAIT Provides a dynamic variable shaped gradient pulse controlled using the AP math functions The statement drives the chosen gradient with the specified pattern scaled to the level defined by the formula level a0 al x1l a2 x2 a3 x3 The pulse is created using a gradient waveform generator and has a pulse shape determined by the pattern width and loops arguments as well as the calculation of level Unlike the shaped rf pulses the shapedincgradient will leave the gradients at the last value in the gradient pattern when the pulse completes The range of the gradient level is 32767 to 32767 If the requested level lies outside the legal range it is clipped at the appropriate boundary value Note that while each variable in the calculation of level must fit in a 16 bit integer intermediate sums and products in the calculation are done with double precision 32 bit integers The following error messages are possible e Machine configuration doesn t allow gradient patterns is displayed if this statement is used on a s
68. Programming 54 example the file vnmr menulib display_1D contains the main choices for the 1D Data Display Menu the corresponding help file is found in vnmr help display_1D Menu Files Menu files are simple text files that can be examined or modified as desired assuming appropriate permission The menuvi command is available for editing a menu file using the UNIX vi editor For example entering menuvi display_1D opens for editing the text file for the 1D data display menu After editing menu files can reside in several places When the user selects a button that opens another menu or if the menu command is entered with the name of a menu as an argument VNMR looks for the menu file name in the following order 1 Inthe user s menulib directory 2 Inthe directory pointed to by the menulibpath parameter if the menulibpath parameter is defined in the user s global parameter file This parameter must contain an absolute path not a relative path 3 Inthe system menulib directory If the file name is not found the command interpreter displays an error message This order of search means that each user can have their own private menu directory menulib in their vnmrsys directory User menus take precedence over the system menus if a menu of the same name exists is in both directories This allows users to modify each menu to their own needs without affecting the operation of other users The system menu directory vnmr me
69. S systems do not have PTS synthesizers with latching but OFF SET_DELAY can be used on these systems Table 30 AP Bus Delay Constants Constant Indicates Duration of ACQUIRE_START_DELAY Overhead at start of acquisition ACQUIRE_STOP_DELAY Overhead at end of acquisition DECMODFREQ_DELAY Overhead for setting modulator frequency GRADIENT_DELAY rgradient zgradpulse two times OBLIQUEGRADIENT_DELAY oblique _gradient applicable only to imaging OFFSET_DELAY decoffset dec2offset obsoffset offset OFFSET_LTCH_DELAY decoffset dec2offset obsoffset offset POWER_DELAY decpower dec2power obspower power rlpower etc PRG_OFFSET_DELAY Time shift of WFG output with obsprgon etc PRG_START_DELAY decprgon dec2prgon obsprgon etc PRG_STOP_DELAY decprgoff dec2prgoff obsprgoff etc PWRF_DELAY decpwrf dec2pwrf obspwrf pwrf SAPS_DELAY dcplrphase dcplr2phase dcplr3phase xmtrphase SETDECMOD_DELAY Overhead for setting modulator mode SPNLCK_START_DELAY Overhead at start of decspinlock spinlock etc SPNLCK_STOP_DELAY Overhead at end of decspinlock spinlock etc VAGRADIENT_DELAY vagradpulse two times WFG_OFFSET_DELAY Time shift of WFG output WFG_START_DELAY Overhead at start of decshaped_pul
70. The interface to status is usually controlled by the status conf file supplied in the vnmxr asm directory This file is duplicated in Listing 15 with the lines numbered for reference Any line in the file that starts with a is a comment line For status to work correctly an out fields parameter must be specified that matches the out fields parameter used by enter as the initiator of the automation run The Listing 15 Text of the status conf File OMNIA UN BWNE OArANnaAuOBPWNER Os WWWWWWWWWNNNNNNNYN DNDN D AAYNaA ONRPWNHFPDWO WANA BWNF OO KB DBD DB BB WW Ww YA OBWNF OC OO Status configuration information outfields identifies the items which will were output by the enter program The order of the listed items must be the same as those used for the enter program set outfields loc user exp solvent textfield userdir data stat separator showfields identifies the items which will be displayed by the status program They must be a subset of outfields The order does not need to be the same as outfields set showfields user loc textfield Button Definitions Possible cntrls are rt locate and quit set cntrls rt locate quit set rt id rt set rt label Retrieve Data set locate id locate set locate label Find Entry set quit id quit set quit label Quit num sets the number of entries to be shown in the scrolling window col sets the width of the scrolling wind
71. User Programming divide 190 double 168 half value 200 increment 204 modulo 2 215 modulo 4 215 modulo n 216 multiply 217 subtract 261 integer type parameter 299 intensity of spectrum at a point 39 interactive dg window 324 interactive parameter adjustment IPA 120 change fine power 209 change linear modulator power 210 change offset frequency 208 delay specified time 80 202 fine power control 93 pulse decoupler 84 201 202 pulse transmitter 82 208 209 210 interferograms 289 interincrement delays 103 internal hardware delays 142 internal variables 98 intertransient delays 103 int type variables 73 74 iobspulse statement 82 208 ioffset statement 91 208 IPA See interactive parameter adjustment IPA ipulse statement 82 209 ipwrf statement 93 209 ipwrm statement 93 210 irgpulse statement 82 210 ix variable 71 J jexp command 32 K keyboard entries recording 46 keyboard focus to VNMR input window 47 keyboard input 41 kill command UNIX 279 kinetic analyses 42 L label field 326 largest integral in region 39 last used parameters text file 284 lastmenu parameter 55 latching on PTS synthesizers 140 LC NMR accessory 311 legrelay parameter 147 length command 47 length of macros 37 lib directory 158 libparam a object library 70 libpsglib a directory 70 157 01 999165 00 A0800 library directory 158 line frequencies and intensities 39 li
72. With IPA oo eee eee cseeeeseeeeeeeeectaeseeeeeees 202 Execute succeeding statements if argument is Zero osses 202 Set real time incremental delay 00 0 eeeeeceeeeeeeteeeeecaeeeneesaeeaes 203 Generate dynamic variable gradient pulse eee eeeeeeeeeeeeeeee 203 Increment an integer valts oo ele eee cee cese cee ceseeeeceseeeeeeeeeeeeeseeeeees 204 Set MAMECt AStSCH OM sss ieve sis seb vedsGek As ences vess Senses sebeanbesnsvasdeed sstesabheoss 205 Create rf patternfile 2 4 scsssiestesni ed esena e nianna ei Ei 205 Create gradient pattern file eee eeeeesecseeseeseceeeeeeseeaeseseeeaeseeeeeaes 206 Initialize real time variable for vscan statement 0 00 0 seeeeeeeeeeeeeeee 207 Initialize incremental delay 00 eee cee cee ceseeeeceseeeeeeeeeeeeeeeeeeeeae 207 Initialize parameters for spectroscopy imaging sequences 207 Initialize a real time variable to specified value ti eeeeeseeeeeeeee 208 Pulse observe transmitter with IPA oo eee eee ceeeeeeceeeeeeeeeeeeeeeee 208 Change offset frequency With IPA eceeeesecseeeceseeseseeeecsaeeteeeees 208 Pulse observe transmitter with IPA oo eee ceeeeeeceeeeeeeeeeeeeeeee 209 Change transmitter or decoupler fine power with IPA n se 209 Change transmitter or decoupler lin mod power with IPA 210 Pulse observe transmitter with IPA oo eee ceeeeeeceeeeeeeeeeeeeeeee 210 Set lock correction circuitry to hold correction 00 0 eee eee eee tees 211 Set lock cor
73. Z gradient G cm extern double gxscale X scaling factor for gmax extern double gyscale Y scaling factor for gmax extern double gzscale Z scaling factor for gnax extern char gpatup MAXSTR Gradient ramp up pattern extern char gpatdown MAXSTR Gradient ramp down pattern extern char gropat MAXSTR Readout gradient pattern extern char gpepat MAXSTR Phase encode gradient pattern extern char gsspat MAXSTR Slice gradient pattern extern char gpat MAXSTR General gradient pattern extern char gpat1 MAXSTR General gradient pattern extern char gpat2 MAXSTR General gradient pattern extern char gpat3 MAXSTR General gradient pattern extern char gpat4 MAXSTR General gradient pattern extern char gpat5 MAXSTR General gradient pattern Delays extern double EX Repetition time per scan extern double te Primary echo time extern double ti Inversion time extern double tm Mid delay for STE extern double at Acquisition time extern double tpe tpe2 tpe3 Phase encode durations for 2D to 4D extern double tcrush Crusher gradient duration extern double tdiff Diffusion encode duration extern double tdelta Diffusion encode duration extern double tDELTA Diffusion gradient separation extern double tflow Flow encode duration extern double tspoil Spoiler duration extern double hold Physiological trigger hold off extern double trise Gradient coil rise time sec extern double satdly Saturation time extern double tau General use delay ext
74. all radio styles are changed to the check style and all xradio styles and changed to the x check check Notice that the small box for the xcheck style exclusive choice is a diamond and the small box for the check style multiple choice is a square If the textent ry style is selected a user simply inputs text VNMR 6 1C User Programming 01 999165 00 A0800 6 1 Customizing the Sample Entry Form Window Sample Entry Form Sample Number Pe Ee Eee Ech PG Fis lee eyes ei FA sie ay ge aay eee r e e ate ee Se e ee B20 B24 of 22 St 23 24 25 26 et 27 of 28 29 ot 30 Epari SZ SS SS eso ea eera Eea SS B40 144 4 42 4 43 J 44 4 45 J 46 4 47 4 48 1 49 I 50 User identification w vnmri Solvent Selection v CDC13 D20 Benzene DMSO Acetone w Cyclohexane w Toluene Methanol Experiment Selection apt Pe I ee Fis P34 a HE H sCOSY a H TOESY H gHSQC H gCOSY gHSQc H gCOSY HSQC gHMBC H gCOSY HSQC gHMBC HSQCTOXY H COSY C DEPT HETCOR H COSY C APT H TOCSY NOESY _ H TOCSY ROESY H TOCSY HMQC Text Customize Parameters Add Entry E and Quit Number of samples submitted 0O Figure 10 Alternate Interface enter Program A col attribute defines how much space to make available for character input You set the col attribute to the maximum number of characters you expect The text field parameter uses this style have allocates space to enter 40 characters The xradiocustom style is a hybrid of the xradio style
75. amplifier modes 82 amplifiers blanking channels 164 duty cycle 81 gating 80 turn off 164 turn on 164 ampmode parameter 82 analyze command 42 analyze inp file 42 and operator 31 angled brackets lt or gt notation 23 27 AP bus commands 93 AP bus delay 91 145 160 AP bus delay constants 139 AP bus instruction 142 AP bus pulse shaping 161 162 163 AP bus registers 97 236 244 273 ap command 304 ap parameter 307 AP table 104 add integer to elements 261 add to another table 263 autoincrement attribute 107 241 VNMR 6 1C User Programming 345 Index divide by second AP table 263 divide integer into elements 262 divn factor 108 file location 105 load from file 107 211 loading statements 105 multiply by a second AP table 264 multiply integer with elements 262 receiver phase cycle 242 receiver variable 108 retrieve element 107 197 scalar operations 108 set divn return and divn factor 242 statement format 105 store integer array 107 243 subtract from second AP table 264 subtract integer from elements 263 table handling statements 107 vector operations 108 apa command 40 apdelay h file 143 146 apovrride statement 89 93 143 160 applicability of statements 69 Applications Laboratory 24 apshaped_dec2pulse statement 162 apshaped_decpulse statement 161 apshaped_pulse statement 163 arc cosine of a number 43 arc sine of a number 43 arc tangent of a number 43 arc tan
76. and Tcl Cmd fields This can be zero or more parameter names MAGICAL expression that is sent to VNMR whenever an item is selected from the drop down menu Any specified VNMR parameters can be used The variable VALUE is set to the value in the Value of choices list of the selected choice 01 999165 00 A0800 6 3 Customizing the Interactive dg Window Tcl Cmd Tcl expression that is evaluated to determine which choice should be identified and displayed in the menu2 button The return value of the expression must match one of the choices in the Value of choices list The menu2 element is useful when making exclusive choices among several items If the choice is among two items a check box is useful three or four items can be handled by radio buttons For more items the menu2 item is useful because the entire list of choices is only displayed where you are making a selection Note that the menu2 item differs from the standard Tcl Tk menu item in that it supports a multiple column display of choices if more than ten choices are specified The following example selects one of several decoupler modulation schemes Label of element modulation Choices ccc CCW CWW Www ccg ccp Value of choices ccc CCW CWW WWW ccg ccp Vnmr Variables dmm Vnmr Cmd dmm SVALUE Tcl Cmd Sdmm Scale Element The scale element adjusts a parameter with a slider A label and the current value of the scale can be displayed to the left of the scale The
77. and the textent ry style Similarly the xcheckcustomstyle is a hybrid of the xcheck style and the textent ry style These two styles provide a set of xradio or xcheck buttons that initialize the textentry field The textentry field can subsequently be edited This is useful for users who like to customize standard experiments For example if the H1 experiment button is pressed the h1 macro is written into the textentry field You might then add temp 40 to the textent ry field If the xradiocustomor the xcheckcustom styles are selected two additional attributes are needed A labe12 attribute specifies a second label to be printed in front of the textentry field A col attribute defines how much space to make available for character input These styles are not used in the default enter conf file but are used in an alternative interface that is commented out Lines 77 to 79 will select this alternative xradiocustom interface Figure 11 shows the interface with this selection File Attribute The file attribute must be present for any parameter listed in infields If file is set to a name then a file of that name in the vnmr asm directory is read to specify the choices available The user exp and solvent parameters specify a file for their set of choices These files are pairs of lines The first line is a label that will be displayed as a choice The second line of each pair is the string that will be output into the file generated 01 99916
78. are created by the set 3dproc command within VNMR The last file is created by the ft 3d program e log isa directory that stores the log files produced by the ft 3d program The file 3 contains all the log output for the f transform For the f and fi transforms there are two log file for each data file one for the i transform 2 and one for the f i 1 The file master contains the log output produced by the master ft 3d program VNMR 6 1C User Programming 01 999165 00 A0800 5 1 VNMR Data Files Data File Structures A data file header of 32 bytes is placed at the beginning of a VNMR data file The header contains information about the number of blocks and their size It is followed by one or more data blocks At the beginning of each block a data block header is stored which contains information about the data within the individual block A typical 1D data file therefore has the following form data file header header for block 1 data of block 1 header for block 2 data of block 2 The data headers allow for 2D hypercomplex data that may be phased in both the f and f2 directions To accomplish this the data block header has a second part for the 2D hypercomplex data Also the data file header the data block header and the data block header used with all data have been slightly revised The new format allows processing of FIDs obtained with earlier versions of VNMR The 2D hypercomplex data files with datafile
79. automation experiments the FID is stored within the experiment regardless of what the parameter file is set to The path username vnmrsys expn acqfil fidis the full UNIX path to that file FIDs are stored as either 16 or 32 bit integer binary data files depending on whether the data acquisition was performed with dp n or dp y respectively After an Fourier transform the experiment file expn datdir data contains the transformed spectra stored in 32 bit floating point format This file always contains complex numbers pairs of floating point numbers except if pnode was selected in processing 2D experiments To speed up the display VNMR stores also the phased spectral information in expn datdir phasefile where it is available only after the first display of the data In arrayed or 2D experiments phasefile contains only those traces that have been displayed at least once after the last FT or phase change Therefore a user program to access that file can only be called after a complete display of the data The directory file expn for current experiment n contains the following files e expn curpar is a text file containing the current parameters e expn procpar is a text file containing the last used parameters expn text is a text file e expn acqfil fidisa binary file that stores the FIDs e expn datdir data is a binary file with transformed complex spectrum e expn datdir phasefile isa binary file with transformed phased spectrum
80. by the channel character evaluating to other than x y or z or by being a string e mult i illegal RT variable multiplier_i is caused by multi mult2 or mult 3 having a value other than a AP math variable v1 tov14 channel is an expression that evaluates to the character x y or z do not confuse characters x y and z with strings x y and z base and incl inc2 inc3 are the base value and increments used in the formula for determining the gradient level mult1 mult2 mult3 are the multipliers used in the gradient level formula These arguments should be AP math variables v1 to v14 Note that AP tables t1 to t 60 are not allowed in this statement See the program inctst c getorientation Read image plane orientation rgradient Set gradient to specified level shapedgradient Provide shaped gradient pulse to gradient channel shaped2Dgradient Generate arrayed shaped gradient pulse shapedvgradient Generate dynamic variable shaped gradient pulse vgradient Generate dynamic variable gradient pulse Increment an integer value incr vi codeint vi real time variable to increment Increments by 1 the integer value given by vi i e vi vit1 204 VNMR 6 1C User Programming 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference Arguments vi is the integer to be incremented It must be a real time variable v1 to v14 oph etc Examples incr v4 Related add Add inte
81. cycled with the parameter oph The attribute SLIDER_LABEL determines whether output is generated for the Acquisition window opened by the acqi command If no label is specified no IPA information is generated by the subroutine The use of the SLIDER_LABEL with the same value for delays or pulses allows multiple delays or pulses to be controlled via one slider This is covered later in this section As an example of a pulse sequence using the general routines Listing 10 shows the source code of i2pul c which can be compiled and run like S2PUL but when go acqi is typed IPA information is generated in vnmr acqqueue acqi IPA The command acqi can be used to adjust the pulses and delays in the sequence Note that G_Pulse covers the statements obspulse pulse decpulse etc Macro definitions have been written to cover these define obspulse G_Pulse 0 define decpulse decpulse phaseptr N G_Pulse PULSE_DEVICE DODEV PULSE_WIDTH decpulse PULSE_PHASE phaseptr PULSE_PRE_ROFF 003 PULSE_POST_ROFF 0 0 See the file vnmr psg macros h for a complete list This file is automatically included when the file st andard h is included in a pulse sequence Note also that the VNMR 6 1C User Programming 01 999165 00 A0800 2 7 Using Interactive Parameter Adjustment Listing 10 Pulse Sequence Listing of File i2pul c I2PUL interactive two
82. dec4power power double power new power level for DO4DEV Changes the third decoupler power It is functionally the same as rlpower value DO4DEV power Sets the power level by assuming values from 0 minimum power to 63 maximum power decpower Change first decoupler power linear amplifier systems dec2power Change second decoupler power linear amplifier systems obspower Change observe transmitter power linear amplifier systems rlpower Change power level linear amplifier systems rftype Type of rf generation End programmable decoupling on first decoupler Systems with a waveform generator on rf channel for the first decoupler decprgoff Terminates any waveform generator controlled programmable decoupling on the first decoupler started by the decprgon statement decprgon Start programmable decoupling on first decoupler dec2prgoff End programmable decoupling on second decoupler dec3prgoff End programmable decoupling on third decoupler 01 999165 00 A0800 dec2prgoff Applicability Syntax Description Related dec3prgoff Applicability Syntax Description Related decprgon Applicability Syntax Description Arguments Examples Related dec2prgon Applicability Syntax 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference End programmable decoupling on second decoupler Systems with a waveform generator on rf channel for the second decoupler dec
83. delays acquires and other scattered instructions are allowed ina hard loop Most notably no real time math statements are allowed thereby precluding any phase cycle calculations The number of events included in the hard loop including the total number of data points if acquisition is performed is subject to the following limitations e 2048 or less for the Data Acquisition Controller board Pulse Sequence Controller board or MERCURY VX and MERCURY STM Output board e 1024 or less for the Acquisition Controller board e 63 or less for the Output board see the description section of the acquire statement for further information about these boards In all cases the number of events must be greater than one No nesting of hard loops is allowed For the Output board a hardware loop must be preceded by some timed event other than an explicit acquisition or another hardware loop If two hardware loops must follow one another it will therefore be necessary to insert a statement like delay 0 2e 6 between the first endhardloop and the second st arthardloop With only a single hardware loop there is no timing limitation on the length of a single cycle of the loop With two hardware loops such as a loop of pulses and delays followed by an implicit acquisition the first hardware loop must have a minimum cycle length of approximately 80 Us With three or more hardware loops loops that are not the first or last must have a minimum cycle l
84. due to be eliminated in future versions of VNMR software Although it is still functional you should not write any new pulse sequences using it and should replace it in existing sequences with shaped_pulse which functions exactly the same as shapedpulse Perform shaped pulse on observe transmitter UNITYTNOVA and UNITY gt plus systems or systems with a waveform generator on the observe transmitter channel shaped_pulse pattern width phase RG1 RG2 char pattern name of RF text file double width width of pulse in sec codeint phase real time variable for phase double RG1 gating delay before pulse in sec double RG2 gating delay after pulse in sec Performs a shaped pulse on the observe transmitter If a waveform generator is configured on the channel it is used otherwise the linear attenuator and the small angle phase shifter are used to effectively perform an apshaped_pulse statement When using the waveform generator the shapes are downloaded into the waveshaper before the start of an experiment When shaped_pulse is called the shape is addressed and started The minimum pulse length is 0 2 us The overhead at the start and end of the shaped pulse varies with the system 244 VNMR 6 1C User Programming 01 999165 00 A0800 Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference e UNITYTNOVA 1 us start 0 end UNITYoplus 5 75 us start 0 end
85. e System with Acquisition Controller board 10 75 us start 4 3 us end e System with Output board 10 95 us start 4 5 us end If the length is less than 0 2 us the pulse is not executed and there is no overhead When using the linear attenuator and the small angle phase shifter to generate a shaped pulse the shaped_pulse statement creates AP tables on the fly for amplitude and phase It also uses the real time variables v12 and v13 to control the execution of the shape It does not use AP table variables For timing and more information see the description of apshaped_pulse Note that if using AP tables with shapes that have a large number of points the FIFO can become overloaded with words generating the pulse shape and FIFO Under flow errors can result file is the name of a text file in the shapelib directory that stores the rf pattern leave off the RF file extension width is the duration in seconds of the pulse on the observe transmitter phase is the phase of the pulse and must be a real time variable RG1 is the delay in seconds between gating the amplifier on and gating the observe transmitter on the phase shift occurs at the beginning of this delay RG2 is the delay in seconds between gating the observe transmitter off and gating the amplifier off shaped_pulse gauss pw vl rofl rof2 apshaped_pulse Observe transmitter pulse shaping via AP bus decshaped_puls Shaped pulse on first decoupler dec2sha
86. e expn sn is saved display number n To access information from one of the experiment files of the current experiment the user must be sure that each of these files has been written to the disk The problem arises because VNMR tries to keep individual blocks of the binary files in the internal buffers as long as possible to minimize disk accesses This buffering in memory is not the same as the disk cache buffering that the UNIX operating system performs The command flush can be used in VNMR to write all data buffers into disk files or at least into the disk cache where it is also available for other processes The command fsave can be used in VNMR to write all parameter buffers into disk files The default directory for the 3D spectral data is curexp datadir3d The output directory for the extracted 2D planes is the same as that for the 3D spectral data except that 2D uses the ext r subdirectory and 3D uses the data subdirectory Within the 3D data subdirectory data are the following files and further subdirectories e datal to data are the actual binary 3D spectral data files If the option nfiles is not entered the number of data files depends upon the size of the largest 2D plane and the value for the UNIX environmental parameter memsize e info is a directory that stores the 3D coefficient text file coef the binary information file procdat the 3D parameter set procpar34d and the automation file auto The first three files
87. ee EEE EEEE EEEE ER ARE 136 Setting Spin Lock Waveform Control ssc cscicccd cascsdecceusentunedscesngs denne soe otceecsed stecestespentiascexesctonsouonss 137 Shaped Pulse Calibration ects decscialsetelssasvevcadevacds ire ees E E eE n ei a aa EE eaves 138 211 Shaped Pulses Using Attenuators 0 ccscessesessssesscseusesecseesesesougscssosessesesesncessestesues osssvessusesendeesesebors 138 AP Bus Delay Constants 063 din deities eian re E E E EA ae east aslo Ani tae 139 Controlling Shaped Pulses Using Attemuators sc ss0ccscisccieccsctsnsensesecusseessevsopeosessvesaausegsnbessuevecesebue 140 Controlling Attenuation scssi eirean Eeen eE rene Ees aE EEE EEC EPEE OEE NEEE VENEN E E EE ES EEE 141 8 VNMR 6 1C User Programming 01 999165 00 A0800 Table of Contents 212 Internal Hardware Delays cciic c cisviceivecssaccasnsesbansnectenecuawecbovesunresvnvesnsvesbecsotdessnestevsaieysadevsonuvalbencceunes sre 142 Delays trom Change Attenuation x seccaisscsezecescssoncs cases ssdsbanerencsstesoenboasuesdbnse zs coaiabatunevesbasoba nsdens 143 Delays trom Changing Status sissies dectieneaiaidta hes dil desde ieee eer Sa iets 143 Waveform Generator High Speed Line Trigger oo ee eeesessesessecececceseecceeceeeeaeseesceeecneeateseeneeaees 145 2 13 Indirect Detection on Fixed Frequency Channel oo eee eeeecceseeeeeeseeeseccesaeceseeaeceeceseseeeeseeeeeeeeseneeas 146 Fixed Frequency DEcoupler ics ics egcictccsscededsavesaussausves i
88. from memory 45 renaming a directory UNIX 278 renaming a file UNIX 278 01 999165 00 A0800 Index repeat until loop 37 reserved words 30 resto parameter 231 results parameter 324 retrieve element from AP table 107 197 retrieving individual parameters 48 Return button 55 return command 37 Return key 23 returning a value 37 reverse a spectrum 298 reverse double quotation marks 56 reverse FID commands 296 reverse mode 147 reverse order of data 297 reverse single quotes C notation 55 revmode c file 147 rf channels control 146 RF file suffix 132 RF monitor errors 77 rf pattern file 205 rf pulse shapes 131 rf pulses waveforms 132 rf shape file 133 rf types 90 rfblk command 296 rfchannel parameter 82 146 rfdata command 296 rftrace command 296 RGI and RG2 delays 80 83 rgpulse statement 80 105 127 128 238 rgradient statement 144 150 152 154 238 rinput command 42 rlpower statement 239 rlpwrf statement 240 rlpwrm statement 92 140 240 rm command UNIX 278 rmdir command UNIX 278 rofl parameter 81 rof2 parameter 81 root directory UNIX 278 rotor period 131 240 rotor position 241 rotorperiod statement 131 241 rotorsync statement 131 241 RS 232 cable 75 rsapply command 298 rt command 27 32 310 rtp command 27 32 rtv command 27 48 run program in background 280 run time statements 102 S safety precautions
89. generates at least three or more depending on the length of the events That is because we generate first a time of rof1 with the amplifier unblanked but transmitter off then a time of pw with the transmitter on and then a time rof2 with the transmitter off but the amplifier unblanked Times that are zero generate no events however For example rgpulse 5 0e 6 v1 0 0 0 0 generates only a single event Although pulses delays and data point acquisitions are the most common things to be in a hardware loop other choices are possible Table 25 lists the number of events that may be generated by each statement On MERCURY VX and MERCURY systems any delay pulse delay decrgpulse etc is limited to 96 seconds within a hardware loop In practice this is not a restriction 01 999165 00 A0800 VNMR 6 1C User Programming 127 Chapter 2 Pulse Sequence Programming Table 25 Number of Events for Statements in a Hardware Loop MERCURY V Statement UNITYTNOVA UNITYplus oie X and mg MERCURY acquire Data Acq 1 to 2048 Controller board acquire Pulse Seq 1 to 2048 Controller board acquire Acq 1 to 1024 Controller board acquire Output 1 to 63 board dcplrphase 1 4 1 6 dcplr2phase dcplr3phase declvlon 1 2 2 high power 2 declvloff decphase 0 0 0 0 0 dec2phase dec3phase decpulse lor2 lor2 lor2 5 or6 decrgpulse 0 3 to6 3
90. hi ablated EE EESO ai 46 axis Provide axis labels and scaling factors esseseeeeseeeesesreseseserrerereerseees 46 beepoff Tor beeper off oreren o kin iia aaah 46 beepon PUN DEC PCT OD we ssscussiscisssessacndveds sqsscsatensetcesonnereesis EE ARR 46 bootup Macro executed automatically when VNMR is started 0 0 0 46 exec Execute a VNMR command 0 eee eeceteceeeeeeee exists Determine if a parameter file or macro exists focus Send keyboard focus to VNMR input window gap Find gap in the current spectrum 00 eee cece csecee cee ceeeeeeeseeeeeneees getfile Get information about directories and files ccceeeseeeeeteeeeeeeees graphis Return the current graphics display status eeeeeeeeseeeeeeeees VNMR 6 1C User Programming 01 999165 00 A0800 Table of Contents length Determine length of a String 0 0 eeeeeeeeseceeeseeseceeeeeeseeaeeereecaeeteeeaes 47 listenoff Disable receipt of messages from send2VnmTt seeeeeeeeeseeeeeeeeeee 47 listenon Enable receipt of messages from send2VnmTr s src 47 login User macro executed automatically when VNMR activated 47 OEE Make a parameter inactive oo eee eeeeceeeeeeeeeeecsecacecaecsseeeeesseeeeeees 48 on Make a parameter active or test its State eee eee eeeeceeeeseeeeeeeee 48 readlk Read current lock l yel sscosiccisccasccssies ascessei beaceedvs beenvesaeetstecansteoetibent 48 PEV Retrieve individual parameters esseseseeseeresssreersrterrrrerere
91. hsdelay Delay specified time with possible homospoil pulse idelay Delay for a specified time with IPA incdelay Real time incremental delay initdelay Initialize incremental delay vfreq Select frequency from table voffset Select frequency offset from table vdelay_list Get delay value from delay list with real time index Get delay value from delay list with real time index Not applicable on MERCURY VX MERCURY and GEMINI 2000 vdelay_list list_number vindex int list_number same index as create_delay_list codeint vindex real time variable Provides a means of indexing into previously created delay lists using a real time variable or an AP table The indexing into the list is from 0 to N 1 where Nis the number of items in the list The delay table has to have been created with the create_delay_list statement It has no return value tlist_number is the number between 0 and 255 for each list This number must match the 1ist_number used when creating the table vindex is a real time variable v1 to v14 or an AP table t1 to t 60 pulsesequence int noffset ndelay listnum double offsets1 256 offsets2 256 delay 256 01 999165 00 A0800 VNMR 6 1C User Programming 269 Chapter 3 Pulse Sequence Statement Reference Related vfreq Applicability Syntax Description Arguments Examples Related vgradient Applicability Syntax Description initialize offset and del
92. il y Vnmr Cmd2 il n Tel Cmd expr il y In the example the Vnmr Variables field requests access to the VNMR parameter i1 The Vnmr Cmd field constructs a MAGICAL expression where i1 is set to y when the check box is selected The Vnmr Cmd2 field constructs a MAGICAL expression where i1 is set to n when the check box is deselected The Tcl Cmd field determines based on the current value of i1 whether the check box should be shown as selected or deselected VNMR 6 1C User Programming 01 999165 00 A0800 6 3 Customizing the Interactive dg Window It is the use of the value of i 1 in this expression as i1 that requires i 1 to be in the Vnmr Variables entry The syntax of the Tcl Cmd field is standard Tcl syntax Whatever the expression it should return a 1 if the check box is to be selected 0 otherwise Radio Element The radio element gives a number of choices only one of which can be selected Whenever one is selected the others are deselected The choices are presented as small diamonds to the left of a label and the choices are presented in a column of rows This is one item where it is useful to use the Row extent so that each choice has its own row The radio element is probably the most difficult item to program correctly The available characteristics are the following Label of element Set of text strings to be displayed to the right of the radio diamonds If the label for a given choice is more than on
93. in the table for Dgroup and factor Note that in Tcl vnmrDgroup returns the key and vnmrUnits returns the scaling factor When the factor is not one already recognized by dg a slightly different procedure is used An example is temp Vnmr Cmd temp SVALUE expr vnmrUnits temp 1 0 0 273 Tcl Cmd expr Stemp vnmrUnits temp 1 0 2 0 273 1 The Tcl ternary if is again used here to convert between the two temperature scales Many variables can be set to a not used condition by setting the variable to n This can be indicated by using the Show Condition characteristic of an entry element An example is lb Vnmr Cmd 1lb SVALUE Tcl Cmd lb Show Condition vnmrOn lb When 1b n the background of the value box is a darker gray or whatever color is specified in dg conf by dgLocal off Note that the background is set dark if the condition is FALSE When we deal with a variable such as sbs a more complex condition may be needed Show Condition expr vnmrOn sb amp amp vnmrOn sbs Here the sbs background is dark when either sb or sbs is n Overall Design of Panes We have used a number of design criteria for our sample panes It is recommended that you stick to the following design rules in order to maintain as much consistency as possible Think of the person who will use the pane when you are not around to explain it e Avoid labels that are just parameter
94. in the user PSG directory When executed seqgen looks first for the user PSG 01 999165 00 A0800 VNMR 6 1C User Programming 157 Chapter 2 Pulse Sequence Programming library vnmrsys psg in the user PSG directory and then in the system library directory vnmr 1lib Modifying a PSG source file and subsequently recompiling the user PSG object directory is done as follows 1 Enter setuserpsg from a UNIX shell done only once Typical output from this command is as follows Creating user PSG directory Copying User PSG library from system directory 2 Copy the desired PSG source file s from Svnmrsystem psg to Svnmruser psg 3 Modify the PSG source files s in the user PSG directory 4 Enter psggen from a UNIX shell or from within Vnmr Typical output from this command is as follows Creating additional source links Compiling PSG Library PSG Library Complete 158 VNMR 6 1C User Programming 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference This chapter contains a detailed reference to the statements used in VNMR pulse sequence programming For a list of statements refer to the Table of Contents For each statement the syntax and a description is provided If the statement contains arguments a description of each argument and an example showing the use of the arguments is also provided For most statements a cross reference to related statements is provided at the end of the listing If the
95. init_rfpattern saves the created pattern as a pattern file with the suffix RF appended to the name in the user s shapelib directory This statement does not have any return value pattern is the name of the pattern file without the RF suffix rfpat_struct is the rf structure that contains the pattern nsteps is the number of steps in the pattern include standard h pulsesequence int nsteps RFpattern pulsel 512 Gpattern gshape 512 pulse2 512 205 VNMR 6 1C User Programming Chapter 3 Pulse Sequence Statement Reference init_gradpattern Not applicable on MERCURY VX MERCURY and GEMINI 2000 nsteps 0 for j 0 j lt 256 j pulsel j phase double 3 0 5 pulsel j amp double 3 2 pulsel j time 1 0 nsteps nsteps 1 init_rfpattern plpat pulsel nsteps nsteps 512 for j 0 j lt nsteps j gshape j amp 32767 0 sin double j 50 0 gshape j time 1 0 init_gradpattern gpat gshape nsteps shaped_pulse plpat pl vl rofl rofl shapedgradient gpat 01 16000 0 Related init_gradpattern pulse shaped_pulse shapedgradient simpulse simshaped_pulse 2 1 WAIT Create gradient pattern file Pulse observe transmitter with amplifier gating Perform shaped pulse on observe transmitter Provide shaped gradient pulse to gradient channel Pulse observe and decouple channels simultaneously Perform simultaneous two pulse shaped pulse
96. int 4095 Maximum value on the slider SLIDER_MIN int 0 Minimum value on the slider SLIDER_UNITS double 1 0 Power in arbitrary units Examples of using G_Power G_Power 0 G_Power POWER_VALUE dpwrf POWER_DEVICE DODEV 0 required terminating zero 2 8 Hardware Looping and Explicit Acquisition The loop and endloop statements described previously generate a soft loop which means that they force the acquisition computer to repeatedly place the information contained within the loop into the pulse program buffer a FIFO If this loop must run extremely fast a condition may arise in which the acquisition computer is not able to provide input to the pulse program buffer as fast as the sequence is required to operate and this technique does not work Because of this problem a different mode of looping known as hardware looping is supported in certain UN YINOVA MERCURY VX MERCURY UNITY plus UNITY and VXR S systems In this mode the pulse program buffer provides its own looping and the speed can be at the maximum possible rate with the only limitation being the number of events that can occur during each repetition of the loop Table 24 lists statements related to hardware looping Hardware looping is not available on GEMINI 2000 01 999165 00 A0800 VNMR 6 1C User Programming 125 Chapter 2 Pulse Sequence Programming 126 Table 24 Hardware Looping Related Statements acquire num_p
97. is handled automatically by the statements dec3rgpulse dec3shaped_pulse and dec3spinlock dec3prgon generally needs to be enabled with an explicit dec3on statement and followed by a dec3o0ff call dec30ff Turn off third decoupler Set quadrature phase of first decoupler decphase phase codeint phase real time variable for quad phase Sets quadrature phase multiple of 90 for the first decoupler rf decphase is syntactically and functionally equivalent to txphase and is useful for a decoupler pulse in all cases where t xphase is useful for a transmitter pulse phase is the quadrature phase for the first decoupler rf The value must be a real time variable v1 to v14 oph ct etc decphase v4 dcplrphase Set small angle phase of first decoupler rf type C or D dec2phase Set quadrature phase of second decoupler dec3phase Set quadrature phase of third decoupler txphase Set quadrature phase of observe transmitter Set quadrature phase of second decoupler Systems with a second decoupler dec2phase phase codeint phase real time variable for quad phase Sets quadrature phase multiple of 90 for the second decoupler rf phase is the quadrature phase for the second decoupler rf The value must be a real time variable v1 to v14 oph ct etc dec2phase v9 dcplr2phase_ Set small angle phase of second decoupler rf type C or D Set quadrature phase of first decoupler decphase Set quadrature
98. is not an ASCII file n abort endif cat n else write error You must select one element abort endif 60 VNMR 6 1C User Programming 01 999165 00 A0800 1 6 Customizing the Files Menus Notice in each case the macro first establishes that the user selected exactly one file and then obtains that file name Each successive example shows how one can program more operations using the file name Several files can be displayed by selecting individual file names with f ilesinfo To avoid obscuring the macro s structure we shall return to the original function of just displaying the selected files not checking for directories or non ASCII files filesinfo number f if Sf lt 1 then write error You must select on lement abort endif i 1 repeat filesinfo name i n write alpha Contents of s Sn cat n write alpha i Sitl until i gt f To illustrate using the redisplay keyword argument we show how one might program a Delete button Again we limit the user to deleting one file at a time filesinfo number Sf n if f 1 then filesinfo name n delete n filesinfo redisplay else write error You must select on lement abort endif Once the macro deletes the selected file it displays again the files in the current directory using filesinfo redisplay 01 999165 00 A0800 VNMR 6 1C User Programming 61 Chapter 1 MAGICAL II Programming 62 VNMR 6
99. is the same as decrgpulse if go is typed width is the duration in seconds of the decoupler transmitter pulse phase sets the decoupler transmitter phase The value must be a real time variable RG1 is the time in seconds that the amplifier is gated on prior to the start of the pulse RG2 is the time in seconds that the amplifier is gated off after the end of the pulse label1 is the short character string to be given to the slider when displayed in the Acquisition window acqi program idecrgpulse pp v5 rofl1l rof2 decpul idecrgpulse pp v4 rofl rof2 pp decrgpulse Pulse decoupler transmitter with amplifier gating Delay for a specified time with IPA All systems except MERCURY VX MERCURY and GEMINI 2000 idelay time label double time delay in sec char label slider label in acqi Works similar to the delay statement but generates interactive parameter adjustment IPA information when gf or go acqi is entered idelay is the same as delay if go is entered time is the length of the delay in seconds label is the short character string to be given to the slider when displayed in the Acquisition window acqi program idelay d1 delay idelay d1 d1 delay Delay for a specified time Execute succeeding statements if argument is zero 1 ifzero vi codeint vi real time variable to check for zero 2 ifzero n vi int n 1 3 must correspond to else
100. loc user solvent exp textfield Ta 8 outfields identifies the items that will be output by the J enter program The order of the listed items is the order 10 in which they will be output 11 set outfields loc user exp solvent textfield userdir data stat separator 12 13 Available input styles include info radio check xradio xcheck 14 xradiocustom xcheckcustom and textentry Toy 16 set loc id loc 17 set loc label Sample Number 18 set loc menulabel Sample Number is 19 set loc style radio 20 set loc file 21 set loc min 1 22 set loc max 50 23 set loc numPerLine 20 24 set loc required 1 25 set loc output SAMPLE 26 set loc duplicates 0 27 set loc errormess No sample locations available 28 set loc errormess2 Sample Tray is Completely Defined 29 30 To select locations instead of allowing a choice 31 uncomment the following lines 32s set loc label Insert Sample at location 33 set loc output SAMPLE 34 set loc style info 353 set loc output SAMPLE 36 set loc value SnextLoc 31 set loc usenextloc 38 39 set user id user 40 set user label User identification 41 set user menulabel User identification is 42 set user style xradio 43 set user file users 44 set user numPerLine 6 45 set user required 1 46 set user output USER 47 48 The following five lines set USER automatically 49 If you do not want USER to appear on the enter screen 50 remov
101. max errormess and usenextloc The syntax of setting attributes is shown on lines 16 to 27 The word set is a command that takes two arguments The first argument is a parameter name and the second is a value For example the line set loc id loc sets the parameter loc id to the word Loc The id attribute should match the name of the item The value of the label attribute is displayed at the top of the window pane used for that selection The label Sample Number shown in Figure 9 is controlled by the line set loc label Sample Number Sample Entry Form 4 5 6 2 18 9 10 aa 22 13 2 15 17 19 20 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 44 45 46 47 48 49 50 User identification Solvent Selection EDEL 020 Benzene DMSO Acetone Cyclohexane Toluene Methanol Experiment Selection H1 c13 F19 pE HC H gCOSY H TOCSY H gHSQC H gCOSY gHSQc H gCOSY HSQC gHMBC H gCOSY HSQC gHMBC HSQCTOxY H COSY C DEPT HETCOR H COSY C APT H TOCSY NOESY H TOCSY ROESY H TOCSY HMQC Text E Customize Parameters Add Entry Number of samples submitted 0 Figure 9 Default Interface enter Program 01 999165 00 A0800 VNMR 6 1C User Programming 315 Chapter 6 Customizing Graphics Windows 316 Note that if a parameter name is to be set to more than one word the words need to be enclosed in double quotes The menulabel attribute is currently unused Setting the Types of Wi
102. memory and compete for space with the acquisition data for each array element If a list is 166 VNMR 6 1C User Programming 01 999165 00 A0800 Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference created the return value is the number of the list 0 to 255 if an error occurs the return value is negative create_freq_list creates what is called a global list Global lists are different from AP tables in that the lists are sent down to the acquisition console when the experiment starts up and are accessible until the experiment completes In working with arrayed experiments be careful when using a 1 in the 1ist_number argument because a list will be created for each array element In this case a list parameter can be created as an arrayed parameter with protection bit 8 256 set To read in the values of this type of parameter use the get array statement To ensure that the list is only created once check the global array counter variable ix and only call create_freq_list to create the list when it equals 1 An example is shown in the entry for the create_delay_list statement list is a pointer to a list of frequencies nvals is the number of values in the list device is OBSch observe transmitter or DECch first decoupler For the UNITYTNOVA and UNITYplus only device can also be DEC2ch second decoupler or DEC3ch third decoupler List_number is 1 or a unique number from 0 to 255 for
103. more information on UNIX refer to the Sun manuals covering Solaris or to UNIX general references found at larger bookstores Command Entry Single command entry Command names Multiple command separator Arguments File Names Typical shorthand names usually used Level separator Individual filenames Characters in filenames First character in filename File Handling Commands Delete unlink a file s Copy a file Rename a file Make an alias link Sort files Tape backup Directory Names Home directory for each user Working directory Shorthand for current directory Shorthand for parent directory Shorthand for home directory Root directory Directory Handling Commands Create or make a directory Rename a directory Remove an empty directory Delete directory and all files in it List files in a directory short list 278 VNMR 6 1C User Programming commandname Generally lowercase case sensitive semicolon or new line commandname argl arg2 vnmr fidlib fidld forward slash Any number of characters 256 unique Underline period often used First character unrestricted rm filenames cp filename newfilenam mv filename newfilenam ln filenamel filename2 sort filenames tar Directory assigned by administrator Current directory user is in single period two periods tilde character forward slash mkdir directoryname mv dirname newdirname rm
104. number of phase encode steps Pulse sequence generation aborts if the DACs on a particular gradient are overrun after the angles and amplitude have been resolved pattern is the name of a gradient shape file width is the length in seconds of the gradient statl stat2 stat3 are values in gauss cm of the components for the static portion of the gradient in the logical reference frame step2 is the value in gauss cm of the component for the step size change in the variable portion of the gradient vmult2 is a real time math variable v1 to v14 ct zero one two three or reference to AP tables t 1 to t 60 whose associated values vary dynamically in a manner controlled by the user 01 999165 00 A0800 VNMR 6 1C User Programming 225 Chapter 3 Pulse Sequence Statement Reference Related wait is a keyword either WAIT or NOWAIT that selects whether or not a delay is inserted to wait until the gradient has completed before executing the next statement tag is a unique integer that tags the gradient element from any other gradient elements used in the sequence These tags are used for variable amplitude pulses phase_encode_shapedgradient Oblique shaped gradient with PE on 1 axis pe2_shapedgradient Oblique shaped gradient with phase encode in two axes Applicability Syntax Description Arguments Related Not applicable on MERCURY VX MERCURY and GEMINI 2000 pe2_shapedgradient pattern
105. of attributes associated with them name group array size basictype display group enumeration subtype max min values protection status active step size The variable s attributes are used by programs when manipulating variables Global Variables The most important global variables used in macros are the VNMR parameters themselves Thus parameters like vs vertical scale nt number of transients at acquisition time etc can be used ina MAGICAL macro Like any variable they can be used on the left side of an equation and hence their value changed or they can be used on the right side of an equation as part of a calculation perhaps to set another parameter The real value parameters r1 r2 r3 r4 r5 r6 and r7 and the string parameter n1 n2 and n3 are not NMR variables but can be used by macros In using these parameters it is important to remember that they are experiment based parameters If you are in exp1 and a macro changes experiments by using the command jexp3 for example a new set of such parameters appears Similarly recalling parameters or data with the rt or rtp commands overwrites the current values of these parameters just as it overwrites the values of all other parameters VNMR 6 1C User Programming 01 999165 00 A0800 1 2 Programming with MAGICAL Within a single experiment and assuming that the rt and rtp commands are not used however these parameters do act like global parameters in that all macr
106. on MERCURY VX MERCURY and GEMINI 2000 Use sim4pulse pwl pw2 pw3 pw4 phasel phase2 phase3 phase4 RG1 RG2 to perform simultaneous pulses on as many as four different rf channels Except for the added arguments pw4 and phase4 for a third decoupler the arguments in sim4pulse are defined the same as sim3pulse If any pulse is set to 0 0 no pulse is executed on that channel sim4pulse has no meaning on MERCURY VX MERCURY and GEMINI 2000 Setting Transmitter Quadrature Phase Shifts The statements txphase decphase dec2phase dec3phase dec4phase control transmitter quadrature phase multiple of 90 Table 10 summarizes these statements Table 10 Transmitter Quadrature Phase Control Statements decphase phase Set quadrature phase of first decoupler dec2phase phase Set quadrature phase of second decoupler dec3phase phase Set quadrature phase of third decoupler dec4phase phase Set quadrature phase of fourth decoupler txphase phase Set quadrature phase of observe transmitter To set the transmitter phase use t xphase phase where phase is areal time variable v1 to v14 etc or a real time constant zero one etc that references the desired phase This enables changing the transmitter phase independently from a pulse 01 999165 00 A0800 VNMR 6 1C User Programming 85 Chapter 2 Pulse Sequence Programming For example knowing that the transmitter phase takes a finite time to shift as muc
107. on observe channel 1446 RF power amp power supply failed on observe channel 1447 RF power monitoring disabled on observe channel 1448 Reflected power monitoring disabled on observe channel 1449 RF power amp monitoring disabled on observe channel 01 999165 00 A0800 VNMR 6 1C User Programming 77 Chapter 2 Pulse Sequence Programming 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1531 1532 1533 1534 1535 Table 5 Acquisition Status Codes continued Reserved RF monitor trip A2 occurred on decouple channel Reserved RF monitor trip B2 occurred on decouple channel Reserved RF monitor trip C2 occurred on decouple channel RF Monitor board PALI TUSUPI missing on decouple channel Excessive reflected power on decouple channel RF amplifier gating disconnected on decouple channel Excessive power detected by PALI on decouple channel RF Monitor system TUSUPI heartbeat stopped on decouple channel Power supply for PALI TUSUPI failed on decouple channel PALI asserted REQ_ERROR on decouple channel should never occur Excessive power detected by TUSUPI on decouple channel RF power amp overdrive on decouple channel RF power amp excessive pulse width on decouple cha
108. operation and the execution of commands returns to the first macro number equals 5 not 10 If the first macro is run again at a later time number starts with an undefined value It is good practice to use local variables whenever possible Local variables can also be created on the command input line These variables are automatically created but are not deleted and hence this is not a recommended practice use r1 r2 etc instead Accessing a variable that does not exist displays the error message Variable variable_name doesn t exist Arrays Both global and local variables whether real or string can be arrayed Array elements are referred to by square brackets such as pw 1 Indices for the array can be fixed numbers pw 3 global variables ow r1 or local variables pw i Of course the index must not exceed the size of the array You can use the s i ze operator to determine the array size For example the statement r1 size d2 sets r1 to number of elements in variable d2 If the variable has only a single value size returns a 1 if the variable doesn t exist it returns a 0 Some arrays such as a pulse width array are user created by keyboard entry Other arrays such as 11 frq and 1lamp are created by the software in this case when a line list is performed In both these cases a macro can refer to any existing element of the array pw 4 or llfrq 5 for example A MAGICAL macro can a
109. others Inclusion in this document does not imply that any particular feature is standard on the instrument UNITYINOVA MERCURY Gemini GEMINI 2000 UNITYplus UNITY VXR XL VNMR VnmrS VnmrX Vnmrl VnmrV VnmrSGI MAGICAL II AutoLock AutoShim AutoPhase limNET ASM and SMS are registered trademarks or trademarks of Varian Inc Sun Solaris CDE Suninstall Ultra SPARC SPARCstation SunCD and NFS are registered trademarks or trademarks of Sun Microsystems Inc and SPARC International Oxford is a registered trademark of Oxford Instruments LTD Ethernet is a registered trademark of Xerox Corporation VXWORKS and VxWORKS POWERED are registered trademarks of WindRiver Inc Other product names in this document are registered trademarks or trademarks of their respective holders Overview of Contents SAFETY PRECAUTIONS siccvssicstinvessctsdsaceatesievesatetlateverisassecseetivestntecteecieceeee 19 ialis elo TION MP E snes wedenatecuideusiedeieasentuleancnaeees 23 Chapter 1 MAGICAL I Programming cssseeeecessseeeeeeeeseeeeenseeeeeeeensneees 25 Chapter 2 Pulse Sequence Programming sssssnsnsunnnnnennnnnnnnnnnnnnnnnnnnnnnnn nnne 63 Chapter 3 Pulse Sequence Statement Reference ccssseeceeeseeeeeeeseees 159 Chapter 4 UNIX Level ProgrammMing sccccssseeeeeeseeeeeeesseeeeeeessseeeeeeeees 277 Chapter 5 Parameters and Data ccsssseeeeeeseeeeeeeseeneeeeeeseneeeeseseeeeeenees 283 Chapte
110. phase ncycles 01 999165 00 A0800 VNMR 6 1C User Programming 137 Chapter 2 Pulse Sequence Programming Table 29 Spin Lock Control Statements decspinlock Set spin lock waveform control on first decoupler dec2spinlock Set spin lock waveform control on second decoupler dec3spinlock Set spin lock waveform control on third decoupler spinlock Set spin lock waveform control on observe transmitter decspinlock name 90_pulselength tipangle_resoln phase ncycles decs2pinlock name 90_pulselength tipangle_resoln phase ncycles decs3pinlock name 90_pulselength tipangle_resoln phase ncycles spinlock name 90_pulselength tipangle_resoln phase ncycles name is the name of the file in shapelib that stores the decoupling pattern leave off the DEC file extension 90_pulselength is the pulse duration for a 90 tip angle tipangle_resolnis the resolution in tip angle degrees to which the decoupling pattern is stored in the waveform generator phase is the phase angle of the spin lock it must be a real time variable and ncycles is the number of times that the spin lock pattern is to be executed e g spinlock mlev16 pw90 90 0 v1 50 Both rf gating and the mixing delay are handled within this statement Spin Lock Waveform Control on Decouplers The decspinlock dec2spinlock and dec3spinlock set spin lock waveform control on the first second and third decouplers respectively The arguments are the same as
111. processing The reformatting routines allow users to compress or uncompress their data f1lashc move data around between experiments and into almost any format mf mfb1k mfdata mftrace reverse data while moving it rfb1k rfdata rft race oruse a table of values in this case an AP table stored in t ablib to sort and reformat scans of data tabc tcapply In this section standard and compressed data are defined reformatting options are described and several examples are presented Table 39 summarizes the reformatting commands described in this section Note that the commands rsapply tcapply tcclose and tcopen are for 2D spectrum data the remaining commands in the table are for FID data Standard and Compressed Formats Usually when discussing standard and compressed data formats standard means the data was acquired using the arrayed parameters ni and ni2 which specify the number of increments in the second and third dimensions and compressed means using parameter nf to specify the increments in the second dimension For multislice imaging standard means using ni to specify the phase encode increments and nf to specify the number of slices and compressed means using nf to specify the phase encode increments while arraying the slices Compressed compressed means using nf to specify the phase encode increments and slices for 2D or to specify the phase encode increments in the second and third dimensions for 3D In compressed co
112. pulse duration in seconds for a 90 tip angle on the first decoupler tipangle_resoln is the resolution in tip angle degrees to which the decoupling pattern is stored in the waveform generator decprgon garp1 1 dmf 1 0 decprgon modt ype pwx90 dres n50ns_ticks decprgon waltz16 1 dmf 90 0 decprgoff End programmable decoupling on first decoupler dec2prgon Start programmable decoupling on second decoupler dec3prgon Start programmable decoupling on third decoupler obsprgon Start programmable control of obs transmitter Start programmable decoupling on second decoupler Systems with a waveform generator on rf channel for the second decoupler dec2prgon pattern 90_pulselength tipangle_resoln name of DEC text file 90 deg pulse length in sec char pattern double 90_pulselength 177 VNMR 6 1C User Programming Chapter 3 Pulse Sequence Statement Reference Description Arguments Examples Related dec3prgon Applicability Syntax Description Arguments Examples Related double tipangle_resoln tip angle resolution Executes programmable decoupling on second decoupler under waveform generator control and returns the number of 50 ns ticks as an integer value in one cycle of the decoupling pattern Explicit gating of the second decoupler with dec2on and dec2of f is generally required Arguments can be variables which require the appropriate get val
113. pulse sequence include lt standard h gt static int phasecycle 4 0 2 1 3 pulsesequence equilibrium period settable t1 4 phasecycle status A hsdelay d1 tau delay aA status B ipulse p1 zero p1 This ipulse statement is equivalent to the following general pulse statement a G_Pulse PULSE_WIDTH pl PULSE_PHASE zero SLIDER_LABEL pl k 0 se G_Delay DELAY_TIME d2 SLIDER_LABEL q2 SLIDER_MAX TO 0 observe period status C ipulse pw t1 pw setreceiver tl same pulse sequence can be used to execute go as well as go acqi however IPA information is only generated when go acqi is used Interactive adjustment of simultaneous pulses is not supported A limit of 10 has been set on the number of calls with a label This limits the number of parameters that can be adjusted within one pulse sequence Note that a subroutine call within a hardware loop is still only one label Parameters are adjusted at the end of a sweep Since this takes a finite amount of time steady state may be affected Of course changing any parameter value also affects the steady state so this should be of little or no consequence Generic Pulse Routine The G_Pulse generic pulse routine has the following syntax G_Pulse PULSE_WIDTH pw PULSE_PRE_
114. pulse sequence suppose you wish to create a new pulse sequence with new variable names and have it fully functional from VNMR Usually the best way to compose a new pulse sequence is to start from a known good pulse sequence 01 999165 00 A0800 VNMR 6 1C User Programming 117 Chapter 2 Pulse Sequence Programming and from a known good parameter set For many pulse sequences s2pul cin vnmr psglib and s2pul par in vnmr par1lib are a good place to start To create a new pulse sequence similar to s2pu1 but with new variable names and using a shaped pulse do the following steps 1 Ina shell window enter cda vnmrsys psglib 2 Use a text editor such as vi to create the file newpul c shown in Listing 9 Listing 9 File newpul c for a New Pulse Sequence newpul c new pulse sequence include lt standard h gt static int ph2 4 0 1 2 3 pulsesequence double dlinew d2new plnew pwnew char patnew MAXSTR dinew getval dlnew d2new getval d2new plinew getval plnew pwnew getval pwnew getstr patnew patnew assign zero vl settable t2 4 ph2 getelem t2 ct v2 equilibrium period status A hsdelay dinew tau delay status B pulse plnew vl hsdelay d2new Va observe period status C shaped_pulse patnew pwnew v2 rofl rof2 If you don t have a waveform generator use the following line apshaped_puls
115. recon statements These statements control the receiver gates except when pulsing the observe channel in which case the receiver is off or during acquisition in which case the receiver is on The recoff and recon statements available only on UNITYTNOVA systems affect the receiver gate only and do not affect the amplifier blanking gate which is the role of rcvroff and rcvron e On YNTYZNOVA and GEMINI 2000 the receiver is on only during acquisition except for certain imaging pulse sequences that have explicit acquires such as SEMS MEMS and FLASH and for the initparms_sis statement that defaults the receiver gate to on e On MERCURY VX MERCURY UNITY and VXR S receiver gating is tied to the amplifier blanking and is normally controlled automatically by the pulse statements rgpulse pulse obspulse decrgpulse decpulse and dec2rgpulse e On UNITYplus the observe amplifier blanking and the receiver gate are tied together Because the decouplers do not affect the receiver and vice versa only the rgpulse pulse and obspulse statements and a shaped pulse statement gate the receiver Amplifier Channel Blanking and Unblanking Amplifier channel blanking and unblanking methods depend on the system e On N TYINOVA the receiver and amplifiers are not linked To explicitly blank and unblank amplifiers the following statements are provided For the amplifier associated with the observe transmitter obsblank and obsunblank
116. register 236 244 273 user device interfacing 97 user library 70 141 user macro 44 user macro directory 27 user_templates directory 328 user created parameters 117 user customized pulse sequence generation 157 usermacrol usermacro8 macros 53 user programmable menus 57 user written weighting function 307 V vl v2 v14 real time variables 73 98 vagradient statement 265 vagradpulse statement 154 266 values of a parameter 302 variable angle gradient 265 variable angle gradient pulse 266 variable angle shaped gradient 266 variable angle shaped gradient pulse 268 variable declaration 33 73 variable gradient pulse generation 248 variable scan 272 variable shaped gradient pulse generation 249 variable types 32 variables using parameters 26 vashapedgradient statement 154 267 vashapedgradpulse statement 154 268 VAST accessory 311 VAX systems 283 vbg shell script UNIX 281 vdelay statement 80 268 vdelay_list statement 157 269 vertical bar notation UNIX 279 vfreq statement 157 270 veradient statement 144 150 155 270 vi command UNIX 279 280 vi command VNMR 280 vi text editor 54 300 VNMR background processing 281 macros executed at startup 46 47 software package 277 source code license 285 versus Vnmr 24 Vnmr command UNIX 281 VNMR Command and Parameter Reference manual 26 VNMR versus Vnmr 24 vnmr_confirmer command 41 vnmrDgroup procedure 342 vnmredito
117. returns the square root of a real number e trunc truncates real numbers VNMR 6 1C User Programming 01 999165 00 A0800 1 2 Programming with MAGICAL Table 2 Order of Operator Precedence Highest First in MAGICAL Group Operation Description Example special sqrt square root a sqrt b trunc truncation 3 trunc 3 6 typeof return argument type if typeof 1 then size return argument size rl size d2 unary negative a 5 multiplicative multiplication a 2 c division b a 2 remainder 1 4 3 mod modulo 3 7 mod 4 additive addition a x 4 subtraction b y sw relational lt less than if a lt b then gt greater than if a gt b then lt less than or equal to if a lt b then gt greater than or equal to if a gt b then equality equal to if a b then lt gt not equal to if a lt gt b then logical not negation if not a b then and logical and if rl and r2 then or logical inclusive or if r1 2 or r2 4 then assignment equal a 3 e typeof returns an identifier 0 or 1 for the type real or string of an argument e size returns the number of elements in an arrayed parameter The unary multiplicative and additive operators apply only to real variables The addition operator can also be used with string variables to concatenate two strings together The mathematical operators can not be used with mixed variable types If the
118. same time and much more Refer to Chapter 3 Pulse Sequence Statement Reference for a full description of dos_show including examples Table 19 Statements for Controlling Graphical Display of a Sequence dps_off Turn off graphical display of statements dps_on Turn on graphical display of statements dps_show options Draw delay or pulses in a sequence for graphical display dps_skip Skip graphical display of next statement dps_show has many options See Chapter 3 Pulse Sequence Statement Reference for the syntax and examples of use 2 5 Real Time AP Tables 104 Real time acquisition phase AP tables can be created under pulse sequence control on all systems except GEMINI 2000 These tables can store phase cycles an array of attenuator values etc In the pulse sequence the tables are associated with variables t1 t2 t 60 The following pulse sequence statements accept the table variables t 1 to t 60 at any place where a simple AP variable such as v1 can be used pulse rgpulse decpulse decrgpulse dec2rgpulse dec3rgpulse simpulse txphase decphase dec2phase dec3phase xmtrphase dcplrphase dcplr2phase dcplr3phase VNMR 6 1C User Programming 01 999165 00 A0800 2 5 Real Time AP Tables phaseshift spinlock decspinlock dec2spinlock dec3spinlock shaped_pulse decshaped_pulse dec2shaped_puls dec3shaped_puls simshaped_pulse sim3shaped_pulse power pwrf For example the statement rgpulse pw
119. scale and set the values correctly The values applied to each gradient axis are as follows x gradivl sin phi sin theta y gradlvl cos phi sin theta z gradlvl cos theta vagradient leaves the gradients at the given levels until they are turned off To turn off the gradients add a vagradient statement with gradlv1 set to zero or include the zero_all_gradients statement vagradient is used if there are actions to be performed while the gradients are on vagradpulse is simpler to use if there are no other actions performed while the gradients are on Arguments gradlv1 is the gradient amplitude in gauss cm theta defines the angle in degrees from the z axis phi defines the angle of rotation in degrees about the xy plane 01 999165 00 A0800 VNMR 6 1C User Programming 265 Chapter 3 Pulse Sequence Statement Reference Examples Related vagradpulse Applicability Syntax Description Arguments Examples Related vagradient 3 0 54 7 0 0 pulse pw oph delay 0 001 pw zero_all_gradients magradient Simultaneous gradient at the magic angle magradpulse Simultaneous gradient pulse at the magic angle mashapedgradient Simultaneous shaped gradient at the magic angle mashapedgradpulse Simultaneous shaped gradient pulse at the magic angle vagradpulse Variable angle gradient pulse vashapedgradient Variable angle shaped gradient vashapedgradpulse Variable angle shaped gradie
120. seqcon 1 vl12 endmsloop End multislice loop loop Start loop peloop Phase encode loop Multiply integer values mult vi vj vk codeint vi real time variable for first factor codeint vj real time variable for second factor codeint vk real time variable for product Sets the value of vk equal to the product of the integer values vi and vj vi is an integer value vj is another integer value and vk is the product of vi and vj All arguments must be real time variables v1 to v14 etc mult v3 v5 v4 add Add integer values assign Assign integer values dbl Double an integer value decr Decrement an integer value divn Divide integer values hivy Half the value of an integer iner Increment an integer value mod2 Find integer value modulo 2 mod4 Find integer value modulo 4 modn Find integer value modulo n sub Subtract integer values O obl_gradient Applicability Syntax Description Arguments Examples Related Execute an oblique gradient Not applicable on MERCURY VX MERCURY and GEMINI 2000 obl_gradient level1 level2 level3 double levell level2 level3 gradient values in G cm Defines an oblique gradient with respect to the magnet reference frame This statement is basically the same as the statement ob lique_gradient except that ob1_gradient uses the parameters psi phi and theta in the parameter set rather than setting them directly It has no return value
121. size of the scale item often requires a Row extent of 2 and a Column extent of 2 or more The value of the scale can be changed by clicking mouse button 1 or 2 in the scale or dragging the slider The available characteristics are the following Label of element Text string to be displayed to the left of the menu box This field is optional Width of element Amount of space reserved to display the value of the scale If the width is 0 the value is not displayed If the center justification is selected the label and value are aligned along the left edge and the scale is aligned along the right edge of the grid rectangle Scale Tcl pars The scale element has many configuration options These can be set here In general an option is a keyword preceded by a minus sign followed by a value Scales include the following options from Value corresponding to left or top of scale to Value corresponding to right or bottom of scale tickinterval Spacing between numerical values below or to left of scale A 0 removes all values resolution Value specifying resolution of values A value greater than zero causes the scale value to be an even multiple of the resolution The default value is 1 which gives integer resolution showvalue Set to 0 or 1 to show the scale value above or to the right of the slide The default is 0 for no orient Set to v for a vertical scale or h for a horizontal scale h is default If v is chosen th
122. statement initval Initialize real time variable to specified value Set real time incremental delay All systems except MERCURY VX MERCURY and GEMINI 2000 incdelay count index codeint count real time variable int index time increment DELAY1 DELAY2 etc Enables real time incremental delays Before incdelay can be used to set a delay an associated initdelay statement must be executed to initialize the time increment and delay index count is a real time variable ct v1 to v14 etc that multiplies the time_increment initialized by the init delay statement to set the delay time index is DELAY1 DELAY2 DELAY3 DELAY4 or DELAYS It identifies which time increment is being multiplied by count to equal the delay incdelay ct DELAY1 incdelay v3 DELAY2 delay Delay for a specified time hsdelay Delay with possible homospoil pulse idelay Delay for a specified time with IPA initdelay Initialize incremental delay vdelay Delay with fixed timebase and real time count Generate dynamic variable gradient pulse Not applicable on MERCURY VX MERCURY and GEMINI 2000 incgradient channel base incl inc2 inc3 multl mult2 mult3 char channel gradient x y or z 01 999165 00 A0800 VNMR 6 1C User Programming 203 Chapter 3 Pulse Sequence Statement Reference Description Arguments Examples Related incr Syntax Description int base
123. statement It can range from 0 to 4095 60 dB on YNTYZNOVA and UNITYplus about 6 dB on other systems device is OBSch observe transmitter or DECch first decoupler On the UNITYINOVA and UNITYplus only device can also be DEC2ch second decoupler or DEC3ch third decoupler pwrf vl OBSch ipwrf Change transmitter or decoupler fine power power Change transmitter or decoupler power linear amp system rlpwrf Set transmitter or decoupler fine power Change transmitter or decoupler linear modulator power UNITYTNOVA and UNITYplus systems only Use of statements obspwrf decpwrf dec2pwrf or dec3pwrf as appropriate is preferred pwrm power device int power new value for fine power control int device OBSch DECch DEC2ch or DEC3ch Changes the linear modulator power of the device specified by adjusting the optional fine attenuators Do not execute pwrm and ipwrm together because they will cancel each other s effect power is the linear modulator power desired It must be a real time variable v1 to v14 etc which means the power level as an integer cannot be placed directly in the pwrm statement power can range from 0 to 4095 60 dB on UNITYINOVA and UNITYplus about 6 dB on UNITY systems device is OBSch observe transmitter or DECch first decoupler For the UNITYTNOVA and UNITYplus only device can also be DEC2ch second decoupler or DEC3ch third decoupler pwrm vl OBSch
124. systems use rgradient and vagradient and MERCURY VX and MERCURY uses the 1k_sample and 1k_hold statements Table 36 lists delays for shaped gradient statements on systems with gradient waveform generators gradt ype w or gradtype q The times for the three axis gradient statements ob1_gradient oblique_gradient pe2_gradient phase_encode3_gradient etc are the overhead times for setting all three gradients The gradients are always set in sequential x y z order It is important to note that starting with VNMR 5 1 some gradient statements use DAC values to set the gradient levels and others use values in gauss cm The lower level gradient statements gradient rgradient shapedgradient etc use DAC values and the obliquing and variable angle gradient statements use gauss cm The gradient statements associated with DAC values are used in single axis PFG pulse sequences and microimaging pulse sequences while the gradient statements associated with gauss cm are used in imaging pulse sequences and triple axis PFG pulse sequences Setting the Gradient Current Amplifier Level To set the gradient current amplifier level use rgradient channel value where channelis X x Y y Z or z only Z or z is supported on MERCURY VX MERCURY and GEMINI 2000 and value is a real number for the amplifier level e g rgradient z 1327 0 For the Performa I PFG module value must be from 2048 to 2047 for Performa II v
125. table Etdiv Divide an AP table into a second table ttmult Multiply an AP table by a second table txphase Set quadrature phase of observe transmitter Syntax txphase phase codeint phase variable for quadrature phase Description Sets the observe transmitter quadrature phase to the value referenced by the real time variable so that the transmitter phase is changed independently from a pulse This may be useful to preset the transmitter phase at the beginning of a delay that precedes a particular pulse For example in the sequence txphase v2 delay d2 pulse pw v2 the transmitter phase is changed at the start of the d2 delay In a normal sequence an rof1 time precedes the pulse to change the transmitter phase Arguments phase is the quadrature phase for the observe transmitter It must be a real time variable v1 to v14 oph ct etc Examples txphase v3 Related decphase Set quadrature phase of first decoupler dec2phase Set quadrature phase of second decoupler dec3phase Set quadrature phase of third decoupler vagradient Variable angle gradient Syntax vagradient gradlvl theta phi double gradlvl gradient amplitude in G cm double theta angle from z axis in degrees double phi angle of rotation in degrees Description Applies a gradient of amplitude gradlv1 at an angle theta from the z axis and rotated about the xy plane at an angle phi Information from a gradient table is used to
126. the button This field is optional Width of the button This field is optional The actual width depends on this entry and the value of the Justify field If any value greater than zero is set in this field a button of roughly that many characters is shown If the entry is set to zero a default size based on the Label of element field is used If the field is empty or a non real value is input it behaves as if the value of zero were set provided Justify is set to left or right If Justify is set to center an empty field or a non real value causes the button to occupy the entire width of the selected grid rectangle MAGICAL expression or command executed when the button is pressed The field is optional however if nothing is specified nothing happens when the button is pressed The entry element is similar to label except that a value is not only displayed but can be directly altered The available characteristics are the following Label of element Units Width of element Vnmr Variables Vnmr Cmd Tcl Cmd 01 999165 00 A0800 Text string to be displayed to the left of the parameter value This field is optional Text string to be displayed to the right of the parameter value This field is optional Width of the recessed entry field In this field the parameter value is displayed and entered This field is optional but is automatically set to 8 if no value or an illegal value is entered List of VNMR param
127. the decoupler board is always open and therefore need not be switched open during RG1 In contrast if homo y the slow gate on the decoupler board is normally closed and must therefore be allowed sufficient time during RG1 to switch open homo is not used on the MERCURY VX MERCURY or GEMINI 2000 For systems with linear amplifiers RG1 for a decoupler pulse is important from the standpoint of amplifier stabilization under either of the following conditions e When tn and dn both equal 3H 1H or 19F high band nuclei e When tn and dn are less than or equal to 31p low band nuclei For these conditions the decoupler amplifier module is placed in the pulse mode in which it remains blanked between pulses In this mode RG1 must be sufficiently long to allow the amplifier to stabilize after blanking is removed 2 Us on MERCURY VX MERCURY and GEMINI 2000 systems or 5 to 10 us for high band nuclei and 10 to 20 us for low band nuclei on other systems On 500 MHz systems that use the ENI 5100 class A amplifier for low band nuclei on the observe channel RG1 should be set for 40 to 60 us If the tn nucleus and the dn nucleus are in different bands such as tn is 1H and dn is 13C the decoupler amplifier module is placed in the continuous wave CW mode in which it is always unblanked regardless of the state of the receiver In this mode RG1 is unimportant with respect to amplifier stabilization prior to the decoupler pulse but
128. the previous version of VNMR Refer to the VVMR 6 1C Release Notes for a description of new features to the software Other Manuals This manual should be your basic source of information on MAGICAL programming pulse sequence programming manipulating parameters and data and customizing graphics windows Other VNMR 6 1 manuals you should have include e Getting Started e Walkup NMR Using GLIDE e User Guide Liquids NUR e User Guide Solid State NMR e User Guide Imaging e VNMR Command and Parameter Reference e VNMR and Solaris Software Installation All of these manuals are shipped with the VNMR software These manuals other Varian hardware and installation manuals and most Varian accessory manuals are also provided online so that you can view the pages on your workstation and print copies Types of Varian Software and Spectrometers VNMR is the trademark name of Varian s NMR software which includes acquisition data processing menus macros and pulse sequences Occasionally you will also see Vnmr mentioned in VNMR manuals as well as in the online help Vnmr is the name of the main NMR program that runs on UNIX forming the nucleus of VNMR Specific applications of VNMR include VNMR for computers using the X Window System VnmrX VNMR for IBM workstations VnmrI and VNMR for Silicon Graphics computers VnmrSGI In parts of this manual the type of system UN TYINOVA MERCURY MERCURY VX GEMINI 2000 UNITYplus UNITY or VX
129. the third decoupler The value must be a real time variable v1 to v14 oph etc or real time constant zero one etc dcplr2phase zero dcplrphase Set small angle phase of first decoupler rf type C or D dec3phase Set quadrature phase of third decoupler stepsize Set small angle phase step size rf type C or D xmtrphase Set small angle phase of obs transmitter rf type C Blank amplifier associated with first decoupler All systems with linear amplifiers except MERCURY VX MERCURY and GEMINI 2000 decblank Disables the amplifier for the first decoupler This is generally used after a call to decunblank decunblank Unblank amplifier associated with first decoupler obsblank Blank amplifier associated with observe transmitter obsunblank Unblank amplifier associated with observe transmitter EEVEOEE Turn off receiver revron Turn on receiver Blank amplifier associated with second decoupler All systems with linear amplifiers dec2blank 01 999165 00 A0800 Description Related dec3blank Applicability Syntax Description Related declvloff Syntax Description Related declvion Syntax Description Related Chapter 3 Pulse Sequence Statement Reference Disables the amplifier for the second decoupler This is generally used after a call to dec2unblank dec2unblank Unblank amplifier associated with second decoupler xevrott Turn off receiver revron Turn on receiver B
130. the value of the string That is the value of St in is simply n w or y and not n w or y The alternative of setting Value of choices n t w ty Vnmr Cmd tin SVALUE could be used but then the Tcl Cmd field is much more complicated The value of tin does not match the characters with single quotes Simply using tin as the value of Tcl Cmd is not a valid Tcl expression 01 999165 00 A0800 VNMR 6 1C User Programming 335 Chapter 6 Customizing Graphics Windows The next example shows the flexibility of this interface However it does take familiarity with Tcl to decipher the value of Tcl Cmd The result of this definition is a series of radio buttons that implement all of the jexp commands Label of element Value of choices Vnmr Variables Vnmr Cmd Tcl Cmd Expl Exp2 Exp3 Exp4 Exp5 Exp6 Exp7 Exp8 Exp9 1234567 8 9 curexp jexp VALUE string range S curexp expr string length Scurexp 1 end Note that the substitution of VALUE is not as a parameter ina MAGICAL expression but to complete a MAGICAL command name The result of the Tcl Cmd field is to return the last character of the curexp parameter which will match one of the Value of choices list It is often the ease in which a 1 entries are put in the Value o cl Cmd entry can be constructed that determines what f choices field For example a second way to implement the same function as the jexp
131. time variables double liml 1lim2 1im3 max gradient value steps double angl ang2 ang3 Euler angles in degrees Sets three oblique phase encode gradients It has no return value Pulse sequence generation aborts if the DACs on a particular gradient are overrun after the angles and amplitude have been resolved 228 VNMR 6 1C User Programming 01 999165 00 A0800 Arguments Examples Related phase_encode_ Applicability Syntax Description Arguments Chapter 3 Pulse Sequence Statement Reference statl stat2 stat3 are values in gauss cm of the components for the static portion of the gradient in the logical reference frame stepl step2 step3 are values in gauss cm of the components for the step size change in the variable portion of the gradient vmulti1 vmult2 vmult3 are real time math variables v1 to v14 ct zero one two three or references to AP tables t 1 to t 60 whose associated values vary dynamically in a manner controlled by the user lim1 1im2 1im3 are values representing the dynamic step that will generate the maximum gradient value for each component This provides error checking in pulse sequence generation and is normally nv 2 ang1 is Euler angle psi in degrees with the range 90 to 90 ang2 is Euler angle phi in degrees with the range 180 to 180 ang3 is Euler angle theta in degrees with the range 90 to 90 phase_encode3_gradient 0 0 0
132. to be used in pulse sequences where the amplitude is arrayed imaging sequences For sequences that array the amplitude it does not use the amount of waveform generator memory that the shapedgradient statement uses but there is a penalty in the amount of overhead time used in setting it up The pulse is created using a gradient waveform generator and has a pulse shape determined by the name width amp and loops arguments pattern is the name of a text file without a GRD extension that describes the shape of the pulse The text file with a GRD extension should be located in Svnmrsystem shapelib or in the users directory Svnmruser shapelib width is the requested length of the pulse in seconds The width of the pulse is affected by two factors 1 the minimum time of every element in the shape file must be at least 200 ns long and 2 the time for every element must be a multiple of 50 ns If the width of the pulse is less than 10 us times the number of steps in the shape a warning message is generated The shaped gradient software will round each element to a multiple of 50 ns If the requested width differs from the actual width by more than 2 a warning message is displayed amp is a value that scales the amplitude of the pulse Only the integer portion of the value is used and it ranges from 32767 to 32767 where 32767 is full scale and 32767 is negative full scale channel selects the gradient coil channel desired and should eva
133. to by the sysmaclibpath parameter if defined 4 Inthe system maclib directory When macros are executed the four locations are searched in this order The first location found is the one that is used For example rt is a standard VNMR macro in the system maclib Ifa user puts a macro named rt in the user s mac1lib the user s rt macro takes precedence over the system rt macro The which macro can search these locations and display on line 3 the information it finds about which location contains a macro For example entering which rt determines the location of the macro rt The system macro directory vnmr mac1ib can be changed by the system operator only but changes to it are available to all users Each user also has their own private macro directory mac1ib in the user s vnmrsys directory These macros take precedence over the system macros if a macro of the same name is in both directories Thus users can modify a macro to their own needs without affecting the operation of other users If the command interpreter does not find the macro it displays an error message to the user Macros are executed in exactly the same way as normal system commands including the possibility of accepting optional arguments shown by angled brackets lt gt macroname lt argumentl lt argument2 gt gt Arguments passed to commands and macros can be constants examples are 5 0 and apt parameters and variables pw and
134. total weighting vector used by VNMR is a vector vector product of this external weighting vector and the internal VNMR weighting vector the latter being calculated from the parameters 1b gf gfs sb sbs and awc The parameter awc still provides an overall additive contribution to the total weighting vector Although the external weighting vector cannot be modified with wt i the total weighting vector can be modified with wti by modifying the internal VNMR weighting vector Note that only a single weighting vector is provided for both halves of the complex data set real and imaginary data points of the complex pair are always weighted by the same factor If the filename program does not exist in a user s wt 1 ib subdirectory VNMR looks for a text file in the current experiment directory with the name filename This file contains the values for the external weighting function in floating point format for example 0 025 but not 2 5e 2 with one value per line If the number of weighting function values in this file is less than the number of complex FID data points that is np 2 the user weighting function is padded out to np 2 points using the last value in the filename text file Writing a Weighting Function Weighting functions must follow this format similar to pulse sequence programs include weight h wtcalc wtpntr npoints delta_t int npoints number of complex data points float wtpntr pointer to weighting vector
135. toultislice loop sciss cssisseccoraschidchscessesachateass csiasessucrsanavoevoctonsesanenace 195 End phase encode LoOp ooo eeeeeeeeesceseeeeceeeeeecaeeeeecasesaecnaeeaeenseeeeeees 195 D vic gating Obsolete e sisicc svsceseaceseeseeSees beaeeedvseseanvessevesdecdsesntseivess 196 Get arrayed parameter values ssssesseseseesesrerssreersrterreereresrerrrsreeesre 196 Retrieve an element from an AP table sseessseeeeeeeeeeeeeeeererserreeresrer 197 Read image plane orientation 0 eee ce eee cee ceseeeeceseeeeeeeeeeeeeeeeeeeees 197 Look up value of string parameter cece eesecsecseeseeeeeeeeeeeaeeeeeeteee 198 Look up value of numeric parameter teeeeeseeseeseeeeceeeeeeeeeeeeeeees 198 Generic delay routine cressa ee ereere inni EER eies 199 Frequency offset routine ssesesseseserseseseronconenceoesenenssnesenserenenes 199 Fine power TOULINE so 05 s3 ce siunc co cvasiduectadlcesseed ieee are ea Ene S e EEN EESE 199 Generic pulse TOutine sis cssescecesessiheesesSepabebonssaeecesieceigassasaceanesdascseestoens 199 Initialize next delay for hardware shimming 0 0 0 cee eeeeeeeeeeeeeeees 200 Find half the value of an integer eee eee eeeeseceeeeeeseeeeeeeeeeeaeeeeeeaes 200 Delay specified time with possible homospoil pulse 00 0 0 eee 201 Pulse first decoupler transmitter with IPA ice eeeeeeseeseeeeeeneeeeeees 201 Pulse first decoupler with amplifier gating and IPA eee 202 Delay for a specified time
136. transposed After the first FT the resulting spectra are transposed to become the FIDs used for the second FT and after the second FT the user might want to work on traces in either the fj or fp direction Furthermore some types of symmetrization and baseline correction algorithms may have to work on traces in both directions at the same time The situation is complicated by the fact that the in place matrix transposition of large data sets is a very complex operation requiring many disk accesses and can therefore not be used in a system that has to transform large non symmetric data sets in a short time Out of place transpositions are not acceptable for large data sets because they double the disk space requirements of the large 2D experiments Therefore VNMR software uses a storage format in the 2D data file that allows access to both rows and columns at the same time Because of the proprietary nature and complexity of the algorithm involved it is not presented here The storage format is used only in datdir data 2D FIDs are stored the same way as 1D FIDs Transformed 2D data is stored in data in large blocks of typically 256K bytes This means that multiple traces are combined to form a block Within one block the data is not stored as individual traces but is scrambled to make access to rows and columns as fast as possible Phased 2D data is stored in phasefile in the same large blocks as in dat a but the traces within each
137. trise mashapedgradient ramp_down 3 0 trise 0 NOWAIT e e magradient Simultaneous gradient at the magic angle magradpulse Simultaneous gradient pulse at the magic angle mashapedgradpulse Simultaneous shaped gradient pulse at the magic angle vagradient Variable angle gradient vagradpulse Variable angle gradient pulse vashapedgradient Variable angle shaped gradient vashapedgradpulse Variable angle shaped gradient pulse zero_all_gradients Zero all gradients mashapedgradpulse Simultaneous shaped gradient pulse at the magic angle Applicability Syntax Description Not applicable on MERCURY VX MERCURY and GEMINI 2000 mashapedgradpulse pattern gradlvl gradtime theta ph char pattern name of gradient shape text file double gradlvl gradient amplitude in G cm double gradtime gradient time in sec double theta angle from z axis in degrees double phi angle of rotation in degrees Applies a simultaneous gradient with shape pat tern and amplitude gradiv1 on the x y and z axes at the magic angle to Bo mashapedgradpulse assumes that the gradient pattern zeroes the gradients at its end and so it does not explicitly zero the gradients Information from a gradient table is used to scale and set values correctly 214 VNMR 6 1C User Programming 01 999165 00 A0800 Arguments Examples Related mod2 Syntax Description Arguments Examples Related mod4
138. two methods with ropes suspended from the ceiling or with the antivibration legs bolted to the floor Refer to the Installation Planning Manual for details WARNING Do not remove the relief valves on the vent tubes The relief valves prevent air from entering the nitrogen and helium vent tubes Air that enters the magnet contains moisture that can freeze causing blockage of the vent tubes and possibly extensive damage to the magnet It could also cause a sudden dangerous release of nitrogen and helium gases from the dewar Except when transferring nitrogen or helium be certain that the relief valves are secured on the vent tubes WARNING On magnets with removable quench tubes keep the tubes in place except during helium servicing On Varian 200 and 300 MHz 54 mm magnets only the dewar includes removable helium vent tubes If the magnet dewar should quench sudden appearance of gases from the top of the dewar and the vent tubes are not in place the helium gas would be partially vented sideways possibly injuring the skin and eyes of personnel beside the magnet During helium servicing when the tubes must be removed carefully follow the instructions and safety precautions given in the manual supplied with the magnet Caution Notices Observe the following precautions during installation operation maintenance and repair of the instrument Failure to comply with these cautions or with specific cautions elsewhere in Varian manuals
139. type C phaseshift base multiplier device 86 VNMR 6 1C User Programming 01 999165 00 A0800 2 3 Spectrometer Control Fixed 90 Settings The first method is the hardwired 90 or quadrature phase setting For both the observe and the decoupler transmitters phases of 0 90 180 and 270 are invoked instantaneously using the obspulse pulse rgpulse simpulse decpulse decrgpulse dec2rgpulse dec3rgpulse dec4rgpulse txphase decphase dec2phase dec3phase and dec4phase statements The receiver phase is actually fixed but is shifted by setting the oph variable which changes the mode of the receiver A 180 receiver phase sets the system to subtract instead of add the data a 90 receiver phase swaps the two channels of the receiver Hardware Control A second method of small angle phase selection is implemented only on spectrometers with direct synthesis This method uses hardware that sets transmitter phase in 0 25 increments on UN TYINOVA and UNITYplus systems 0 5 increments on UNITY and VXR S systems or 1 41 on MERCURY VX and MERCURY systems independently of the phase of the receiver Unlike the phase pulse technique described below this method is an absolute technique e g if a phase of 60 is invoked twice the second phase selection does nothing The obsstepsize base statement sets the step size of the small angle phase increment to base for the observe transmitter Simi
140. use vdelay timebase count where timebase is NSEC defined below USEC microseconds MSEC milliseconds or SEC seconds and count is one of the real time variables v1 to v14 For predictable acquisition the real time variable should have a value of 2 or more If t imebase is set to NSEC the delay depends on the type of acquisition controller board see page 72 for a list in the system e On systems with a Data Acquisition Controller board the minimum delay is a count of 0 100 ns and a count of n corresponds to a delay of 100 12 5 7 ns e On systems with a Pulse Sequence Controller board or an Acquisition Controller board the minimum delay is a count of 2 200 ns and a count greater than 2 is the minimum delay plus the resolution 25 ns of the board e On systems with Output boards the minimum delay is a count of 2 200 ns and a count greater than 2 is the minimum delay plus the resolution 100 ns of the board The vdelay statement is not available on the MERCURY VX MERCURY and GEMINI 2000 Use initdelay time_increment index or incdelay count index to enable a real time incremental delay A maximum of five incremental delays set by index can be defined in one pulse sequence The following steps are required to set up an incremental delay initdelay and incdelay are not available on the MERCURY VX MERCURY and GEMINI 2000 1 Enter initdelay time_increment index to initialize
141. used with spinlock except that 90_pulselength is the pulse duration for a 90 tip angle on the decoupler controlled by the statement Arguments to spinlock decspinlock dec2spinlock and dec3spinlockcan be variables which would need the appropriate get val and get st r statements to permit changes via parameters Shaped Pulse Calibration Macros bandinfo and pulseinfo can be run interactively without arguments to give a table with shaped pulse information for calibration bandinfo takes the name of the shape and the bandwidth desired for the pulse and gives a table containing the duration of that pulse and a predicted 90 pulse power setting pul seinfo takes the name of the shape and the duration of the pulse and gives the bandwidth of that pulse and a predicted 90 pulse power setting Both macros can also be called from another macro For more information refer to the VVMR Command and Parameter Reference 2 11 Shaped Pulses Using Attenuators 138 UNITYTNOVA MERCURY VX MERCURY UNITYplus and UNITY systems are equipped with computer controlled attenuators 0 dB to 79 dB on YNTYZNOVA and UNITYplus 0 dB to 63 dB on MERCURY VX MERCURY and UNITY on the observe and decouple channels linear amplifiers and T R transmit receive switch preamplifiers that allow low level transmitter signals to be generated and pass unperturbed into the probe Similarly GEMINI 2000 broadband systems are equipped with 0 dB to 63 5 dB computer controll
142. value in pp1v1 and declvlon does not set the power to full output On GEMINI 2000 thy Be systems however declvlon does set the decoupler to full power MERCURY VX and MERCURY systems do not use declvlon or declvloff To distinguish between GEMINI 2000 and MERCURY VX and MERCURY use declvlflag e g see vnmr psglab dept c On UNITY systems with a class C amplifier decpwr level changes the decoupler high power level to the value set by level which can assume real values from 0 lowest to 255 full power these units are monotonically increasing but neither linear nor logarithmic To reset the power back to the standard dhp level use decpwr dhp On GEMINI 2000 H 3C systems the power is fixed decpwr has no meaning Controlling Status and Gating Statements to control decoupler and homospoil status are status and set status Explicit transmitter and receiver gating control statements are xmt roff xmt ron decoff decon dec2off dec2on dec30ff dec30n rcvroff and rcvron Statements for amplifier blanking and unblanking are obsblank obsunblank decblank decunblank dec2blank dec2unblank dec3blank 01 999165 00 A0800 VNMR 6 1C User Programming 93 Chapter 2 Pulse Sequence Programming 94 dec3unblank blankingoff and blankingon Finally statements for user dedicated lines are sp off and sp on Table 14 summarizes these statements Table 14 Gating Control Statements blankingof
143. values before acquisition this must be done explicitly e For systems with rf type D UNITYplus the frequency shift time is 14 95 us latching with or without over range No 100 us delay is inserted into the sequence by the offset statement Offset frequencies are not returned automatically to their normal values before acquisition this must be done explicitly as in the example below e For YN YINOVA systems the frequency shift time is 4 us e For GEMINI 2000 systems rf types F or E on broadband systems only the decoupler can be shifted 8 6 us on tH Be systems observe 6 48 us decoupler 8 6 us and homodecoupler 8 6 us can be set e For MERCURY VX and MERCURY systems the setup time is 86 4 us and the shift time is 1 us e On systems with the Output board only all of fset statements by default are preceded internally by a 0 2 us delay Other frequency control statements are variations of offset e To set the offset frequency of the observe transmitter the same as of f set but generate interactive parameter adjustment IPA information when gf or go acqi is 90 VNMR 6 1C User Programming 01 999165 00 A0800 2 3 Spectrometer Control entered use ioffset frequency device string where string is used as a label for the slider in acqi If go is entered instead the IPA information is not generated For details on IPA see Using Interactive Parameter Adjustment page 120 IPA is not available on
144. violates safety standards of design manufacturing and intended use of the instrument Varian assumes no liability for customer failure to comply with these precautions CAUTION Keep magnetic media ATM and credit cards and watches outside the 5 gauss perimeter from the centerline of the magnet The strong magnetic field surrounding a superconducting magnet can erase magnetic media such as floppy disks and tapes The field can also damage the strip of magnetic media found on credit cards automatic teller machine ATM cards and similar plastic cards Many wrist and pocket watches are also susceptible to damage from intense magnetism Refer to the manuals supplied with the magnet for the size of a typical 5 gauss stray field This gauss level should be checked after the magnet is installed 01 999165 00 A0800 VNMR 6 1C User Programming 21 SAFETY PRECAUTIONS Caution Notices continued CAUTION CAUTION CAUTION CAUTION Keep the PCs including the LC STAR workstation beyond the 5 gauss perimeter of the magnet Avoid equipment damage or data loss by keeping PCs including the LC workstation PC well away from the magnet Generally keep the PC beyond the 5 gauss perimeter of the magnet Refer to the Installation Planning Guide for magnet field plots Check helium and nitrogen gas flowmeters daily Record the readings to establish the operating level The readings will vary somewhat because of changes in barometric
145. which uses two input arguments offset argl arg2 Increment vertical position vp and horizontal position sc vp 1 vp sc 2 sc The typeof operator returns a zero FALSE if the variable is real or does not exist and returns a non zero TRUE if the variable is a string For example in the conditional statement if typeof 1 then the then part is executed only if 1 isa string Name Replacement An identifier surrounded by curly braces results in the identifier being replaced by its value before the full expression is evaluated If the name replacement is on the left side of the equal sign the new name is assigned a value If the name replacement is on the right 01 999165 00 A0800 VNMR 6 1C User Programming 35 Chapter 1 MAGICAL II Programming 36 side of the equal sign the value of the new name is used The following are examples of name replacement Sa pw variable a is set to string pw a 10 3 ow is set to 10 3 pw 20 5 pw is set to 20 5 b Sa variable b is set to 20 5 Sa 2 5 pw 2 is set to 5 0 b a 2 variable b is set to 5 0 Scmd wft Scmd is set to the string wft cmd execute wft command The use of curly braces for command execution is subject to a number of constraints In general using the VNMR command exec for the purpose of executing an arbitrary command string is recommended In this last example this would be exec cmd Condition
146. width statl stat2 stat3 step2 step3 vmult2 vmult3 char pattern name of gradient shape file double width length of gradient in sec double stat1l stat2 stat3 static gradient components double step2 step3 variable gradient step size codeint vmult2 vmult3 real time math variables Sets two oblique phase encode shaped gradients otherwise this statement is the same as pe3_shapedgradient Pulse sequence generation aborts if the DACs on a particular gradient are overrun after the angles and amplitude have been resolved pattern is the name of a gradient shape file width is the length in seconds of the gradient statl stat2 stat3 are values in gauss cm of the components for the static portion of the gradient in the logical reference frame step2 step3 are values in gauss cm of the components for the step size change in the variable portion of the gradient vmult2 vmult3 are real time math variables v1 to v14 ct zero one two three or references to AP tables t 1 to t 60 whose associated values vary dynamically in a manner controlled by the user pe3_shapedgradient Oblique shaped gradient with phase encode in 3 axes pe3_shapedgradient Oblique shaped gradient with phase encode in three axes Applicability Syntax Description Not applicable on MERCURY VX MERCURY and GEMINI 2000 pe3_shapedgradient pattern width statl stat2 stat3 stepl step2 step3 vmultl vmult2
147. with the appropriate real time variables The value of ss in low core is associated with real time variables ssval and ssctr e ssval is never modified by the acquisition computer unless specifically instructed by statements within the pulse sequence e ssctr is automatically initialized to ssval For the first increment only if ssval is greater than zero or else before every increment in a arrayed 1D or 2D experiment ssctr is decremented after each steady state transient until it reaches 0 When ssctr is 0 all subsequent transients are collected as data The value of bs in low core is associated with real time variables bsval and bsctr e bsval is never modified by the acquisition computer unless specifically instructed by statements within the pulse sequence e bsctr is automatically initialized to bsval after each block of transients has been completed 102 VNMR 6 1C User Programming 01 999165 00 A0800 2 4 Pulse Sequence Statements Phase and Sequence Control During the acquisition of a block of transients bsct r is decremented after each transient If bsval is non zero a zero value for bsctr signals that the block of transients is complete The ability within a pulse sequence to modify the values of these low core acquisition variables can be used to add various capabilities to pulse sequences As an example the following pulse sequence illustrates the cycling of pulse and receiver phases during steady state pulses
148. with values d2 0 1 sw1 2 swl 3 swl 4 swl 5 swl 6 swl 7 sw1 is generated Eight FIDs each using the corresponding d2 delay will be acquired For the second indirect dimension the analogous parameters are ni2 sw2 and d3 For the third indirect dimension the analogous parameters are ni3 sw3 and d4 When creating a new 2D pulse sequence in standard form the pulse sequence should contain a d2 delay To create the appropriate parameters use the par2d macro It is usually convenient to call par2d from within the macro used to set up the pulse sequence and to set the parameters to appropriate values with the set 2d macro Examples of 2D pulse sequences are given in the standard software in vnmr psglib and vnmr maclib When creating a new 3D pulse sequence in standard form the pulse sequence should contain the delays d2 and d3 and parameters can be created with the par3d macro Similarly a 4D pulse sequence should contain the delays d2 d3 and d4 with parameters created by the par4d macro Each indirect dimension of data can be acquired in a phase sensitive mode Examples of this include the hypercomplex method and the TPPI method see the chapter on multidimensional NMR in User Guide Liquids NMR for more details For each indirect dimension a phase parameter selects the type of acquisition For the first indirect dimension the corresponding phase parameter is phase For the second indirect dimension the parameter is phase
149. 0 0 decstepsize Set step size of first decoupler dec2stepsize Set step size of second decoupler obsstepsize Set step size of observe transmitter stepsize Set small angle phase step size rf type C or D Unblank amplifier associated with first decoupler All systems except MERCURY VX MERCURY and GEMINI 2000 decunblank Explicitly enables the amplifier for the first decoupler This overwrites the implicit blanking and unblanking of the amplifier before and after pulses decunblank is generally followed by a call to decblank decblank Blank amplifier associated with first decoupler obsblank Blank amplifier associated with observe transmitter obsunblank Unblank amplifier associated with observe transmitter revrott Turn off receiver revron Turn on receiver Unblank amplifier associated with second decoupler Systems with a second decoupler dec2unblank Explicitly enables the amplifier for the second decoupler This overwrites the implicit blanking and unblanking of the amplifier before and after pulses dec2unb1ank is generally followed by a call to dec2blank dec2blank Blank amplifier associated with second decoupler HevVnoft Turn off receiver revron Turn on receiver Unblank amplifier associated with third decoupler UNITYINOVA and UNITYplus systems with a third decoupler dec3unblank Explicitly enables the amplifier for the third decoupler This overwrites the implicit blanking and unblanking of the amplifier before and aft
150. 0 0 2 0 gcrush ne zero zero vl2 0 0 0 psi phi theta pe3_gradient Oblique gradient with PE in 3 axes phase_encode_shapedgradient Oblique sh gradient with PE on 1 axis phase_encode3_shapedgradient Oblique sh gradient with PE on 3 axes shapedgradient Oblique shaped gradient with PE in one axis Not applicable on MERCURY VX MERCURY and GEMINI 2000 phase_encode_shapedgradient pattern width statl stat2 stat3 step2 vmult2 lim2 angl ang2 ang3 vloops wait tag char pattern name of gradient shape file double width width of gradient in sec double statl stat2 stat3 static gradient components double step2 var gradient step size codeint vmult2 real time math variable double lim2 max gradient value steps double angl ang2 ang3 Euler angles in degrees codeint vloops number of loops int wait WAIT or NOWAIT int tag tag to a gradient element Sets static oblique shaped gradients plus one oblique phase encode shaped gradient The phase encode gradient is associated with the second axis of the logical frame This corresponds to the convention read phase slice for the functions of the logical frame axes One gradient shape is used for all three axes It has no return value Pulse sequence generation aborts if the DACs on a particular gradient are overrun after the angles and amplitude have been resolved pattern is the name of a gradient shape fi
151. 00 VNMR 6 1C User Programming 131 Chapter 2 Pulse Sequence Programming 132 e A text file describing the shape of a waveform e A pulse sequence statement applying that waveform in an appropriate manner The power of rf shape or decoupler pattern is controlled by the standard power and fine power control statements for that rf channel For example obspower and obspwrf will scale the overall power of a shape on the observe channel File Specifications The macro sh2pul1 sets up a shaped two pulse SH2PUL experiment This sequence behaves like the standard two pulse sequence S2PUL except that the normal hard pulses are changed into shaped pulses from the waveform generator To find pulse shape definitions the pulse sequence generation PSG software looks in a user s vnmrsys shapelib directory and then in the system s shapelib Each shapelib directory contains files specifying the defined shapes for rf pulses decoupling and gradient waveforms To differentiate the files ina shapelib directory each type uses a different suffix Pattern Type Suffix Example rf pulses RF gauss RF decoupling DEC mlev16 DEC gradient GRD hard GRD Each pattern file is a set of element specifications with one element per line Therefore a 67 element pattern contains 67 lines Any blank lines and comments characters after a sign on a line in a specification are ignored Shapes can be created by macro by programs or by hand The spec
152. 04 date and time UNIX 279 FID file 290 file headers 290 macros 44 memory usage 290 part of file UNIX 279 pulse sequences 104 dividing an AP table into a second AP table 263 dividing an integer into AP table elements 262 dividing integer values 190 divn factor 106 108 242 divn statement 190 divn return attribute 106 108 242 dll command 28 dm parameter 94 147 dm2 parameter 94 dm3 parameter 94 dmm parameter 83 94 143 145 243 dmm2 parameter 94 143 dmm3 parameter 94 143 DODEV DO2DEV DO3DEYV constants 82 dof parameter 90 dof2 parameter 90 dof3 parameter 90 01 999165 00 A0800 Index dollar sign notation 29 33 done codes 74 75 doneQ file 322 double integer value 168 double quotation marks notation 31 56 double precision 32 double type variables 73 74 dp parameter 284 dps command 65 70 104 191 dps_off statement 104 190 dps_on statement 104 191 dps_ps_gen command 70 dps_show statement 191 dps_skip statement 193 dpwr parameter 92 93 142 171 dpwr2 parameter 92 dpwr3 parameter 92 draw pulses for graphical display 191 dres command 38 ds command 58 288 dsn command 38 dsnmax command 38 du command UNIX 279 duplicates attribute 318 duty cycle 81 dynamic range of shaped pulse 139 dynamic variable gradient pulse generation 203 248 dynamic variable scan 272 dynamic variable shaped gradient pulse generation 249
153. 1 v14 oph etc RG1 is the delay in seconds between gating on the amplifier and turning on the first transmitter all phases set at beginning of RG1 even if pwn is 0 0 RG2 is the delay in seconds between the final transmitter off and gating the amplifier off 252 VNMR 6 1C User Programming 01 999165 00 A0800 Examples Related Chapter 3 Pulse Sequence Statement Reference sim4pulse pw 2 pw pl 2 pl oph v3 ZERO TWO RG1 RG2 sim4pulse pw 0 0 0 0 2 p1 oph ZERO ZERO TWO RG1 RG2 rgpulse Pulse observe channel with amplifier gating simpulse Pulse observe and decoupler channel simultaneously sim3pulse Pulse simultaneously on 2 or 3 channel s simshaped_pulse Perform simultaneous two pulse shaped pulse Applicability Syntax Description Arguments Systems with a waveform generator on two or more rf channels simshaped_pulse obsshape decshape obswidth decwidth obsphase decphase RG1 RG2 char obsshape decshape names of RF shape files double obswidth decwidth pulse lengths in sec codeint obsphase decphase variables for phase double RG1 gating delay before pulse double RG2 gating delay after pulse Performs a simultaneous two pulse shaped pulse on the observe transmitter and the first decoupler under waveform generator control The overhead at the start and end of the two pulse shaped pulse varies with the system e UNITYTNOVA 1 45 us sta
154. 11 with divn factor 4 i e 00001111000022220000222200002222 t4 0 1 2 3 8 t4 table with autoincrement and divn factor 8 i e 00000000111111112222222233333333 with index VNMR 6 1C User Programming 01 999165 00 A0800 2 5 Real Time AP Tables incremented at each reference to table not at each ct Handling AP Tables Table 20 lists statements for handling AP tables None of these statements apply to GEMINI 2000 systems Table 20 Statements for Handling AP Tables settable tablename numelements intarray getelem tablename APindes APdest Retrieve an element from an AP table loadtable file Load AP table elements from table text file setautoincrement tablename Set autoincrement attribute for an AP table setdivnfactor tablename divnfactor Set divn return attribute and divn factor setreceiver tablename Associate revr phase cycle with AP table settable Store array of integers in real time AP table tsadd tablename scalarval moduloval Add an integer to AP table elements tsdiv tablename scalarval moduloval Divide an AP table into a second table tsmult tablename scalarval moduloval Multiply an integer with AP table elements tssub tablename scalarval moduloval Subtract an integer from AP table elements ttadd Add an AP table to a second table Etdiv Divide an AP table into a second table ttmult Multiply an AP table by a second table ttsub Subtract an AP table from a second table tt
155. 131 synchronous decoupling 243 Synchronous Line Interface SLI board 157 255 213 sysgcoil parameter 153 sysmaclibpath parameter 27 system identification 279 system macro 45 system macro library 27 systemglobal type parameter tree 299 T T analyses 42 t1 t60 table names 105 T analyses 42 T2PUL pulse sequence 108 tab fields 326 tabc command 298 table names 105 table of delays 165 table of frequencies 166 table of frequency offsets 167 tablib directory 105 tail command UNIX 279 tallest peak in region 39 tan command 44 tangent value of angle 44 tape backup UNIX 278 tar command UNIX 278 tcapply command 298 tcl command 343 tcl directory 328 Tcl procedures 342 Tcl script 343 Tcl Tk tool command language tool kit 311 template parameters 304 temporary variables 26 29 32 33 terminating a calling macro 37 terminating zero 120 test4acq procedure 86 text display status 49 text editor 280 text file 284 text file lookup 41 text format files 283 text window 40 textedit command UNIX 279 280 textentry style 316 VNMR 6 1C User Programming 359 Index textfield parameter 317 textis command 49 thermal shutdown 81 theta angle 154 theta parameter 155 218 third attenuator 139 third decoupler blank associated amplifier 171 fine power 180 fine power adjustment 92 gating 95 homodecoupler gating 84 offset frequency 90 91 173
156. 153 creating directories UNIX 279 FDF files 294 new parameter 299 slider in Acquisition window 124 user macros 44 variable without value 32 credit cards caution 21 ct variable 98 105 curly braces notation 35 73 curpar file 284 288 299 current directory 59 current experiment files 284 current parameter tree 299 current parameters text file 284 current type parameter tree 299 cursor mode 39 cursor position 38 curve fitting 42 cycling phases entry 67 D dO parameter 103 d2 parameter 99 148 d3 parameter 99 148 d4 parameter 99 148 DANTE sequence 139 Data Acquisition Controller boards 72 73 160 data acquisition statements 74 data block 285 data block header 285 data buffers 284 data directory 284 data file 284 288 289 data file header 285 data file in current experiment 290 data point acquisition 129 data portion of FDF file 291 data transposition 289 data h file 285 datablockhead structure 286 datadir3d directory 284 datafilehead structure 285 date command UNIX 279 dbl statement 99 168 dc drift correction 288 dconi command 57 dcphase statement 144 168 dcplr2phase statement 87 128 144 169 dcplr3phase statement 87 128 144 170 dcplrphase statement 87 128 144 169 VNMR 6 1C User Programming 347 Index ddf command 290 ddff command 290 ddfp command 290 debug command 37 DEC file suffix 132 dec2blank statement 96
157. 1C User Programming 01 999165 00 A0800 Chapter 2 Pulse Sequence Programming Sections in this chapter e 2 1 Programming Pulse Sequences from Menus this page e 2 2 Overview of Pulse Sequence Programming page 69 e 2 3 Spectrometer Control page 79 e 2 4 Pulse Sequence Statements Phase and Sequence Control page 98 e 2 5 Real Time AP Tables page 104 e 2 6 Accessing Parameters page 110 e 2 7 Using Interactive Parameter Adjustment page 120 e 2 8 Hardware Looping and Explicit Acquisition page 125 e 2 9 Pulse Sequence Synchronization page 131 e 2 10 Pulse Shaping page 131 e 2 11 Shaped Pulses Using Attenuators page 138 e 2 12 Internal Hardware Delays page 142 e 2 13 Indirect Detection on Fixed Frequency Channel page 146 e 2 14 Multidimensional NMR page 148 e 2 15 Gradient Control for PFG and Imaging page 150 e 2 16 Programming the Performa XYZ PFG Module page 153 e 2 17 Imaging Related Statements page 155 e 2 18 User Customized Pulse Sequence Generation page 157 Programming pulse sequences on VNMR based spectrometer systems is a process called pulse sequence generation PSG To simplify this process the software includes a menu driven mode for writing new pulse sequences This mode allows generation of the most common pulse sequences and presents a useful starting point even for those users who wish to make use of pulse se
158. 2 elsenz Execute succeeding statements if argument is nonzero ifzero Execute succeeding statements if argument is zero End loop 1 endloop index codeint index real time variable 01 999165 00 A0800 Description Arguments Examples Related endmsloop Applicability Syntax Description Arguments Examples Related endpeloop Applicability Syntax Description Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference 2 endloop n int n 1 2 3 same as corresponding loop Ends a loop that was started by a Loop statement Syntax 1 is used with UNTYINOVA MERCURY VX MERCURY UNITY plus UNITY and VXR S systems Syntax 2 is used with GEMINI 2000 systems index is a real time variable used as a temporary counter to keep track of the number of times through the loop It must not be altered by any statements within the loop nis the same value 1 2 or 3 as used in the corresponding loop statement endloop v2 endloop 2 loop Start loop End multislice loop Not applicable on MERCURY VX MERCURY and GEMINI 2000 endmsloop state apv2 char state compressed or standard codeint apv2 current counter value Ends a loop that was started by amsloop statement state is either c to designate the compressed mode or s to designate the standard arrayed mode It should be the same value that was in the state argume
159. 2 For the third indirect dimension the parameter is phase3 The total number of FIDs in a given multidimensional data set is stored in the parameter arraydim For a 2D experiment arraydim is equal to ni number of elements of the phase parameter When programming the multidimensional pulse sequences it is convenient to have access to the current increment in a particular indirect dimension and to know what the phase element is Table 34 lists these PSG variables see Table 22 for the full list of Vnmr parameters and their corresponding PSG variable names and types Some pulse sequences such as heteronuclear 2D J HET2DJ can be used as is for phase sensitive 2D NMR however the hypercomplex and TPPI experiments require more information compared to normal pulse sequences and this is presented here Hypercomplex 2D Hypercomplex 2D States Haberkorn Ruben requires only that a pulse sequence be run using an arrayed parameter that generates the two required experiments While this can be any parameter for consistency we recommend the use of a parameter phase which can VNMR 6 1C User Programming 01 999165 00 A0800 2 14 Multidimensional NUR Table 34 Multidimensional PSG Variables PSG Variable PSG type Vnmr parameter Description d2_index int 0 to ni 1 Current index of the d2 array id2 real time 0 to ni 1 Current real time index of the d2 array inc2D double 1 0 swl Dwell time for first indirect dimension ph
160. 2 is the delay in seconds between gating the final rf transmitter off and gating the amplifier off 01 999165 00 A0800 VNMR 6 1C User Programming 253 Chapter 3 Pulse Sequence Statement Reference Examples Related simshaped_pulse gauss hrm180 pw pl v2 v5 N rofl rof2 decshaped_puls Shaped pulse on first decoupler dec2shaped_puls Shaped pulse on second decoupler shaped_pulse Shaped pulse on observe transmitter sim3shaped_pulse Simultaneous three pulse shaped pulse sim3shaped_pulse Perform a simultaneous three pulse shaped pulse Applicability Syntax Description Arguments Systems with a waveform generator on three or more rf channels sim3shaped_pulse obsshape decshape dec2shape obswidth decwidth dec2width obsphase decphase dec2phase RG1 RG2 char obsshape name of obs RF file char decshape name of dec RF file char dec2shape name of dec2 RF file double obswidth obs pulse length in sec double decwidth dec pulse length in sec double dec2width dec2 pulse length in sec codeint obsphase obs real time var for phase codeint decphase dec real time var for phase codeint dec2phase dec2 real time var for phase double RG1 gating delay before pulse in sec double RG2 gating delay after pulse in sec Performs a simultaneous three pulse shaped pulse under waveform generator control on three independ
161. 2109 value of third weighting vector element 0 4567 value of fourth weighting vector element etc 0 1234 value of last weighting vector element Compiling the Weighting Function The macro shellscript wt gen is used to compile filename as set by parameter wt file into an executable program The source file is filename c stored ina user s vnmrsys wt lib directory The executable file is in the same directory and has the same name as the source file but with no file extension The syntax is for wtgen is wtgen file lt c gt from VNMR or wtgen file lt c gt from UNIX The wt gen macro allows the compilation of a user written weighting function that subsequently can be executed from within VNMR The shellscript wt gen can be run from within UNIX by typing the name of the shellscript file name where the c file extension is optional wt gen can also be run from within VNMR by executing the macro wt gen with the file name in single quotes The following functions are performed by wt gen 1 Checks for the existence of the bin subdirectory in the VNMR system directory and aborts if the directory is not found 2 Checks for files usrwt o and weight h in the bin subdirectory and aborts if either of these two files cannot be found there 3 Checks for the existence of the user s directory and creates this directory if it does not already exist 4 Establishes in the wt 1ib directory soft links to usrwt o and weig
162. 2D plane 01 999165 00 A0800 VNMR 6 1C User Programming 39 Chapter 1 MAGICAL II Programming Input Output Tools apa Description banner Syntax Description clear Syntax Description confirm Syntax Description echo Syntax Description flip Syntax Description format Syntax Description 40 VNMR 6 1C User Programming Plot parameters automatically Selects the appropriate command on different devices to plot the parameter list Display message with large characters banner message lt color gt lt font gt Displays the text given by message as large size characters on the VNMR graphics windows Clear a window clear lt window_number gt Clears window given by window_number on the Sun or GraphOn terminal With no argument clears the text screen Confirm message using the mouse confirm message Srespons Displays dialog box with message and two buttons Confirm and Cancel response is if the user clicks the mouse on Confirm response is 0 if the user clicks the mouse on Cancel Display strings and parameter values in text window echo lt lt n gt stringl string2 gt Functionally similar to the UNIX echo command Arguments to VNMR echo can be strings or parameter values such as pw The n option suppresses advancing to the next line Flip between graphics and text window flip lt graphics text lt off on autooff autoo
163. 2prgoff Terminates any waveform generator controlled programmable decoupling on the second decoupler set by the dec2prgon statement dec2prgon Start programmable decoupling on second decoupler End programmable decoupling on third decoupler UNITYTNOVA and UNITYplus systems with a waveform generator on rf channel with the third decoupler dec3prgoff Terminates any waveform generator controlled programmable decoupling on the third decoupler set by the dec3prgon statement dec3prgon Start programmable decoupling on third decoupler Start programmable decoupling on first decoupler Systems with a waveform generator on rf channel for the first decoupler decprgon pattern 90_pulselength tipangle_resoln name of DEC file 90 deg pulse length in sec tip angle resolution char pattern double 90_pulselength double tipangle_resoln Executes programmable decoupling on the first decoupler under waveform generator control and returns the number of 50 ns ticks as an integer value in one cycle of the decoupling pattern Explicit gating of the first decoupler with decon and decof f is generally required Arguments can be variables which require the appropriate get val and get st r statements to permit changes by the parameters see the second example pattern is the name of the text file in the shape1lib directory that stores the decoupling pattern leave off the DEC file extension 90_pulselength is the
164. 3 Fine Power SUBMOUUNE csces sas cies cate seteicieldea rs ceteabesieebevsonsabboev end E OESTE EE EE E Nr bine EASES NATS K EE 125 2 8 Hardware Looping and Explicit Acquisition oo eee eee ee cee ceeeceeeteeeeeeeeeecaeeacecaeesaecaeesaesaeceaseeseeeeeees 125 Controlling Hardware Loopia csc ccriclsiseb cehewtestistlivisabteethtateiatisdulesssesbine EASE ESE ERE TEE EES 126 Number of Eventsin Hardware Loops scsivsecssesschccseseuscebssssesesveasesah ces EE e EE EEr E E ESE 127 Explicit ACgUISIIOM sionc iino aE E EE dad ia R E E as 129 Receiver Phase For Explic t ACuUSiNONS ssc sccssctsdescesssceveseivesngevscsccssessccsdesspecoce scsnscttvestestacteesereest 130 Multiple PUD AECJMSIMOR oci esisiini ense re oaar E E E AE E E ee as 130 29 Pulse Sequence Synchronization sscccscesazessccccssecoisessegseseipsusesssegncescesegectaswes seed cedcegaadueeics suagnis sdnepsrensseyeses 131 External Time Base eis sesesihes Hats cuscselstssaets cade aot vaeck E else tsa etieadidaeasce acest Renew ae eee 131 Controlling Rotor Symenronizauon cicdssn a ete it E eE e EE E til ental 131 2 10 Pulse Shaping ecissicsdss Gassesicevin seeds aoinne EnEn E nET EE E EREE Ee EEE EAEE E E EERE aE E RE EE ESE EE ES EORR 131 File SpeciNCa NONS cersetori ine E a E ES EEEE TEENER daha Ne E S E 132 Perionmme Shaped Pulses os isssiesshestiaccadiisesoseesncsvesaceuscceuasbabasiaatisaians AEE EREE EE E EEEE SaR 134 Programmable Transmitter Comirol caceres arrere neee sE E ESEN e
165. 3 are user created program variables of type char single characters The address operator amp is used with these arguments to pass the address rather than the values of these variables to getorientation search_stringjisa literal string that get orientation will search for in the VNMR parameter set i e the parameter name For example if search_string orient the value of parameter orient will be 01 999165 00 A0800 VNMR 6 1C User Programming 197 Chapter 3 Pulse Sequence Statement Reference Examples Related getstr Syntax Description Arguments Examples Related getval Syntax Description accessed The value of the parameter should not exceed three characters and should only be made up of characters from the set n x y and z The message can t find variable in tree aborts getorientation This means there is no string associated with search_string or the parameter name cannot be found 1 pulsesequence char phase read slice getorientation amp read amp phase amp Slice orient 2 pulsesequence char rd ph sl int error rror getorientation rd amp ph amp sl ort shapedvgradient Dynamic variable shaped gradient function rgradient Set gradient to specified level vgradient Dynamic variable gradient function Look up value of string parameter getstr parameter_name internal_name char parameter_name name of paramete
166. 31 Table 27 Shaped Pulse Statements 20 0 0 eee cecesececeseeseceseeecseseeesceseecaecnaecaecsaesaessaeeseseeeeeeseetees 134 Table 28 Programmable Control Statements 00 eee esceseeee cece ceecaecaeceaeeseeeseeeeeeeeeeeeetees 137 Table 29 Spin Lock Control Statements 00 eee eeeeceeeeeeceseeeeceseecaecaaecaecsaeaeseseeeseseeeeeeetees 138 Table 30 AP Bus Delay Constants scc siecicceeselsesaesisvees tes visebevenashevnsviaeseledabivosssbssedeansbnerbesesviges 140 Table 31 Statements for Pulse Shaping Through the AP Bus 0 0 cc seeeeeesseceeeseeseceeeeceseeeeeeeeees 141 Table 32 AP Bus Overhead Delays iccccssisiicsssiessecatcha cose sob EEEE E EE n E Eri E EEE EEEE 144 Table 33 Example of AP Bus Overhead Delays for status Statement esseere 145 Table 34 Multidimensional PSG Variables 0 cece ec eeeeeeseeseecseesnecaeceaeceeceaeeeeeseeeeseeeeeeeeetees 149 Table 35 Gradient Control Statements sccesccsececsccceous vec secnseneSedessrieccsecdsceeteesnsarecsesess ssscsvnsvessssgensis 151 Table 36 Delays for Obliquing and Shaped Gradient Statements 0 0 eee eect ee cece tee eneeeeees 152 Table 37 Performa XYZ PFG Module Statement i eeeseseeeceecseeeeeeceeceeeeceaeceeeeseeesaeeeseees 154 Table 38 Imaging Related Statement 0 sees csecseeceeceseesecseeseceeeeseeeeeeercaeeaecasesaesneesaees 156 Table 39 Commands for Reformatting Data 0 eeesecsseceseeseeeceeceseeeeseceecseeaeesecnecaeeeeeaeeasenes 296 Table 40 Commands for Wo
167. 5 full power These values in this range increase monotonically but are neither linear nor logarithmic decpwr 255 0 decpwr levell declvloff Return first decoupler back to normal power Set first decoupler fine power Systems with fine power control on the first decoupler Not available on MERCURY VX MERCURY or GEMINI 2000 decpwrf power double power new fine power value for DODEV Changes first decoupler fine power It is functionally the same as rlpwrf value DODEV power is the fine power desired 01 999165 00 A0800 VNMR 6 1C User Programming 179 Chapter 3 Pulse Sequence Statement Reference Examples Related dec2pwrf Applicability Syntax Description Arguments Examples Related dec3pwrf Applicability Syntax Description Arguments Examples Related decr Syntax Description Arguments Examples Related 180 VNMR 6 1C User Programming decpwrf 4 0 dec2pwrf Set second decoupler fine power dec3pwrf Set third decoupler fine power obspwrf Set observe transmitter fine power rlpwrf Set transmitter or decoupler fine power Set second decoupler fine power Systems with fine power control on the second decoupler dec2pwrf power double power for DO2ZDEV new fine power valu Changes the second decoupler fine power It is functionally the same as rlpwrf value DO2DEV power is the fine power desired dec2pw
168. 5 00 A0800 VNMR 6 1C User Programming 317 Chapter 6 Customizing Graphics Windows 318 Sample Entry Form E23 Ja e Je Jz e Ja 10 aal 12 1415 1617 4819 2 21 22 23 24 25 26 27 28 29 30 34 32 33 34 35 36 37 381 39 40 41 42 43 44 45 46 47 48 49 50 User identification Solvent Selection enera D20 Benzene pmso Acetone _ Cyclohexane Toluene _ Methano1 Experiment Selection N CA F19 Raa HC H gCosy H TOCSY H gHSQC H gCOSY gHSgc H gCOSY HSQC gHMBC H gCOSY HSQC gHMBC HSQCTOXY H COSY C DEPT HETCOR H COSY C APT H TOCSY NOESY H TOCSY ROESY H TOCSY HMQC Selected Experiment JAuHexp i O OOO Customize Parameters Add Entry Number of samples submitted O0 Figure 11 Second Alternate Interface enter Program by the enter command If the file attribute is set to a null string the min and max attributes can be selected for choices of integers This is used by the loc selection The numPerLine attribute provides some control over the layout of the enter program This attribute specifies how many choices are presented on a line You may notice that the numPerLine attribute for the loc selection differs between Figure 9 and Figure 10 The required attribute specifies whether a particular selection must be made In the default configuration file the required attribute for text fieldis set to 0 This means that users do not need to enter descriptive text in orde
169. 5 us delay except PFG which has a 1 0 us delay e On MERCURY VX and MERCURY 1 2 us delay e On UNITYplus 1 15 us delay On GEMINI 2000 UNITY and VXR S 2 15 us delay VNMR 6 1C User Programming 01 999165 00 A0800 2 12 Internal Hardware Delays Delays from Changing Attenuation The pulse sequence statement power which is used to change the level of attenuation produced by a 63 dB rf attenuator in the system leads to the following values e On UN TYINOVA 1 AP bus instruction 0 5 us concomitant internal delay WFG start takes 1 AP bus instructions at 0 5 us and extra board delay of 0 75 us total 1 25 us e On MERCURY VX and MERCURY 4 AP bus instructions 4 8 us concomitant internal delay e On UNITYplus 2 AP bus instructions 2 3 us concomitant internal delay WFG start takes 5 AP bus instructions at 5 75 us e On VXR S and UNITY 2 AP bus instructions 4 3 us concomitant internal delay WFG start takes 7 AP bus instructions at 15 00 us Table 32 lists all pulse sequence statements that lead to an internal delay and the magnitude of this delay Similar information to the table is contained in the PSG header file apdelay h which resides in the VNMR system PSG directory On systems with the Output board Table 32 indicates that the pulse sequence statement power incurs a 4 5 us internal delay not a 4 3 us delay as previously stated Of the 4 5 us delay 0 2 us is to allow any high speed line for example the transmit
170. 57 216 mstat command 45 290 mstring parameter 55 56 mult statement 99 217 multidimensional NMR 148 multiple command separator UNIX 278 multiple FID acquisition 130 multiple trace or arrayed experiments 289 multiply AP table by second AP table 264 multiply integer values 217 354 VNMR 6 1C User Programming multiply integer with AP table elements 262 multislice loops 157 216 multiuser protection 281 mv command UNIX 278 279 N nl n3 parameters 32 name replacement 35 natural logarithm of a number 43 nested macros 37 nested multiple hardloops 129 newmenu command 55 nf parameter 130 ni parameter 99 ni2 parameter 99 ni3 parameter 99 nitrogen contact with body 20 nitrogen gas flowmeters caution 22 nll command 39 NMR algorithms 25 NMR language 25 noise modulation 243 noninteractive dg window selecting 328 notational conventions 23 notebook number 322 np parameter 76 nrecords command 41 nth2D variable 227 null string 32 33 56 number of arguments 35 numeric parameter value lookup 117 198 numPerLine attribute 318 numreg command 39 O object code 70 object file 157 object libraries 70 obl_gradient statement 217 obl_shapedgradient statement 218 oblique gradient 217 218 oblique gradient statements 155 oblique gradient with phase encode in 1 axis 223 228 oblique gradient with phase encode in 2 axes 224 oblique gradient with phase en
171. 7 508 509 510 511 512 513 514 515 525 526 527 528 529 530 531 532 533 534 535 593 594 595 596 597 598 Table 5 Acquisition Status Codes continued Invalid sample number during retrieve Invalid temperature during retrieve Gripper abort during retrieve Sample out of range during automatic retrieve Illegal command character during retrieve Robot arm failed to find home position during retrieve Sample tray size is not consistent Sample changer power failure during retrieve Illegal sample changer command during retrieve Gripper failed to open during retrieve Air supply to sample changer failed during retrieve Tried to insert invalid sample number Invalid temperature during sample changer insert Gripper abort during insert Sample out of range during automatic insert Illegal command character during insert Robot arm failed to find home position during insert Sample tray size is not consistent Sample changer power failure during insert Illegal sample changer command during insert Gripper failed to open during insert Air supply to sample changer failed during insert Failed to remove sample from magnet Sample failed to spin after automatic insert Sample failed to insert properly Sample changer not turned on Sample changer not connected to RS 232 interface Sample changer not responding 600 Shimming errors 601 602 604 608 Shimming user aborted Los
172. 74 precedence of operators 30 presaturation 92 print files UNIX 279 print working current directory UNIX 279 prioritySample button 319 private help files 54 55 private menu library 54 probe damage caution 92 procdat file 284 process status UNIX 279 processed type parameter tree 299 procpar file 284 288 290 291 299 procpar3d file 284 program execution 26 programmable control of transmitter 221 programmable control statements 136 programmable decoupling ending 176 starting 177 programmable phase and amplitude control 136 programmable pulse modulation 243 programming imaging pulse sequences 152 menus 55 Performa XYZ PFG module 153 pulse sequence 63 prompt for user input 41 propagation delay 145 prosthetic parts warning 19 protection bits 27 300 302 prune command 301 ps command UNIX 279 PSG pulse sequence generation 63 psg directory 157 158 psg macro 102 psggen shell script 157 158 psglib directory 69 psgset command 41 psi parameter 155 218 356 VNMR 6 1C User Programming PTS synthesizers with latching 140 pulse channels simultaneously 251 pulse control 131 pulse decoupler 179 pulse decoupler with IPA 201 202 pulse decoupler with receiver gating 181 pulse four channels simultaneously 252 pulse interval time 137 pulse observe transmitter 80 pulse program buffer 125 pulse routine 199 pulse sequence control statements 100 Pulse Sequence Controller board 72
173. Cch DEC2ch or DEC3ch on is TRUE or FALSE mode is a decoupler mode c g p etc sync is TRUE or FALSE and mod_freq is the modulation frequency e g set status DECch TRUE w FALSE dmf The setstatus statement is not available on the MERCURY VX MERCURY or GEMINI 2000 set status provides a way to set transmitters independent of the parameters one channel at a time For example set status OBSch TRUE g TRUE obs_mf turns the observe transmitter OBSch on TRUE using GARP modulation g in synchronized mode TRUE with a modulation frequency of obs_mf The obs_mf parameter will need to be calculated from a parameter set with an appropriate get val statement Note Be sure to set the power to a safe level before calling set status Timing for set status is the same as for the status statement except that only one channel needs to be taken into account To ensure that the timing is constant for the status use the statusdelay statement e g statusdelay A 2 0e 5 Homospoil gating is treated somewhat differently than decoupler gating If a particular homospoil code letter is y delays coded as hsdelay that occur when the status corresponds to that code letter will begin with a homospoil pulse the duration of which is determined by the parameter hst Thus if hs ny all hsdelay delays that occur during status B will begin with a homospoil pulse The final status always occurs during
174. Change offset frequency of third decoupler dec4offset frequency Change offset frequency of fourth decoupler obsoffset frequency Change offset frequency of observe transmitter offset frequency device Change offset frequency of transmitter or decoupler ioffset frequency device string Change offset frequency with IPA The main statement to set the offset frequency of the observe transmitter parameter tof first decoupler dof second decoupler dof 2 or third decoupler do f 3 is the statement offset frequency device where frequency is the new value of the appropriate parameter and device is OBSch observe transmitter DECch first decoupler DEC2ch second decoupler or DEC3ch third decoupler For example use offset to2 OBSch to set the observe transmitter offset frequency DEC2ch can be used only on systems with three rf channels Likewise DEC3ch is used only on systems with four rf channels e For systems with rf types A or B the frequency typically changes in 10 to 30 us but 100 us is automatically padded into the sequence by the of fset statement so that the time duration of the of fset statement is constant and not frequency dependent e For systems with rf type C which necessarily use PTS frequency synthesizers the frequency shift time is shown in Table 32 No 100 us delay is padded into the sequence for systems with rf type C or D Offset frequencies are not automatically returned to their normal
175. Cmd A Tcl expression that is evaluated to determine the value that is displayed by this label item Any legitimate Tcl expression is allowed To access the values of any VNMR parameters specified in the Vnmr Variables list prepend a dollar sign to the parameter name For example the value of sfrqis sfrq 332 VNMR 6 1C User Programming 01 999165 00 A0800 6 3 Customizing the Interactive dg Window The following examples show Tcl expressions possible for Tcl Cmd hello expr np 2 0 Ssw expr acos 1 Sct Button Element A simple string that will not be updated and is not very useful It would be better to use a title for this case An expression to calculate acquisition times Parameters np and sw need to be listed as Vnmr Variables is order to get access to their values A calculator for pi Probably the most common use The value of a VNMR parameter is displayed and updated as it changes ct needs to be listed as Vnmr Variables to get access to its value During an acquisition this value would be updated as block size transfers of data occur The button element is the first interactive item It provides a mechanism to send any MAGICAL command to VNMR As a mouse button passes over a button the button changes color to indicate that it is an active item The available characteristics are the following Label of element Width of element Vnmr Cmd Entry Element Text string to be displayed inside
176. Generator Offset Delay on YN YINOVA Systems 01 999165 00 A0800 VNMR 6 1C User Programming 145 Chapter 2 Pulse Sequence Programming On UNITY plus the time overhead for the AP bus is 5 75 us The offset delay is an additional 0 45 us for a total delay of 6 20 Us Note that if the shaped pulse is followed by a delay say d3 then the end of the delay is at 1 7 pshape 0 5 d3 Similarly on UNITYplus the end of the delay is at 6 20 pshapet d3 On UNITY it shifts 1 5 us so the offset delay depends on the type of system To obtain the proper offset delay available in apdelay h are macros WFG_OFFSET_DELAY WFG2_OFFSET_DELAY and WFG3_OFFSET_DELAY Another delay is incurred between transients on systems other than UN YINOVA At the end of data collection 3 5 ms is inserted to give the acquisition computer time to check lock temperature spin etc If the solids ADC is used so that sw is greater than 100000 this delay is extended to 15 5 ms on UNIT Yplus systems or extended by 10 ms per kilobyte points on UNITY and VXR S systems The VNITYZN OVA has a 0 004 ms delay at the start of a transient to initialize the data collection hardware and a 2 006 ms delay at the end of a transient for data collection error detection For systems with gradients the end of scan delays do not include the times to turn off gradients which is done at the end of every scan 2 13 Indirect Detection on Fixed Frequency Channel 146
177. H half value of integer 200 half transformed spectra 289 hardloop nesting 129 hardware loop 125 194 end of loop 194 start of loop 258 hardware phase control 87 hardware shimming iniitializing next delay 200 hardware WALTZ decoupling 86 hardwired 90 phase 87 head command UNIX 279 header of FDF file 291 helium contact with body 20 helium gas flowmeters caution 22 Help button 53 54 help command 53 54 help directory 53 54 help files for menus 53 54 helppath variable 54 HET2DJ pulse sequence 148 hidden delay 142 hidecommand command 44 high band nuclei 83 high noise signal 75 high power amplifiers cautions 22 high power decoupling 96 high speed device control 97 high speed line propagation delay 145 hlv statement 99 102 200 HMOQC experiment 82 hom2dj macro 64 hom2dj c sequence listing 69 HOM2DIT pulse sequence 109 home directory for user UNIX 278 homo parameter 83 84 homo2 parameter 84 homo3 parameter 84 homodecoupler gating 84 homonuclear J resolved pulse sequence 109 homonuclear 2D J pulse sequence 64 69 homospoil gating 94 95 259 homospoil pulse 64 66 79 201 host disk errors 77 hs parameter 79 94 hsdelay statement 79 95 128 201 VNMR 6 1C User Programming 351 Index hst parameter 79 95 hwlooping c module 86 hypercmplxbhead structure 287 hypercomplex 2D 148 I i2pul c pulse sequence 120 id2 pointer 71 99 150 id3 pointer 71 99 id4 poi
178. IDER_MAX 1000 SI SI LIDER_MIN 0 LIDER_UNITS le 6 PULSE_PHASE oph 0 See Generic Pulse Routine page 121 H hdwshiminit Applicability Syntax Description Examples Related hlv Syntax Description Arguments Examples Related Initialize next delay for hardware shimming UNITYINOVA systems hdwshiminit Enables hardware shimming during the following delay or during the following presaturation pulse defined as a power level change followed by pulse hdwshiminit is not necessary for the first delay or presaturation pulse in a pulse sequence which is automatically enabled for hardware shimming hdwshiminit delay d2 hardware shim during d2 if hdwshim y hdwshiminit obspower satpwr rgpulse satdly v5 rofl rof2 hardware shim during satdly if hdwshim p delay Delay for a specified time Find half the value of an integer hlv vi vj codeint vi real time variable for starting value codeint vj real time variable for 1 2 starting value Sets vj equal to the integer part of one half of vi vi is the starting value and vj is the integer part of one half of the starting value Both arguments much be real time variables v1 to v14 oph etc hlv v2 v5 add Add integer values assign Assign integer values dbl Double an integer value decr Decrement an integer value divn Divide integer values incr Increm
179. Indirect detection experiments in which the observe nucleus is 1H and the decouple nucleus is a low frequency nucleus usually 13C are easily done on systems with two broadband channels not available on GEMINI 2000 systems Systems with a fixed frequency decoupler depend on the type of system Fixed Frequency Decoupler For systems with a fixed frequency H decoupler the implementation depends on whether the system is a UNTYINOVA MERCURY VX MERCURY UNITYplus or GEMINI 2000 or instead is a UNITY or VXR S UNITYINOVA MERCURY UNITY plus GEMINI 2000 Systems A UNTTYINOVA or UNITYplus system with the label Type of RF set to U H1 Only in the CONFIG window or any MERCURY VX MERCURY or GEMINI 2000 broadband system can use the same parameter sets and pulse sequences as a dual broadband system e g HMQC as long as the pulse statements in a sequence do not use the channel identifiers TODEV DODEV DO2DEV and DO3DEV This restriction is negligible because statements obspower decpower dec2power and dec3power are available that specify an rf channel without requiring the these channel identifiers Each of these statements require only the power level and can be remapped to different rf channels The rfchannel parameter enables remapping rf channel selection Refer to the description of rfchannel in the VWMR Command and Parameter Reference for details Internal logic on this system checks if the first decoupler is U H1
180. It works on both compressed compressed and compressed 3D data The reverse FID commands rfblk rftrace and rfdata are similar to their respective mfblk mft race and mfdata commands except that rfblk rftrace VNMR 6 1C User Programming 01 999165 00 A0800 5 3 Reformatting Data for Processing Listing 12 Code from a Move FID Macro if seqcon 3 c and seqcon 4 c then x x x x Compressed compressed 3d Sarraydim arraydim if Sindex gt Sarraydim then write error Index greater than arraydim abort endif mfblk Sindex Sworkexp 1 jexp Sworkexp setvalue arraydim 1 processed setvalue arraydim 1 current setvalue array processed setvalue array current fesad jexp cexpn else if seqcon 3 c and seqcon 4 s then xx x x x Compressed 3d if ni lt 1 5 then write error seqcon ni mismatch check parameters abort endif Sarraydim arraydim ni if Sindex gt Sarraydim then write error Index greater than arraydim abort endif i 1 k Sindex while i lt ni do mfblk k Sworkexp i k k Sarraydim Si i 1 endwhile jexp workexp setvalue arraydim ni processed setvalue arraydim ni current setvalue array processed setvalue array current ft3d jexp cexpn and rfdata also reverse the order of the data The rfblk rftrace and rfdata c
181. MERCURY VX MERCURY and GEMINI 2000 systems To set the offset frequency of the observe transmitter parameter tof use obsoffset frequency which functions the same as offset frequency OBSch To set the offset frequency of the first decoupler parameter dof use decoffset frequency which functions the same as offset frequency DECch To set the offset frequency of the second decoupler parameter dof 2 use dec2offset frequency which functions the same as offset frequency DEC2ch dec30ffset freque To set the offset frequency of the third decoupler parameter dof 3 use ncy which functions the same as offset frequency DEC3ch e To set the offset frequency of the deuterium decoupler used as the fifth channel parameter dof4 use dec4offset frequency which functions the same as offset frequency DI EC4ch Controlling Observe and Decoupler Transmitter Power Statements to control power by adjusting the coarse attenuators on linear amplifier systems are power obspower decpower dec2power dec3power and dec4power Statements to control fine power are pwrf pwrm rlpwrm obspwrf decpwrf dec2pwrf and dec3pwrf Statements to control decoupler power level switching are declvlon declvloff and decpwr The apovrride statement overrides an AP bus delay the delay before AP bus access Table 13 summarizes these statements Only the declvloff declvlon obspower and decpower state
182. PI The following construct which was taken from an older version of hmqc c generates the warning if iphase 3 tl_counter int ix 1 arraydim ni initval double tl counter v14 Changing these lines to if iphase 3 initval double int ix 1 arraydim ni le 6 v14 avoids the warning and also provides for roundoff of the floating point expression to give proper TPPI phase increments Even the above expression can fail under some circumstances That construction will not work for 3D and 4D experiments With the availability of increment counters such as id2 id3 and id4 and the predefined phasel variable this example can be rewritten as if phasel 3 assign id2 vl14 j The second warning generally suggests an uninitialized variable parameter_name may be used before set 01 999165 00 A0800 VNMR 6 1C User Programming 71 Chapter 2 Pulse Sequence Programming 72 This should be corrected otherwise unpredictable execution of the pulse sequence is likely A common cause is the use of a user variable without first using a get val or getstr statement on the variable The third warning generally suggests that a variable is defined within the pulse sequence that has the same name as one of the standard PSG variables parameter_name redefinition hides earlier one This warning is normally avoided by renaming the variable in the pulse sequence or if the variable co
183. Programming 01 999165 00 A0800 6 1 Customizing the Sample Entry Form Window Prepend a character to the front of the attribute name to access the value of that attribute In addition four other variables are provided e Sindex the index of the selected or deselected radio or check button e Slabel the label of the selected or deselected radio or check button e Svalue the value of the selected or deselected radio or check button e filename the name of the file where output from enter will be written For example set loc set_rtoutput write alpha Sloc label value selected set loc unset_rtoutput write alpha Sloc label value de selected If any variables are included in the value of the attribute the value must be enclosed in braces Using xradio and xcheck with rtoutput Attribute Selections of type xradio and xcheck have an optional attribute rt out put This attribute is a magical command that will be sent to VNMR when the button is selected The value of the attribute can include any other attribute from that group Prepend a character to the front of the attribute name to access the value of that attribute In addition four other variables are provided e Sindex the index of the selected xradio or xcheck button e Slabel the label of the selected xradio or xcheck button e value the value of the selected xradio or xcheck button e filename the name of the file where output from en
184. Pulse Sequence Object Code The ability to modify or customize acquisition parameters to fit a given user created pulse sequence is provided by a small number of commands These commands make it possible to perform the following operations on an existing parameter table e Create new parameters e Control the display and enterability of parameters e Control the limits of the parameter e Create a parameter table for two dimensional experiments The commands that enable the creation and modification of parameters are discussed in Chapter 5 of this manual C Framework for Pulse Sequences Each pulse sequence is built onto a framework written in the C programming language Look again at the hom2dj sequence in Listing 6 The absolutely essential elements of this framework are these VNMR 6 1C User Programming 01 999165 00 A0800 2 2 Overview of Pulse Sequence Programming include lt standard h gt pulsesequence This framework must be included exactly as shown Between the two curly braces are placed pulse sequence statements each statement ending with a semicolon The majority of pulse sequence statements allow the user to control pulses delays frequencies and all functions necessary to generate pulse sequences Most are in the general form statement argument1 argument2 where statement is the name of the particular pulse sequence statement and argument1 argument 2 is the information needed by that statemen
185. Pulse Sequence Statement Reference Arguments Examples Related dcplr3phase Applicability Syntax Description Arguments Examples Related decblank Applicability Syntax Description Related dec2blank Applicability Syntax 170 VNMR 6 1C User Programming multiplier is a small angle phaseshift multiplier for the second decoupler The value must be a real time variable v1 to v14 oph etc or real time constant zero one etc dcplr2phase zero dcplrphase Set small angle phase of first decoupler rf type C or D dec2phase Set quadrature phase of second decoupler stepsize Set small angle phase step size rf type C or D xmt rphase Set small angle phase of obs transmitter rf type C Set small angle phase of 3rd decoupler rf type C or D Systems using a third decoupler with rf type C or D dcplr3phase multiplier codeint multiplier multiplies phase step Sets the third decoupler phase in units set by the stepsize statement If stepsize has not been used the default step size is 90 The small angle phaseshift is a product of multiplier and the preset stepsize The full small angle phase is set by dcplr3phase Unlike dec3phase dcplr3phase is needed any time the third decoupler phase shift is to be set to a value that is not a multiple of 90 dec3phase sets quadrature phase shift only which is rarely needed multiplier is asmall angle phaseshift multiplier for
186. Pulse observe transmitter with amplifier gating 0 eee eeeeeeeeee Set gradient to specified level ote ee eeeeeseeseeseeseceeeecsseeeeeeeeeeseenees Change power level linear amplifier systems 0 0 eeeeseeesseeeeeeeee Set transmitter or decoupler fine power Set transmitter or decoupler linear modulator power 0 eeeee Obtain rotor period Of MAS rotor cece eeeeeeseceeeeeeeseeeeeeeeaeseeeeeees Gated pulse sequence delay from MAS rotor position Set autoincrement attribute for an AP table Set divn return attribute and divn factor for AP table Associate the receiver phase cycle with an AP table Set status of observe transmitter or decoupler transmitter Store an array of integers in a real time AP table Set user AP register wescsssscscescesscsssessseaseaseseseseanes Perform shaped pulse on observe transmitter Perform shaped pulse on observe transmitter Generate shaped gradient pulse eee eceseeeseeeeteeceecaeeeeeaes Generate arrayed shaped gradient pulse 0 eee eeeeeeeeeeeeereeeeeeee 01 999165 00 A0800 Table of Contents shapedincgradient Generate dynamic variable gradient pulse eee eeeeeeee eee eeee 248 shapedvgradient Generate dynamic variable shaped gradient pulse 0 0 eee 249 simpulse Pulse observe and decouple channels simultaneously ee 251 sim3pulse Pulse simultaneously on 2 or 3 rf channels 20 0 0 eeeeseeeeeeeeeeeeeeeeee 251 sim4pulse Simultaneous puls
187. R EE e er taR Era E E a 279 4 3 UNIX Commands Accessible from VNMR o ccccecssssssseesscessecesecesseceseecueesseesseeecseceeecsaesesaeceeeecsseseneees 280 Opening a UNIX Text Editor from YNMR 2ssiscsiccceessctsescesccogevsconcssssssesscsotessusccousistiescusbostersnsenst 280 Opening a UNIX Shell from VNMR rissies it tena iator i a aaeei 280 4 4 Background VNMR 00 eceeecessecesseceececssceencecencecsecesneesecesaecsscecsseeeaaeceeecseceeaeessecesaecsucecsaceeneeceseeeneeeeneees 280 Running VNMR Command as a UNIX Background Task oo ee eee eeeeeeeee cece cee cneeeecaeeseeeeeseens 281 Running VNIMR Processing im the Background 0 0 00 cscsesssassceicsbuedetvessscbesssdscbescnsennvesdseavievsceee 281 45 gt Shell Pro stam IN S joi 5 5s2edeedhcscees edhesdeveseusesedhecenss ences censeccestaasvandasaussoacsescastsaavesascaeave dass E ea E EEr BEERE arot 282 Shell Variables and Control Ori ats 5 503s cesisvetesdhecedecscssbbservaaetveess onievsess EE EEE EE EErEE REIESE 282 OTIC UL CHAPS E E E succanzs sbbasdsiseebaestags axa shapsbnaacs 282 Chapter 5 Parameters and Data ccccssseccccssseeeeeesseeeeeesseeneesesneneeseensneneeensaneeeeessenneeseees 283 Sel VINMIR Wate Biles ca E E EAE A E EA E a EE 283 Binary Data FIIS csccccssceensscaissviesocusevaccvaseszenachascnsennseus ch vias EE E E EEE S 283 Data PIS SUC MES eie E E EE OE E nade ana REE E E 285 YNMR Useof Bimary Data Files sosisini e apee eitea oes seuss suceecusss
188. R S must be considered in order to use the software properly e UNITYINOVA and MERCURY VX are the current systems sold by Varian e UNITYplus UNITY and VXR S are spectrometer lines that preceded the UN YINOVA e GEMINI 2000 is a separate line of spectrometers that preceded the MERCURY and MERCURY VX Help Us to Meet Your Needs We want to provide the equipment publications and help that you want and need To do this your feedback is most important If you have ideas for improvements or discover a problem in the software or manuals we encourage you to contact us You can reach us at the nearest Varian Applications Laboratory or at the following address Palo Alto Applications Laboratory Varian Inc NMR Systems 3120 Hansen Way MS D 298 Palo Alto CA 94304 1030 24 VNMR 6 1C User Programming 01 999165 00 A0800 Chapter 1 MAGICAL II Programming Sections in this chapter e 1 1 Working with Macros this page e 1 2 Programming with MAGICAL page 29 e 1 3 Relevant VNMR Commands page 38 e 1 4 Using Dialog Boxes from a Macro page 49 e 1 5 Customizing the Menu System page 52 e 1 6 Customizing the Files Menus page 58 Many of the actions performed on an NMR spectrometer are performed many times day after day To make these actions easier on the user VNMR software provides for the use of macros and a high level programming language designed for NMR 1 1 Working with Macros A macro is a us
189. RCURY and GEMINI 2000 dec2rgpulse dec3rgpulse and dec4rgpulse have no meaning and homo is not used Pulsing Channels Simultaneously Statements for controlling simultaneous non shaped pulses are simpulse sim3pulse and sim4pulse Table 9 summarizes these statements Simultaneous pulses statements using shaped pulses are covered in a later section Table 9 Simultaneous Pulses Statements simpulse Pulse observe and decoupler channels simultaneously sim3pulse Pulse simultaneously on two or three rf channels sim4pulse Simultaneous pulse on four channels sim3pulse pwl pw2 pw3 phasel phase2 phase3 RG1 RG2 sim3pulse pwl pw2 pw3 phasel phase2 phase3 RG1 RG2 sim4pulse pwl pw2 pw3 pw4 phasel phase2 phase3 phase4 RG1 RG2 Use simpulse obswidth decwidth obsphase decphase RG1 RG2 to simultaneously pulse the observe and first decoupler rf channels with amplifier gating e g simpulse pw pp vl v2 0 0 rof2 Figure 4 illustrates the action of simpulse on YN YINOVA MERCURY VX MERCURY GEMINI 2000 UNITYplus UNITY and VXR S systems The shorter of the two pulses is centered on the longer pulse while the amplifier gating occurs before the start of the longer pulse even if it is the decoupler pulse and after the end of the longer pulse The absolute difference in the two pulse widths must be greater than or equal to 0 2 us 0 4 us on the MERCURY VX MERCURY UNITYplus and GEMINI 2000 otherwise
190. RCURY VX MERCURY and GEMINI 2000 for high band nuclei and 10 to 20 Us 2 Us typical for MERCURY VX MERCURY and GEMINI 2000 for low band nuclei Solids require at least 1 5 us On 500 MHz systems that use the ENI 5100 class A amplifier for low band nuclei on the observe channel RG should be 40 60 us If the tn nucleus and the dn nucleus are in different bands e g tn is H and dn is 13C the decoupler amplifier module is placed in the cw mode in which it is always unblanked regardless of the state of the receiver In this mode RG is unimportant with respect to amplifier stabilization prior to the decoupler pulse width is the duration in seconds of the decoupler transmitter pulse phase is the phase of the pulse It must be a real time variable v1 to v 14 etc or a real time constant zero one etc RG1 is the time in seconds before the start of the pulse that the amplifier is gated off RG2 is the time in seconds after the end of the pulse that the amplifier is gated on decrgpulse pp v3 rofl rof2 decrgpulse pp zero 1 0e 6 0 2e 6 decpulse Pulse first decoupler with amplifier gating dec2rgpulse Pulse second decoupler with amplifier gating dec3rgpulse Pulse third decoupler with amplifier gating 01 999165 00 A0800 VNMR 6 1C User Programming 181 Chapter 3 Pulse Sequence Statement Reference dec2rgpulse Applicability Syntax Description Arguments Examples Related d
191. ROFF rofl PULSE_POST_ROFF rof2 PULSE_DEVICE TODEV SLIDER_LABEL NULL SLIDER_SCALE 1 SLIDER_MAX 1000 01 999165 00 A0800 VNMR 6 1C User Programming 121 Chapter 2 Pulse Sequence Programming v IDER_MIN SLIDER_UNITS PULSE_PHASE 0 0 le 6 oph The following table describes the attributes used with G_Pulse Attribute Type Default Description PULSE_WIDTH double pw As specified in parameter set PULSE_PRE_ROFF double rofl As specified in parameter se PULSE_POST_ROFF double rof2 As specified in parameter set PULSE_DEVICE int TODEV TODEV for observe channel or DODEV for 1st decoupler On UNITYplus also DO2DEV or DO3DEV for 2nd 3rd decoupler SLIDER_LABEL char NULL Label 1 6 characters for acqi or NULL for no output to acqi SLIDER_SCALE int 1 Decimal places 0 to 3 on slider SLIDER_MAX int 100 Maximum value on the slider SLIDER_MIN int 0 Minimum value on the slider SLIDER_UNITS double 1le 6 Pulses are in us scale factor PULSE_PHASE int oph Real time variable Examples of using G_Pulse G_Pulse 0 equals obspulse G_Pulse PULSE_WIDTH PULSE_PHASE 0 pw vl equals pulse pw v1 required terminating zero Frequency Offset Subroutine The G_Offset routine adjusts the offset frequency It has the follo
192. RY GEMINI 2000 system decouplers are rf type F and E dcplrphase multiplier codeint multiplier real time phase step multiplier Sets first decoupler phase in step size units set by the stepsize statement The small angle phaseshift is a product of multiplier and the step size If stepsize has not been used default step size is 90 If the product of the step size set by the stepsize statement and multiplier is greater than 90 the sub 90 part is set by dcp1lrphase Only on systems with an Output board are carryovers that are multiples of 90 automatically saved and added in at the time of the next 90 phase selection such as at the time of the next pulse or decpulse On systems with a Data Acquisition Controller board a Pulse Sequence Controller board or an Acquisition Controller board this is done by dcplrphase see the description section of the acquire statement for further information about these boards Unlike decphase dcplrphase is needed any time the first decoupler phase shift is to be set to a value not a multiple of 90 decphase sets quadrature phase shift only which is rarely needed multiplier isa small angle phaseshift multiplier for the first decoupler The value must be a real time variable v1 tov14 oph etc or real time constant zero one etc dcplrphase zero dcplr2phase Set small angle phase of second decoupler rf type C or D dcplr3phase Set small angle phase of third decoupler rf t
193. SAMPLE 6 USER dan MACRO h1 SOLVENT cdcl3 TEXT USERDIR usr24 dan vnmrsys DATA usr24 dan tstness tcl auto 0101 Complete Mon Jul 29 15 25 54 1996 Experiment started Mon Jul 29 15 26 55 1996 Acquisition complete Retrieve Data Find Entry Quit Figure 12 Default Interface status Program Acquisition Observe Channel Sample Spect width 5558 8 Nucleus ii Date Jul 29 96 Acq tine i Spect Freq 400 075 Miz File fidld fid Acquired complex pts offset cr Hz zaf Solvent feia Recycle delay s obs pulse Tra us zl temperature Transients power 55 Steady state Calibration Channel Nucl pi 2 pulse rr us Observe HL power 55 Decoupler H Decoupler2 Decoupler3 Gradient Type mq Figure 13 dg Window 01 999165 00 A0800 VNMR 6 1C User Programming 325 Chapter 6 Customizing Graphics Windows 326 Normally a setting displayed in dg is associated with a parameter You can alter the setting by typing into the command line in the normal way or as outlined above A number of editing operations can be used on an entry e A single click of the left mouse button positions the entry cursor between characters at about the mouse position Typing characters insert them at this point The backspace key deletes characters to the left of the cursor and the Del key deletes characters to the right e Double clicking the left mouse button highlights a string of characters bounded by white space or punctuation such as a word
194. SET SLI_OR SLI_XOR or SLI_AND address is the address of the SLI board in the system It must match the address specified by jumper J7R on the board Note that the jumpers 19 20 through 2 specify bits 2 through 11 respectively Bits 0 and are always zero An installed jumper signifies a one bit and a missing jumper a zero The standard addresses for the SLI in the VME card cage e Digital left side is C90 hex 3216 e Analog right side is 990 hex 2448 mode determines how to combine the specified value with the current output of the SLI to produce the new output The four possible modes e SLI_SET is to load the new value directly into the SLI e SLI_ORis to logically OR the new value with the old e SLI_AND is to logically AND the new value with the old e SLI_XOR is to logically XOR the new value with the old value as modified by the mode argument specifies the bit pattern to be set in the SLI board This should be a non negative number between 0 all lines low and 232 1 all lines high pulsesequence int SLIaddr Address of SLI board unsigned SLIbits 32 bits of SLI line settings ri Libits getval s address Liaddr getval Ns uv sli SLIaddr SLI_SET SLIbits Note that sli and address are not standard parameters but need to be created by the user if they are mentioned in a user pulse sequence for details see the descripti
195. Sht or expressions 2 pwt5 0 Recursive calls to procedures are allowed Single quotes must be used around constant strings Macros can also be executed three other ways When the VNMR program is first run a system macro boot up is run This macro in turn runs a user macro named login in the user s local mac1lib directory if such a macro exists e When any parameter x is entered if that parameter has a certain protection bit set see Format of a Stored Parameter page 301 a macro by the name _x that is the same name as the parameter with an underline as a prefix is executed For example changing the value of sw executes the macro _sw e Whenever parameters are retrieved with the rt rtp or rtv commands a macro named fixpar is executed 01 999165 00 A0800 VNMR 6 1C User Programming 27 Chapter 1 MAGICAL II Programming 28 If the macro needs to know what macro invoked it that information is stored by the string parameter macro available in each experiment Transferring Macro Output Output from many commands and macros in addition to being displayed on the screen or placed in a file can also be transferred into any parameter or variable of the same type To receive the output of a program of this type the program name and arguments if any are followed by a colon and one or more names of variables and parameters that are to take the output macroname lt argl lt arg2 gt gt variablel vari
196. TEENE E eE EES 59 Sckeine and Accessing FIOS secssccssccsss ciysccsshaveescssecuvavnsaisdsenessadeneannssuseanseSbpuscesessdaescnis Seaansdagbenaeesys 59 Using the Files Program with the Menu Systemi csscsessescsscssssseetscisaeeessocieiccttsees caorna a cbaeseandecsnen seas 59 Chapter 2 Pulse Sequence Programming sssnsnssssnnnrnnnnnrnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnan nnn 63 2 1 Programming Pulse Sequences from Menus ccssesessssesseeeeeseeseeesecsseseeseesecseeseeseaecaseeceaesaeeeeeessaeaees 63 Pulse Sequence Programme Menus sos ccscisescseceshasericbesser ad tel ncket hoc E R EET 65 Pulse Sequence Entry Main Mem ssid 5ccesceeccgonsecesospesctdesiecinctsesuee canteviqoccd sx eeocesnssnacedssdevvoutyseneseeets 66 Pulse Sequence Entry Delay Menu cisse aee iea ae E Gian ashn nai aeaas 66 Pulse Sequence Entry Phases MICO ci 5 5 scscicsdesspenscesvecacuscesnseaduentss jevuteoviesiss oi EE Oa TEE EEES 67 Pulse Sequence Entry Phases Secondary Ment 2s csccc scssccsesseeescacieeescocsetecetsosscaeebocecbnaseubdeesaceaney 67 Pulse Sequence Entry Pulses MGM s 2o ss lt ccscsecssecsacesccvssassesvecssctscsusccangsvsesecssiesocessssptesissutesenieesdeneites 67 Pulse Sequence Entry Decoupler Pulses Ment 2 2 2 5 csc scicssescssssessescasest sareguneobaadscautsansebesaevsaecsersosns 68 Pulse Sequence Entry Status MGM ccse scsi citceces bi scdyucuesnsstevien ntvacsthasieos as vlaneuses sides nri reenn ESEE 68 2 2 Overv
197. Turn off third decoupler UNITYINOVA and UNITYplus systems with a third decoupler dec3o0fFf Explicitly gates off the third decoupler in the pulse sequence dec3on Turn on third decoupler Change offset frequency of first decoupler decoffset frequency double frequency offset in Hz Changes the offset frequency of the first decoupler parameter dof It is functionally the same as of fset frequency DODEV frequency is the offset frequency desired in hertz decoffset dol dec2offset Change offset frequency of second decoupler dec30ffset Change offset frequency of third decoupler obsoffset Change offset frequency of observe transmitter offset Change offset frequency of transmitter or decoupler Change offset frequency of second decoupler dec2offset frequency double frequency offset frequency in Hz Changes the offset frequency of the second decoupler parameter dof 2 It is functionally the same as of fset frequency DO2DEV frequency is the offset frequency desired in hertz dec2offset do2 decoffset Change offset frequency of first decoupler dec3o0ffset Change offset frequency of third decoupler obsoffset Change offset frequency of observe transmitter offset Change offset frequency of transmitter or decoupler 01 999165 00 A0800 dec30ffset Syntax Description Arguments Examples Related dec4offset Applicability Syntax Description Arguments Examples Re
198. User Programming 01 999165 00 A0800 Examples Related sli Applicability Syntax Description Chapter 3 Pulse Sequence Statement Reference dec2width is the length of the pulse in seconds on the second decoupler obsphase is the phase of the pulse on the observe transmitter The value must be a real time variable v1 to v14 oph etc decphase is the phase of the pulse on the first decoupler The value must be a real time variable v1 to v14 oph etc dec2phase is the phase of the pulse on the second decoupler The value must be a real time variable v1 to v14 oph etc RG1 is the delay in seconds between gating the amplifier on and gating the first rf transmitter on all phase shifts occur at the beginning of this delay RG2 is the delay in seconds between gating the final rf transmitter off and gating the amplifier off sim3shaped_pulse gauss hrm180 sinc pw pl p2 v2 v5 v6 rofl rof2 sim3shaped_pulse dumy hrm180 sinc 0 0 pl p2 v2 v5 v6 rofl rof2 decshaped_puls Shaped pulse on first decoupler dec2shaped_puls Shaped pulse on second decoupler shaped_pulse Shaped pulse on observe transmitter simshaped_pulse Simultaneous two pulse shaped pulse Set SLI lines Systems with imaging capability and the Synchronous Line Interface SLI board an option that provides an interface to custom user equipment sli address mode value int address SLI board address
199. _list delay2 n 1 vdelay_list list2 v5 Use v5 from list2 vfreq 1 v2 Use v2 from list 1 voffset 2 v1 Use v1 from list 2 vdelay_list listl vl Use vl from listl create_freq_list Create table of frequencies create offset list Create table of frequency offsets delay Delay for a specified time getarray Retrieves all values of an arrayed parameter vdelay Select delay from table create_freq list Create table of frequencies Applicability Syntax Description Not applicable on MERCURY and GEMINI 2000 create_freq_list list nvals device list_number double list pointer to list of frequencies int nvals number of values in list int device OBSch DECch DEC2ch or DEC3ch int list_number number 0 255 for each list Stores global lists of frequencies that can be accessed with a real time variable or table element for dynamic setting of frequencies Frequency lists use frequencies in MHz such as from s frq df rq The lists need to be created in order starting from 0 using the 1ist_number argument or by setting the list_number argument to 1 which makes the software allocate and create the next free list and give the list number as a return value Each list must have a unique and sequential 1ist_number There can be a maximum of 256 lists depending on the size of the lists The lists are stored in data
200. a loop of pulses and delays followed by an implicit acquisition the first hardware loop must have a minimum cycle length of approximately 80 us With VNMR 6 1C User Programming 01 999165 00 A0800 2 8 Hardware Looping and Explicit Acquisition three or more hardware loops loops that are not the first or last must have a minimum cycle length about 100 us For MERCURY VX and MERCURY STM Output boards Data Acquisition Controller boards Acquisition Controller boards and Pulse Sequence Controller boards there are no timing restrictions between multiple back to back hard loops There is one subtle restriction placed on the actual duration of a hard loop if back to back hard loops are encountered the duration of the ith hard loop must be N i 1 0 4 ms where N i 1 is the number of events occurring in the i 1 th hard loop Number of Events in Hardware Loops As indicated above a limit of 63 events can occur in a hardware loop for Output boards a limit of 1024 events for Acquisition Controller boards and a limit of 2048 events for the MERCURY VX and MERCURY STM Output Data Acquisition Controller and Pulse Sequence Controller boards with a requirement in all cases that the number of events be greater than 1 see Types of Acquisition Controller Boards page 72 for a description of board types But what is meant by an event An event is a single activation of the timing circuitry Pulses delays phase shifts etc set or r
201. a timed event of less than the minimum value 0 1 us on UN YINOVA 0 2 us on other systems would be produced In such cases a short time 0 2 us on UN TYINOVA 0 4 us on other systems is added to the longer of the two pulse widths to remedy the problem or the pulses are made the same if the difference is less than half the minimum less than 0 1 us on UN TYINOVA less than 0 2 us on other systems sim3pulse pwl pw2 pw3 phasel phase2 phase3 RG1 RG2 performs a simultaneous three pulse pulse on three independent rf channels where pw1 pw2 and pw3 are the pulse durations on the observe transmitter first decoupler and second decoupler respectively phasel phase2 and phase3 are real time variables for the VNMR 6 1C User Programming 01 999165 00 A0800 2 3 Spectrometer Control Observe pulse gt Decoupler pulse Decoupler pulse gt Observe pulse Transmitter obswidth Decoupler deewialn gating gating decwidth obswidth Decoupler l Transmitter gating i gating RG1 RG2 Amplifier Amplifier gating gating Figure 4 Pulse Observe and Decoupler Channels Simultaneously phases of the corresponding pulses for example sim3pulse pw p1 p2 oph VL0 vi Lotl rot2 A simultaneous two pulse pulse on the observe transmitter and the second decoupler can be achieved by setting the pulse length for the first decoupler to 0 0 for example sim3pulse pw 0 0 p2 oph vl10 vl1 rofl1 rof2 sim3pulse has no meaning
202. abel 3 Broaden mstring 3 lb sw fn 2 set to digital resolution if dmg ph then mlabel 4 gt AV mstring 4 av else mlabel 4 gt PH mstring 4 ph endif mlabel 5 FN Small mstring 5 fn np 4 mlabel 6 Normal mstring 6J fn n mlabel 7 Large mstring 7 fn 2 np mlabel 8 Return mstring 8 menu process_1D e The label and action of button 4 depend on the value of a particular parameter dmg If the spectrum is in the phase sensitive mode button 4 displays the label gt AV clicking on the button switches the spectrum to the absolute value mode If the spectrum is in the absolute value mode button 4 displays gt PH clicking on it switches the spectrum to the phase sensitive mode Menus are redisplayed after any choice is made from the menu and also after any other action such as entering a parameter For this reason menus can respond dynamically to changed conditions by displaying different choices or taking different actions in response to different situations Consider the menu in Listing 5 that allows the user to display the experiment library join different experiments and create and delete experiments Of course we only want to allow experiments that exist to be joined It is meaningless to join the current experiment The macro that sets up the menu evaluates the current situation and prepares the menu accordingly Note that if you select this menu
203. able 1 Reserved Words in MAGICAL ooo cece ceeeseeseceseeseceeceseceeeeseecaeeseecoeesaecaeesaesnessaeeseeeaees 30 Table 2 Order of Operator Precedence Highest First in MAGICAL ou ce ceeeeeeeteeeeeeeeeeeeeees 31 Table 3 Menu Related Commands and Parameters 00 0 0 eceeceeceesseseeeeeeseeeeecseeaecseesaecneseaeeneeenees 52 Table 4 Variable Types in Pulse Sequences cece ec eeceeeeeeceeeeeeceseeeeeeseeeeecaeesaecaaesaecseseseeneeenees 74 Table 3 Acquisition Status Codes sicoor e ienaa r ids EE E SEE RESES SE 75 Table 6 Delay Related Statements sc cscescovce nscek steep ivsccd so vaevacetess bvbsebuesetebasSardeaseacdeutesunessivecssasveess 79 Table 7 Observe Transmitter Pulse Related Statements s sssesssesesseeessstrrrsrrrisrrerrrreresrneerrnsenees 81 Table 8 Decoupler Transmitter Pulse Related Statements eee eeeeecseeceececesaecneetaeeneensees 83 Table 9 Simultaneous Pulses Statements 20 0 0 ee cece ceseeeeceeeeeeceeeeeeecaeeeeecaeesaecaeesaecesesesneeeaees 84 Table 10 Transmitter Quadrature Phase Control Statements cccccccssececsseeeeseceeesneeeeseeeeess 85 Table 11 Phase Shift Statement 00 0 ee cseseesececsceccesecaseeceeesaecesseceecneesessecnecaeeseeaeceeseeeaeeaeeees 86 Table 12 Frequency Control Statements 200 00 eee ceeeeeeseeseceeeeseceeeeseeeaeeseecoeesaecsaesaesnesaeeneesaees 90 Table 13 Power Control Statements sc csitscscss deeseiaseicsees Sonsecvecdsvnaieussebusavivess bosse
204. able for vscan Execute an oblique gradient Execute an oblique gradient Execute a shaped oblique gradient Execute a shaped oblique gradient Provides a sequence switchable loop Oblique gradient with PE in 1 axis Oblique gradient with PE in 2 axes Oblique gradient with PE in 3 axes Oblique shaped gradient with PE in 1 axis Oblique shaped gradient with PE in 2 axes Oblique shaped gradient with PE in 3 axes Oblique gradient with PE in 1 axis Oblique gradient with PE in 3 axes Oblique shaped gradient with PE in 1 axis Oblique shaped gradient with PE in 3 axes Set frequency based on position Set frequency from position list Set frequency from position list Provide shaped gradient pulse Arrayed shaped gradient function Dynamic variable gradient function Dynamic variable shaped gradient function Set SLI lines Variable angle gradient Pulse controlled variable angle gradient Variable angle shaped gradient Variable angle pulse controlled shaped gradient Select delay from table Get delay value from delay list with real time index Select frequency from table Dynamic variable gradient Select frequency offset from table Dynamic variable scan function Set SLI lines from real time variable Sets all gradients to zero For the argument list refer to the statement reference in Chapter 3 VNMR 6 1C User Programming 01 999165 00 A0800 2 18 User Customized Pulse Sequence Generation Global List and Position Statements The globa
205. able name may be used only once within the table file If a table name is used twice within the table file an error message is displayed and pulse sequence generation PSG aborts Each table statement must be written as an integer number and separated from the next statement by some form of white space such as a blank space tab or carriage return The maximum number of statements per table is 8192 For the average pulse sequence the maximum number of table statements per experiment is approximately 10 000 The table name is separated from the table statements by an or a sign the sign is explained below and there must be a space between the table name and either of these two signs For example if a table file contains the table name t 1 with statements 0 1 2 3 2 3 0 1 it would be writtenastl 012323041 The index into a table can range from 0 to 1 less than the number of statements in the table Note that an index of 0 will access the first statement in the table Unless the autoincrement attribute described below is imparted to the table the index into the table is given by ct the completed transient counter If the number of transients exceeds the length of the table access to the table begins again at the beginning of the table Thus given a table of length n with statements numbered 0 through n 1 this numbering is strictly a way to think about the numbering and does not imply the statements are actually nu
206. able2 For example the command peak described below in more detail finds the height and frequency of the tallest peak Entering the command peak rl r2 results in r1 containing the height of the tallest peak and r2 its frequency Therefore entering the command peak Sht cr would set ht equal to the height of the tallest peak and set the cursor parameter cr equal to its frequency and thus would be the equivalent of a tallest line command similar to but different than the command n1 to position the cursor at the nearest line It is not necessary to receive all of the information For example entering peak Speakht puts the height of the tallest peak into the variable peakht and does not save the information about the peak frequency The command that displays a line list d1 1 also produces one output the number of lines Entering dll n reads the number of lines into variable n d11 alone is perfectly acceptable although the information about the number of lines is then lost Loading Macros into Memory Every time a macro is used it is parsed before it is executed This parsing takes time If a macro is used many times or if faster execution speed is desirable the parsed form of the macro user or system can be loaded into memory by the macrold command When that macro is executed it runs substantially faster You can even pre load one or more macros automatically when you start VNMR by ins
207. acquisition at which time a homospoil pulse is not permitted Thus if a particular pulse sequence uses status A status B and status C dm and other decoupler parameters may have up to three letters but hs will only have two since hs y during status C would be meaningless and is ignored Transmitter Gating On all systems transmitter gating is handled as follows e Explicit transmitter gating in the pulse sequence is provided by xmt roff and xmt ron Transmitter gating is handled automatically by obspulse pulse rgpulse simpulse sim3pulse shaped_pulse simshaped_pulse sim3shaped_pulse and spinlock The obsprgon statement should generally be enabled with an explicit xmt ron statement followed by xmt roff e Explicit gating of the first decoupler in the pulse sequence is provided by decof f and decon First decoupler gating is handled automatically by decpulse decrgpulse declvlon declvloff simpulse sim3pulse decshaped_pulse simshaped_pulse sim3shaped_pulse and decspinlock The decprgon function should generally be enabled with explicit decon statement and followed by a decof f call e Explicit gating of the second decoupler in the pulse sequence is provided by dec2o0ff and dec2on Second decoupler gating is handled automatically by dec2pulse dec2rgpulse sim3pulse dec2shaped_pulse sim3shaped_pulse and dec2spinlock The dec2prgon function should generally be enabled with an explicit d2con stat
208. add tablenamedest tablenamemod moduloval ttdiv tablenamedest tablenamemod moduloval ttmult tablenamedest tablenamemod moduloval ttdiv tablenamedest tablenamemod moduloval The loadtable file statement loads AP table statements from table text file file specifies the name of the table file a UNIX text file in the user s personal tablib directory or in the VNMR system t ablib directory loadt able can be called multiple times within a pulse sequence Care should be taken to ensure that the same table name is not used more than once by the pulse sequence The settable tablename numelements intarray statement stores an array of integers in a real time AP table tablename specifies the name of the table t 1 to t60 numelements specifies the size of the table intarray is aC array that contains the table elements These elements can range from 32768 to 32767 The user must predefine and predimension this array in the pulse sequence using C language statements prior to calling settable The getelem tablename APindex APdest statement retrieves an element from an AP table tablename specifies the name of the Table t 1 to t 60 APindex isan AP variable v1 to v14 oph ct bsctr or ssctr that contains the index of the desired table element Note that the first element of an AP table has an index of 0 APdest is also an AP variable v1 to v14 and oph into which the retrieved table element is placed For tables for wh
209. ain hidden Arguments width specifies the width of the observe transmitter pulse phase sets the phase and must be a real time variable Examples pulse pw v2 Related dps_show Draw delay or pulses in a sequence for graphical display obspulse Pulse observe transmitter with IPA ipulse Pulse observe transmitter with IPA irgpulse Pulse observe transmitter with IPA obspulse Pulse observe transmitter with amplifier gating rgpulse Pulse observe transmitter with amplifier gating simpulse Pulse observe decoupler channels simultaneously sim3pulse Simultaneous pulse on 2 or 3 rf channels pwrf Change transmitter or decoupler fine power Applicability Systems with fine attenuators Not available on MERCURY VX MERCURY and GEMINI 2000 systems Syntax pwrf power device int power new value for fine power control int device OBSch DECch DEC2ch or DEC3ch 234 VNMR 6 1C User Programming 01 999165 00 A0800 Description Arguments Examples Related pwrm Applicability Syntax Description Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference Changes the fine power of the device specified by adjusting the optional fine attenuators Do not execute pwr f and i pwr f together because they will cancel each other s effect power is the fine power desired It must be a real time variable v1 to v14 etc which means it cannot be placed directly in the pwrf
210. al Statements The following forms of conditional statements are allowed if booleanexpression then endif if booleanexpression then else endif Any number of statements including none can be inserted in place of the ellipses If booleanexpression is TRUE the then statements are executed if booleanexpression is FALSE the else statements if any are executed instead Note that endi f is required for both forms and that no other delimiters such as BEGIN or END are used even when multiple statements are inserted Nesting of if statements the use of if statement as part of another if statement is allowed but be sure each if has a corresponding endif The following example uses a simple if then conditional statement error Check for error conditions if pw gt 100 or d1 gt 30 or tn H1 and dhp y then write line3 Problem with acquisition parameters endif This example adds an else conditional statement checkpw Check pulse width against predefined limits if pw lt l then pw 1 write line3 pw too small else if pw gt 100 then pw 100 write line3 pw too large endif endif Loops Two types of loops are available The while loop has the form while booleanexpression do endwhile This type of loop repeats the statements between do and endwhi le as long as booleanexpression is TRUE if booleanexpression is FALSE from the start the statements are not ex
211. alarval is an integer to be added to each element of the table is the modulo value taken on the result of the operation if is greater than 0 moduloval moduloval tsadd t31 4 4 tsdiv Divide an integer into AP table elements tsmult Multiply an integer with AP table elements tssub Subtract an integer from AP table elements Divide an integer into AP table elements All systems except the GEMINI 2000 tsdiv table scalarval moduloval real time table variable integer divisor modulo value of result codeint table int scalarval int moduloval A run time scalar operation that divides an integer into the elements of an AP table table specifies the name of the table t 1 to t 60 is an integer to be divided into each element of the table must not equal 0 otherwise an error is displayed and PSG aborts scalarval scalarval is the modulo value taken on the result of the operation if is greater than 0 moduloval moduloval tsdiv t31 4 4 tsadd Add an integer to AP table elements tsmult Multiply an integer with AP table elements tssub Subtract an integer from AP table elements Multiply an integer with AP table elements All systems except the GEMINI 2000 tsmult table scalarval moduloval real time table variable integer multiplier modulo value of result codeint table int scalarval int moduloval A run time
212. alue must be from 32768 0 to 32767 0 To set the gradient current amplifier level but determine the value instead by real time math use vgradient channel intercept slope rtval where channel is used the same as in rgradient and amplifier level is determined by intercept slope rtval e g vgradient z 5000 0 2500 0 v10 This statement not available on the Performa I PFG module VNMR 6 1C User Programming 01 999165 00 A0800 2 15 Gradient Control for PFG and Imaging Table 35 Gradient Control Statements 1k_hold 1k_sample obl_gradient oblique_gradient obl_shapedgradient oblique_shapedgradient pe_gradient pe2_gradient pe3_gradient pe_shapedgradient pe2_shapedgradient pe3_shapedgradient Set lock correction circuitry to hold Set lock correction circuitry to sample Execute an oblique gradient Execute an oblique gradient Execute a shaped oblique gradient Execute a shaped oblique gradient Oblique gradient with PE in 1 axis Oblique gradient with PE in 2 axes Oblique gradient with PE in 3 axes Oblique shaped gradient with PE in 1 axis Oblique shaped gradient with PE in 2 axes Oblique shaped gradient with PE in 3 axes phase_encode_gradient Oblique gradient with PE in 1 axis phase_encode3_gradient Oblique gradient with PE in 3 axes phase_encode_shapedgradient Oblique shaped gradient with PE in 1 axis phase_encode3_shapedgradient Oblique shaped gradient with PE i
213. alue of sb is 0 6666666 Tcl Cmd format 3f Ssb This displays sb with 3 decimal places A more complex example can be found with fn Vnmr Cmd fn SVALUE 2 Tel Cma expr Sfn gt 2000 format Sdk expr fn 2000 fn 2 This complex expression checks to see if fn is greater than 1024 If fn gt 1024 itis displayed as nk but if not the display is the full number of complex points This introduces the Tcl expression for true and false The expression in parentheses is evaluated for truth or the value 1 If found true the result is the value of the expression between the question mark and the colon otherwise the result is the value of the expression that follows the colon Allowing the units of an entry to change requires some more Tcl Take sw for example We may wish to display and enter this either as Hz or as ppm Vnmr Cmd sw SVALUE vnmrUnits sw Tcl Cmd expr sw vnmrUnits sw 340 VNMR 6 1C User Programming 01 999165 00 A0800 6 3 Customizing the Interactive dg Window The Tcl procedure vnmrUnits takes the string sw note not sw as an argument and returns a scaling factor for sw The scaling factor is chosen through an adjacent menu2 widget The key definitions for this widget are the following Choices Hz ppm Value of choices 14 Vnmr Variables sw Vnmr Cmd setdgroup sw SVALUE Tcl Cmd vnmrDgroup sw The values that can be set in Dgroup are shown
214. alues can be interrogated by entering the name of the parameter followed by a question mark e g rof1 width specifies the duration in seconds of the observe transmitter pulse phase sets the observe transmitter phase and must be a real time variable RG1 is the time in seconds the amplifier is gated on prior to the start of the pulse typically 10 us for 1H 19F 40 us for other nuclei and 2 us for the MERCURY VX MERCURY and GEMINI 2000 RG2 is the time in seconds before the amplifier is gated off after the end of the pulse typically 10 us on the MERCURY VX MERCURY and GEMINI 2000 and about 10 to 20 us on other systems rgpulse pw vl rofl rof2 rgpulse 2 0 pw v2 1 0e 6 0 2e 6 iobspulse Pulse observe transmitter with IPA ipulse Pulse observe transmitter with IPA irgpulse Pulse observe transmitter with IPA obspulse Pulse observe transmitter with amplifier gating pulse Pulse observe transmitter with amplifier gating simpulse Pulse observe decoupler channels simultaneously sim3pulse Simultaneous pulse on 2 or 3 rf channels Set gradient to specified level Systems with imaging or PFG modules rgradient channel value char channel gradient x y or fz double value amplitude of gradient amplifier Sets the gradient current amplifier to specified value In imaging rgradient sets a gradient to a specified level in DAC units 238 VNMR 6 1C User Programming 01 999165 00 A0800 Arguments Exa
215. amplifiers an rf pulse can be unexpectedly curtailed if the amplifier goes into thermal shutdown Thermal shutdown can be brought about if the amplifier duty cycle becomes too large for the average power output In addition on GEMINI 2000 MERCURY VX and MERCURY systems the pulse length is limited to 1 ms The remaining statements for pulsing the observe transmitter are variations of rgpulse e To pulse the observe transmitter the same as rgpulse but with RG1 and RG2 set to the parameters rof1 and rof2 respectively use pulse width phase Thus pulse width phase and rgpulse width phase rofl rof2 are exactly equivalent 01 999165 00 A0800 VNMR 6 1C User Programming 81 Chapter 2 Pulse Sequence Programming 82 e To pulse the observe transmitter the same as pulse but with width preset to pw and phase preset to oph use obspulse Thus obspulse is exactly equivalent to rgpulse pw oph rofl rof2 e To pulse the observe transmitter with rgpulse pulse or obspulse but generate interactive parameter adjustment IPA information when gf or go acqi is entered use irgopulse width phase RG1 RG2 string ipulse width phase string or iobspulse string respectively The st ring argument is used as a label in acqi If go is entered the IPA information is not generated For details on IPA see Using Interactive Parameter Adjustment page 120 IPA is not available on MERCURY VX MERCURY and GEMINI 2000 system
216. amplitude and phase tables respectively If apshaped_pulse is called more than once different table names should be used in each call RG1 is the amplifier gating time in seconds before the pulse RG2 is the amplifier gating time in seconds after the pulse apshaped_pulse gauss pw vl rofl rof2 apshaped_decpulse First decoupler pulse shaping via the AP bus apshaped_dec2pulse Second decoupler pulse shaping via the AP bus shaped_pulse Perform shaped pulse on observe transmitter xmtrphase Set small angle phase of observe transmitter rf C or D 01 999165 00 A0800 VNMR 6 1C User Programming 163 Chapter 3 Pulse Sequence Statement Reference assign Assign integer values Syntax assign vi vj codeint vi real time variable for starting value codeint vj real time variable for assigned value Description Sets vj equal to the integer value vi Arguments vi and vj are real time variables v1 to v14 oph etc Examples assign v3 v2 Related adad Add integer values dbl Double an integer value decr Decrement an integer value divn Divide integer values hlv Half the value of an integer incr Increment an integer value mod2 Find integer value modulo 2 mod4 Find integer value modulo 4 modn Find integer value modulo n mult Multiply integer values sub Subtract integer values blankingoff Unblank amplifier channels and turn amplifiers on Applicability MERCURY VX MERCURY and GEMINI 2000 systems only Syntax blankingoff
217. an be zero or more parameter names 338 VNMR 6 1C User Programming 01 999165 00 A0800 6 3 Customizing the Interactive dg Window Vnmr Cmd MAGICAL expression sent to VNMR whenever the scroll updates to the next item in the list Any specified VNMR parameters can be used The variable SVALUE is set to the value of the scroll Tcl Cmd Tcl expression that is evaluated to determine the value of the scroll Any legitimate Tcl expression is allowed To access the values of any VNMR parameters specified in the Vnmr Variables list prepend a dollar sign to the front of the parameter name The scroll element is a useful mechanism to modify a numerical or string parameter It prevents errors in parameter entry This item is most useful if there is an obvious up down notion about the parameter An example with Fourier Numbers is the following Label of element Fourier Number Choices 128 256 512 1024 2048 4096 8192 16384 32768 65536 131072 Width of element 6 Vnmr Variables fn Vnmr Cmd fn SVALUE Tcl Cmd Sin Tips for dg Design The key to designing dg panes is to have a clear understanding of the operation of the two entries Vnmr Cmd and Tcl Cmd The contents of these two fields are passed as strings via the Tcl set command in the form set dgTemplate string What VNMR Sees In the case of Vnmr Cmd the string is sent to VNMR for evaluation Thus the final string needs to be something that makes sense to MAGICAL Howe
218. an item causes it to occupy a corresponding number of grid rectangles to the right of the currently selected rectangle The Justify menu selects whether the item is aligned along the left edge of its grid space centered within the grid space or aligned along the right edge of the grid space 01 999165 00 A0800 VNMR 6 1C User Programming 331 Chapter 6 Customizing Graphics Windows Below this menu are twelve entry fields These are used to define the label and actions of the interaction items Each type of interaction item has its own set of adjustable characteristics Entry fields that are not appropriate for the selected type of element are shaded and you can not enter a value in the shaded field Interaction Elements The Type of Element choices and the associated characteristics define the actions of the dg pane The available elements are none title label button entry check radio menu menu2 scale scroll and list For each of these elements the Row Extent Column Extent and Justify options are available Also for each of these elements the Color of Label choice is available It must be filled in with the name of any legitimate X windows color The UNIX command showrgb lists the available color names If an unknown color name or no color name is present it defaults to black None Element The none element removes any interaction item from the selected grid rectangle Title Element The title element places a non interac
219. an the offset frequency Frequencies are in Hz Default value is described in the description column for this attribute Examples of using G_Offset G_Offset OFFSET_DEVICE TODEV OFFSET_FREQ tof equivalent to a offset tof TODEV 0 required terminating zero G_Offset OFFSET_DEVICE ODEV OFFSET_FREQ tof basic interactive offset statement SLIDER_LABEL TOF for fine adjustment of 0 transmitter frequency Generic Delay Routine The G_Delay generic delay routine has the following syntax G_Delay DELAY_TIME dl SLIDER_LABEL NULL SLIDER_SCALE 1 SLIDER_MAX 60 SLIDER_MIN 0 SLIDER_UNITS ieg 0 01 999165 00 A0800 VNMR 6 1C User Programming 123 Chapter 2 Pulse Sequence Programming 124 The following table describes the attributes used with G_Delay Attribute Type Default Description DELAY_TIME double dl As specified in parameter set SLIDER_LABEL char NULL Label 1 to 6 characters for acqi or NULL for no output to acqi SLIDER_SCALE int 1 Decimal places 0 to 3 displayed SLIDER_MAX int 60 Maximum value on the slider SLIDER_MIN int 0 Minimum value on the slider SLIDER_UNITS double 1 0 Delays are in seconds Examples of using G_Delay G_Delay 0 equals delay dl
220. and get st r statements to permit changes by the parameters see the second example below pattern is the name of the text file in the shape1ib directory that stores the decoupling pattern leave off the DEC file extension 90_pulselength is the pulse duration in seconds for a 90 tip angle on the second decoupler tipangle_resoln is the resolution in tip angle degrees to which the decoupling pattern is stored in the waveform generator 1 dec2prgon waltz16 1 dmf2 90 0 2 dec2prgon modt ype pwx290 dres2 n50ns_ticks dec2prgon garpl 1 dmf2 1 0 decprgon Start programmable decoupling on first decoupler dec2prgoff End programmable decoupling on second decoupler obsprgon Start programmable control of obs transmitter Start programmable decoupling on third decoupler UNITYTNOVA and UNITYplus systems with a waveform generator on rf channel for the third decoupler dec3prgon pattern 90_pulselength tipangle_resoln char pattern name of DEC text file double 90_pulselength 90 deg pulse length in sec double tipangle_resoln tip angle resolution Executes programmable decoupling on third decoupler under waveform generator control It returns the number of 50 ns ticks as an integer value in one cycle of the decoupling pattern Explicit gating of the third decoupler with dec3on and dec3of f is generally required Arguments can be variables which require the appropriate get val and get st r st
221. and unblank both amplifier channels as well as turn the amplifiers off and on Interfacing to External User Devices All consoles provide some means of interfacing to external user devices Table 15 lists the statements available for this feature Table 15 Interfacing to External User Devices readuserap rtvalue Read input from user AP register setuserap value nreg Set user AP register sp off sp on Turn off and on specified spare line vsetuserap rtvalue nreg Set user AP register using real time variable User Dedicated Spare Lines One or more user dedicated spare lines are available for high speed device control e UNITYTNOVA consoles have five spare lines in the Breakout panel on the rear of the left cabinet Each spare line is a BNC connector The sp on and sp off statements control specified SPARE lines e GEMINI 2000 consoles have a single user dedicated spare line e UNITYplus consoles have two spare line on the front panel of the Pulse Sequence Controller board in the digital cardcage Each spare line is a SMB connector The sp on and sp off statements control specified SPARE lines LEDs between the two connectors indicate activity on each line e UNITY and VXR S consoles have spare lines on the Interface board User AP Analog Port Lines UNITYINOVA consoles have two 24 pin user AP connectors J8212 and J8213 in the Breakout panel on the rear of the left cabinet Each connector has 16 us
222. are to sort chronologically which is the std sort to sort by location numbers loc to sort by user names user or to sort by experiment status st at This attribute only defines the default sort The locate button provides access to the other sort criteria 6 3 Customizing the Interactive dg Window 324 The interactive dg window brings a new level of functionality to VNMR This window is readily customizable and so can be designed for the specific needs of individual pulse sequences The window consists of a series of panes Any pane can be selected by clicking on the label tab normally found to the right of the window Figure 13 shows this window Each pane of the window deals with settings and actions associated with a particular phase of operating the spectrometer The most common display element on a pane is a labeled value of a setting This value may be altered by clicking on it with the mouse editing the value in the normal manner and then either pressing Return or moving the mouse cursor to another value and clicking on that shifting the focus VNMR 6 1C User Programming 01 999165 00 A0800 6 3 Customizing the Interactive dg Window Samples Queued Active Complete Error Total 2 0 S 0 8 USER SAMPLE TEXTS USER SAMPLE TEXT USER SAMPLE TEXT USER vnmri SAMPLE 5 TEXT USER SAMPLE TEXT USER SAMPLE TEXT USER SAMPLE TEXT USER SAMPLE TEXT Log information
223. ary dynamically in a manner controlled by the user phase_encode3_shapedgradient Oblique sh gradient with PE on 3 axes Phase encode loop Not applicable on MERCURY VX MERCURY and GEMINI 2000 peloop state max_count apvl apv2 char state compressed or standard double max_count initializes apvl codeint apvl maximum count codeint apv2 current counter value Provides a sequence switchable loop that can use real time variables in what is known as acompressed loop or it can use the standard arrayed features of PSG In the imaging sequences it uses the third character of the seqcon string parameter seqcon 2 for the state argument The statement is used in conjunction with the endpeloop statement peloop differs from ms 1oop in how it sets the apv2 variable in standard arrayed mode state is s In standard arrayed mode apv2 is set to nth2D 1 if max_count is greater than zero nt h2D is a PSG internal counting variable for the second dimension When in the compressed mode apv2 counts from zero to max_count 1 state is either c to designate the compressed mode or s to designate the standard arrayed mode apv1 is a real time variable that holds the maximum count apv2 is a real time variable that holds the current counter value If state is s and max_count is greater than zero apv2 is set to nth2D 1 otherwise it is set to zero peloop seqcon 2 nv v5 v6 msloop segqcon 1 nv vl1 v12
224. asel int phase Acquisition mode for first indirect dimension d3_index int 0 to ni2 1 Current index of the d3 array id3 real time 0 to ni2 1 Current real time index of the d3 array inc3D double 1 0 sw2 Dwell time for second indirect dimension phase2 int phase2 Acquisition mode for second indirect dimension d4_index int 0 to ni3 1 Current index of the d4 array id4 real time 0 to ni3 1 Current real time index of the d4 array inc4D double 1 0 sw3 Dwell time for third indirect dimension phase3 int phase3 Acquisition mode for third indirect dimension ix int 1toarraydim Current element of an arrayed experiment be set by the user to 0 to give a non phase sensitive experiment or to an array as in phase 1 2 to generate the two desired experiments The parameter phase is automatically made available to a pulse sequence as the integer phase1 Typical code as part of the pulse sequence might look like this pulsesequence if phasel 0 Phase calculation for eae normal experiment else if phasel 1 Phase calculation for Sey first of two arrays else if phasel 2 Phase calculation for second of two arrays This code usually can be condensed because the phases are obviously related in the three experiments and three separate phase calculations are not needed One possibility is to write down the phase cycle for the entire experiment interspersing the real and imagi
225. at end These values hold regardless of the values for obswidth and decwidth If either obswidth or decwidth is 0 0 no pulse occurs on the corresponding channel If both obswidth and decwidth are non zero and either obsshape or decshape is set to the null string then a hard pulse occurs on the channel with the null shape name If either the pulse width is zero or the shape name is the null string then a waveform generator is not required on that channel Simultaneous Three Pulse Shaped Pulse The sim3shaped_pulse statement performs a simultaneous three pulse shaped pulse under waveform generator control on three independent rf channels The arguments to sim3shaped are the same as defined previously for simshaped_pulse except that dec2shape is the name of the text file that contains the rf pattern to be executed on the second decoupler dec2width is the duration of the pulse on the second decoupler and dec2phase is the phase a real time variable of the pulse on the second decoupler e g sim3shaped_pulse gauss hrm180 sinc pw pl v2 v5 v6 rofl rof2 The overhead at the beginning and end of the simultaneous three pulse shaped pulse varies with the system and acquisition controller board OnNTYINOVA 1 95 Us at start 0 at end e On UNITYplus 17 25 us at start 0 at end e On systems with an Acquisition Controller board 32 25 us at start 12 9 us at end e On systems with an Output board 32 45 us at start 13 1 us at
226. ata determines the value of the receiver phase To perform run time scalar operations of an integer with AP table elements use the following statements tsadd tablename scalarval moduloval tssub tablename scalarval moduloval tsmult tablename scalarval moduloval tsdiv tablename scalarval moduloval where tablename specifies the name of the table t 1 tot 60 and scalarval is added to subtracted from multiplied with or divided into each element of the table The result of the operation is taken modulo moduloval if moduloval is greater than 0 tsdiv requires that scalarval is not equal to 0 otherwise an error is displayed and PSG aborts To perform run time vector operations of one AP table with a second table use the following table to table statements ttadd tablenamedest tablenamemod moduloval ttsub tablenamedest tablenamemod moduloval ttmult tablenamedest tablenamemod moduloval ttdiv tablenamedest tablenamemod moduloval where tablenamedest and tablenamemodare the names of tables t 1 to t 60 Each element in tablenamedest is modified by the corresponding element in tablenamemod The result stored in tablenamedest is taken modulo moduloval if moduloval is greater than 0 The number of elements in tablenamedest must be greater than or equal to the number of elements in t ablenamemod tt div requires that no element in tablenamemod equal 0 Examples of Using AP Tables This section contains a two puls
227. atement Reference position_offset_list posarray grad nslices resfrq device list_number apv1 double posarray position values in cm double level gradient level in G cm double nslices number of slices double resfrq resonance offset in Hz int device OBSch DECch DEC2ch or DEC3ch int list_number number for global list codeint vi real time variable or AP table Sets the rf frequency from a position list conjugate gradient value and dynamic math selector The dynamic math selector apv1 holds the index for required slice offset value as stored in the array The arrays provided to this statement must count zero up that is array 0 must have the first slice position and array ns 1 the last It has no return value position_array is a list of position values in cm level is the gradient level in gauss cm used in the slice selection process nslices is the number of slices or position values resfrq is the resonance offset in Hz for the nucleus of interest device is OBSch observe transmitter or DECch first decoupler For the UNITYTNOVA and UNITYplus only device can also be DEC2ch second decoupler or DEC3ch third decoupler list_number is a value for identifying a global list The first global list must begin at zero and each created list must be incremented by one vi is a dynamic real time variable v1 to v14 or AP table t1 to t 60
228. atements to permit changes by parameters see second example below pattern is the name of the text file in the shape1lib directory that stores the decoupling pattern leave off the DEC file extension 90_pulselength is the pulse duration in seconds for a 90 tip angle on the third decoupler tipangle_resoln is the resolution in tip angle degrees to which the decoupling pattern is stored in the waveform generator 1 dec3prgon waltz16 1 dmf3 90 0 2 dec3prgon modt ype pwx390 dres3 n50ns_ticks dec3prgon garpl1 1 dmf3 1 0 decprgon Start programmable decoupling on first decoupler dec2prgoff End programmable decoupling on second decoupler obsprgon Start programmable control of obs transmitter 178 VNMR 6 1C User Programming 01 999165 00 A0800 decpulse Syntax Description Arguments Examples Related decpwr Applicability Syntax Description Arguments Examples Related decpwrf Applicability Syntax Description Arguments Chapter 3 Pulse Sequence Statement Reference Pulse first decoupler transmitter with amplifier gating decpulse width phase double width width of pulse in sec codeint phase real time variable for phase of pulse Pulses the first decoupler at its current power level The amplifier is gated off during decoupler pulses as it is during observe pulses The amplifier gating times see RGI and RG2 for decrgpulse are interna
229. aveform generator controlled spin lock on the third decoupler Both the rf gating and the mixing delay are handled within this function Arguments can be variables which would need the appropriate get val and get str statements to permit changes via parameters see the second example below pattern is the name of the text file in the shape1lib directory that stores the decoupling pattern leave off the DEC file extension 90_pulselength is the pulse duration in seconds for a 90 tip angle tipangle_resoln is the resolution in tip angle degrees to which the decoupling pattern is stored in the waveform generator phase is the phase of the spin lock It must be a real time variable v1 to v14 etc or a real time constant zero one etc ncycles is the number of times that the spin lock pattern is to be executed dec3spinlock mlev16 p390 dres3 vl1 42 dec3spinlock lock2 pwx2 dres3 vl cycles decspinlock Set spin lock waveform control on first decoupler spinlock Set spin lock waveform control on observe transmitter Set step size for first decoupler All systems except the GEMINI 2000 decstepsiz double step_size step_size phase step size of DODEV Sets the step size of the first decoupler It is functionally the same as stepsize base DODEV step_size is the phase step size desired and is a real number or a variable decstepsize 30 0 dec2stepsize Set step size of second decoupler de
230. ay These overhead delays and associated functions are placed outside the hardware loop when acquire statements are within a hardware loop and before the first acquire and after the last acquire when more than one acquire statement is used to acquire a FID Once an explicit acquisition is invoked even if for one pair of data points the standard implicit acquisition is turned off and the user is responsible for acquiring the full number of data points Failure to acquire the correct number of data points before the end of the pulse sequence generates an error The total number of data points acquired before the end of the sequence must equal the specified number np An example of the programming necessary to program a simple explicit acquisition analogous to the normal implicit acquisition would look like this revron txphase zero decphase zero delay alfa 1 0 beta fb acquire np 1 0 sw Although generally not needed the clearapdatatable statement is available to zero the acquired data table at times other than at the start of the execution of a pulse sequence when the data table is automatically zeroed The limitation that multiple hardloops cannot be nested has consequences for the use of the acquire statement inside a hardloop Depending on its arguments and how it is built into 01 999165 00 A0800 VNMR 6 1C User Programming 129 Chapter 2 Pulse Sequence Programming 130 a pulse sequence the acqu
231. ay lists create_offset_list offsets1 noffset OBSch 0 create_delay_list delay ndelay 1 create_offset_list offsets2 noffset DECch 2 voffset 0 v4 get v4 from observe offset list vdelay_list 1 v5 get v5 from delay list voffset 2 v4 get v4 from decouple offset list create_delay_list Create table of delays delay Delay for a specified time hsdelay Delay specified time with possible homospoil pulse idelay Delay for a specified time with IPA incdelay Real time incremental delay initdelay Initialize incremental delay vfreq Select frequency from table voffset Select frequency offset from table vdelay Set delay with fixed timebase and real time count Select frequency from table Not applicable on MERCURY VX MERCURY and GEMINI 2000 vfregq list_number vindex int list_number same index as for create_freq_list codeint vindex real time variable Provides a means of indexing into previously created frequency lists using a real time variable or an AP table The indexing into the list is from 0 to N 1 where N is the number of items in the list The frequency table must have been created with the create_freq_list statement It has no return value list _number is the number between 0 and 255 for each list This number must match the 1ist_number used when creating the table vindex is a real time variable v1 to v14 or an AP table t1 to t 60 See the example for the vdel
232. ay statement create_freq_list Create table of frequencies vdelay Select delay from table voffset Select frequency offset from table Set gradient to a level determined by real time math Systems with imaging or PFG modules Not applicable to MERCURY VX MERCURY and GEMINI 2000 systems vgradient channel intercept slope mult char channel gradient channel x Ty or z int intercept initial gradient level int slope gradient increment codeint mult real time variable Provides a dynamic variable gradient controlled using the AP real time math functions It has no return value The statement drives the chosen gradient to the level defined by the formula level intercept slope mult 270 VNMR 6 1C User Programming 01 999165 00 A0800 Arguments Examples Chapter 3 Pulse Sequence Statement Reference The gradient level ranges from 2047 to 2047 for systems with 12 bit DACs or from 32767 to 32767 for gradients using the waveform generators which have 16 bit DACs If the requested level lies outside this range it is rounded to the appropriate boundary value After vgradient the action of the gradient is controlled by the gradient power supply The gradient level is ramped at the preset slew rate 2047 DAC units per millisecond to the value requested by vgradient This fact becomes a concern when using vgradient ina loop with a delay element in order to produce a modulated g
233. back n2 wftda e Plotting is possible e g Vnmr mback n3 pl pscale pap page e Printing is possible e g Vnmr mback printon dg printoff Running VNMR Processing in the Background The UNIX shell script vbg runs VNMR processing in the background The main requirements are that vbg must be run from within a UNIX shell and that no foreground or other background processes can be active in the designated experiment From UNIX vbg is entered in the following form vbg command_string lt prefix gt where is the number of an experiment from to 9 in the user s directory in which the background processing is to take place command_st ring is one or more VNMR commands and macros to be executed in the background double quotes surrounding the string are mandatory and prefix is the name of the log file making the full log file name prefix_bgf 1log e g to perform background plotting from experiment 3 enter vbg 3 vsadj pl pscale pap page plotlog The default log file name is _bgf 1og where is the experiment number The log file is placed in the experiment in which the background processing takes place Refer to the VNMR Command and Parameter Reference for more information on vbg 01 999165 00 A0800 VNMR 6 1C User Programming 281 Chapter 4 UNIX Level Programming 4 5 Shell Programming The shell executes commands given either from a terminal or contained in a file Files containing commands and control flow
234. base value int incl inc2 inc3 increments codeint multl mult2 mult3 multipliers Provides a dynamic variable gradient pulse controlled using the AP math functions It drives the chosen gradient to the level defined by the formula level basetincl multlt inc2 mult2 inc3 mult3 with increments incl inc2 inc3 and multipliers mult1 mult2 mult3 The range of the gradient level is 2047 to 2047 if the gradients are run through the DAC board and 32767 to 32767 if the gradient waveform generator package is installed If the requested level lies outside the legal range it is clipped at the appropriate boundary value Note that while each variable in the level formula must fit in a 16 bit integer partial sums and products in the calculation are done with double precision 32 bit integers The action of the gradient after the use of the incgradient statement is controlled by the gradient power supply and optional gradient compensation boards The gradient level is ramped at the maximum slew rate to the value requested by incgradient This fact becomes a concern when using the incgradient statement in a loop with a delay statement to produce a modulated gradient The delay statement should be sufficiently long so as to allow the gradient to reach the assigned value that is new_level old_levell gt ay full_scale xX risetime The following error messages are possible e Bad gradient specified channel is caused
235. between the if zero statement on the MERCURY and GEMINI 2000 systems compared to other Varian spectrometers On the MERCURY and GEMINI 2000 the sequence above must be written as follows mod2 ct vl ifzero 1 vl note different syntax on GEMINI 2000 pulse pw v2 delay d3 elsenz 1 note different syntax on GEMINI 2000 pulse 2 0 pw v2 delay d3 2 0 endif 1 note different syntax on GEMINI 2000 If numbers other than those easily accessible in integer math such as ct oph three are needed any variable can be initialized to a value with the initval number vi statement e g initval 4 0 v9 The real number input is rounded off and placed in the variable vi This statement unlike the statements such as add and sub described above is executed once and only once at the start of a non arrayed 1D experiment or at the start of each increment in a 2D experiment or an arrayed 1D experiment not at the start of each transient Real Time vs Run Time When Do Things Happen It may help to explain the pulse sequence execution process in more detail When you enter go the go program is executed This program looks up the various parameters examines the name of the current pulse sequence and looks in seqlib for a file of that name The file in seqlib is acompiled C program which was compiled with the seqgen command This program which is run by the go program combines the param
236. ble nf Number of FIDs in pulse sequence extern double np Number of data points to acquire extern double nt Number of transients extern double sfrq Transmitter frequency mix extern double dfrq Decoupler frequency MHz extern double dfrq2 2nd decoupler frequency MHz extern double dfrq3 3rd decoupler frequency MHz extern double dfrq4 4th decoupler frequency MHz extern double fb Filter bandwidth extern double bs Block size extern double tof Transmitter offset extern double dof Decoupler offset extern double dof2 2nd decoupler offset extern double dof3 3rd decoupler offset extern double dof4 4th decoupler offset extern double gain Receiver gain value or n for autogain extern double dlp Decoupler low power value extern double dhp Decoupler low power value extern double tpwr Transmitter pulse power extern double tpwrf Transmitter fine linear attenuator for pulse extern double dpwr Decoupler pulse power extern double dpwrf Decoupler fine linear attenuator for pulse extern double dpwrf2 2nd decoupler fine linear attenuator extern double dpwrf3 3rd decoupler fine linear attenuator extern double dpwrf4 4th decoupler fine linear attenuator extern double dpwr2 2nd decoupler pulse power extern double dpwr3 3rd decoupler pulse power extern double dpwr4 4th decoupler pulse power extern double filter Pulse amp filter setting extern double xmf Transmitter modulation frequency extern double dmf Decoupler modulation frequency extern doub
237. block are stored sequentially in their natural order Both traces along f4 and f2 are stored in the same file The first block s contain traces number 1 to n along the f4 axis the next block s contains traces number to fn1 along the fp axis Note again that phasefile will only contain data if the corresponding display operation has been performed Therefore in most typical situations where only a display along one of the two 2D axes is done phasefile will contain only the block s for the traces along f4 or a hole followed by the block s for the traces along f2 Furthermore in large 2D experiments where multiple blocks must be used to store the whole data only a full display will ensure that all blocks were actually calculated 01 999165 00 A0800 VNMR 6 1C User Programming 289 Chapter 5 Parameters and Data Header and Data Display The VNMR commands ddf ddf f and ddfp display file headers and data ddf displays the data file in the current experiment Without arguments only the file header is displayed Using ddf lt block_number trace_number first_number gt ddf displays a block header and part of the data of that block is displayed block_number is the block number default 1 t race_number is the trace number within the block default 1 first is the first data element number within the trace default 1 The ddf f command displays the FID file in the current experiment and the ddfp command displays the phase f
238. bsprgon except they apply to the decoupler controlled by the statement Each statement returns the number of 50 ns ticks as an integer value in one cycle of the decoupling pattern Similarly explicit gating of the selected decoupler is generally required and termination of the control is done by the decprgoff dec2prgoff and dec3prgoff statements respectively Arguments to obsprgon decprgon dec2prgon and dec3prgon can be variables which need the appropriate get val and get st r statements to permit changes via parameters The macro pwsadj shape_file pulse_parameter adjusts the pulse interval time so that the pulse interval for the shape specified by shape_file a file from shapelib is an integral multiple of 100 ns This eliminates a time truncation error in the execution of the shaped pulse by the programmable pulse modulators pulse_parameter is a string containing the adjusted pulse interval time Setting Spin Lock Waveform Control Statements for spin lock control on UN TYINOVA UNITYplus and UNITY systems with optional waveform generators are spinlock decspinlock dec2spinlock and dec3spinlock for the observe transmitter first decoupler second decoupler and third decoupler respectively Table 29 provides a summary of these statements Spin Lock Waveform Control on Observe Transmitter To execute a waveform generator controlled spin lock on the observe transmitter use spinlock name 90_pulselength tipangle_resoln
239. button action is complete the Pulse Sequences Entry Main Menu page 66 is displayed Button Description A B C D RevrOn RevrOff Set Revr Phase Return Change status of decoupler to A at this point in the sequence This corresponds to the first letter of parameters dm decoupler mode and dmm decoupler modulation mode Thus if dm yny the decoupler will be turned on because of the first y during status A Select status B at this point in the sequence Select status C at this point in the sequence Select status D at this point in the sequence Turn receiver on at this point in the sequence Turn receiver off at this point in the sequence Display Pulse Sequences Entry Phases Menu page 67 to set receiver phase different than default 0123 0 90 180 270 Display Pulse Sequence Entry Main Menu page 66 without changing status at this point in the sequence 68 VNMR 6 1C User Programming 01 999165 00 A0800 2 2 Overview of Pulse Sequence Programming 2 2 Overview of Pulse Sequence Programming Pulse sequences are written in C a high level programming language that allows considerable sophistication in the way pulse sequences are created and executed New pulse sequences are added to the software by writing and compiling a short C procedure This process is greatly simplified however and need not be thought of as programming if you prefer not to As shown in the previo
240. by selecting Workspace in the Main menu and then create an experiment with the Create New button the menu changes immediately Note also in this menu the creation of menu strings is not by simple assignments but with string concatenation operations Those interested in exploring the limits of creating complex macros should find this menu an interesting model User Programmable Menus in Interactive Programs Many of the various interactive programs that are part of VNMR such as dconi and df have user programmable menus Entering a command to start one of these programs displays a menu from the menulib directory For example e dconi automatically brings up the menu dconi when started e df or dfid automatically brings up the menu dfid when started 01 999165 00 A0800 VNMR 6 1C User Programming 57 Chapter 1 MAGICAL II Programming Listing 5 Typical Menu with Dynamic Changes mlabel mstring mlabel 1 Library mstring 1 explib Sx y jexp x i 2 e 1 firstfree 10 repeat format e 1 0 y exists userdir exp y file expexists if NOT Sexpexists and firstfree 10 then firstfree y endif if expexists AND y lt gt x then mlabel i Exp y mstring i jexp y menu main i i 1 endif e e 1 until i gt 7 or e gt 9 if firstfree lt gt 10 AND i lt 8 then mlabel i Create New mstring i cexp firstfree i i 1 endif mlabel i D
241. c analyses Also displays polynomial curves from diffusion or other types of analysis Plot exponential or polynomial curves pexpl lt lt options gt lt linel line2 gt Plots exponential curves from T T gt or kinetics analysis Also plots polynomial curves from diffusion or other types of analysis Display mean of the data in the file regression inp Calculates and displays the mean of data in the file regression inp Input data for a regression analysis Formats data for regression analysis and places it into the file regression inp Set limits for scales in regression scalelimits x_start x_end y_start y_end Causes the command exp 1 to use typed in scale limits 01 999165 00 A0800 1 3 Relevant VNMR Commands Mathematical Functions abs Syntax Description acos Syntax Description asin Syntax Description atan Syntax Description atan2 Syntax Description averag Syntax Description cos Syntax Description exp Syntax Description in Syntax Description 01 999165 00 A0800 Find absolute value of a number abs number lt value gt Finds absolute value of a number Find arc cosine of a number acos number lt value gt Finds arc cosine of a number The optional return value is in radians Find arc sine of a number asin number lt value gt Finds arc sine of a number The optional return value is in radians Find arc tangent of a number atan number lt val
242. c3stepsize Set step size of third decoupler obsstepsize Set step size of observe transmitter stepsize Set small angle phase step size rf type C or D Set step size for second decoupler Systems with a second decoupler dec2stepsiz double step_size step_size phase step size of DO2DEV Sets the step size of the first decoupler This statement is functionally the same as stepsize base DO2DEV step_size is the phase step size desired and is a real number or a variable dec2stepsize 30 0 decstepsize Set step size of first decoupler dec3stepsize Set step size of third decoupler obsstepsize Set step size of observe transmitter stepsize Set small angle phase step size rf type C or D 01 999165 00 A0800 dec3stepsize Applicability Syntax Description Arguments Examples Related decunblank Applicability Syntax Description Related dec2unblank Applicability Syntax Description Related dec3unblank Applicability Syntax Description Related Chapter 3 Pulse Sequence Statement Reference Set step size for third decoupler UNITYTNOVA and UNITYplus systems with a third decoupler dec3stepsize step_size double step_size phase step size of DO3DEV Sets the step size of the third decoupler This statement is functionally the same as stepsize base DO3DEV step_size is the phase step size desired and is a real number or a variable dec3stepsize 3
243. cale of the spectrum so that the tallest peak is 180 mm high The following macro or MAGICAL program that we call vsadj illustrates how the MAGICAL tools can be used to quickly and simply find a solution vsadj Adjust scale of spectrum peak height frequency Find largest peak if Sheight lt 0O then Sheight If negative make positive Sheight endif vs 180 vs Sheight Adjust the vertical scale As written the macro vsadj has four lines The material in double quotation marks the first line and parts of other lines are comments MAGICAL permits comments and as is good programming practice this example is filled with comments to explain what is happening e The second line of the macro peak height illustrates the ability of MAGICAL to extract spectral information The peak command looks through the spectrum and returns to the user the height and frequency of the tallest peak in the spectrum which are then stored in this example in temporary variables named Sheight and frequency The third line of the macro if Sheight lt 0O illustrates that MAGICAL is a high level programming language with conditional statements e g if then loops etc This particular line ensures that the peak height we measure is always a positive value which is necessary for the calculation in the next line The last line vs 180 vs illustrates the use of NMR parameters like vs wh
244. ce dec2prgon dec3prgon decshaped_pulse dec2shaped_pulse dec3shaped_pulse decspinlock dec2spinlock dec3spinlock obsprgoff obsprgon power rlpower shaped_pulse simshaped_pulse sim3shaped_pulse spinlock and xmtrphase apshaped_decpulse First decoupler pulse shaping via AP bus Applicability Syntax Description Arguments Examples Related UNITYINOVA and UNITYplus systems On MERCURY VX and MERCURY only shapes with no phase shifts are supported apshaped_decpulse shape pulse_width pulse_phase power_table phase_table RG1 RG2 char shape name of RF shape file double pulse_width pulse width in sec codeint pulse_phase real time phase of pulse codeint power_table table variable to store power codeint phase_table table variable to store phase double RG1 gating time before pulse in sec double RG2 gating time after pulse in sec Provides first decoupler fine grained waveform generator type pulse shaping through the AP bus A pulse shape file for the waveform generator vnmr shapelib RF is used This statement overrides any existing small angle phase shifting i e a preceding dcp1lrphase and step size setting on the first decoupler channel After apshaped_decpulse first decoupler channel small angle phase shifting is reset to zero and the step size is set to 0 25 degrees apshaped_decpulse capability is now integrated into th
245. ce Statement Reference The logic levels on the SLI lines are not all set simultaneously The four bytes of the 32 bit word are set consecutively the low order byte first The delay between setting of consecutive bytes is 1 AP bus cycle 100 ns This 100 ns timing jitter is non cumulative The following error messages are possible e Illegal mode n is caused by the mode argument not being one of SLI_SET SLI_OR SLI_XOR or SLI_AND e Illegal real time variable nis caused by the var argument being outside the range v1 to v13 Arguments address is the address of the SLI board in the system It must match the address specified by jumper J7R on the board Note that the jumpers 19 20 through 2 specify bits 2 through 11 respectively Bits 0 and 1 are always zero An installed jumper signifies a one bit and a missing jumper a zero The standard addresses for the SLI in the VME card cage e Digital left side is C90 hex 3216 e Analog right side is 990 hex 2448 mode determines how to combine the specified value with the current output of the SLI to produce the new output The four possible modes e SLI_SET is to load the new value directly into the SLI e SLI_ORis to logically OR the new value with the old e SLI_AND is to logically AND the new value with the old e SLI_XOR is to logically XOR the new value with the old var specifies the real time variables to use to set the SLI
246. char homo3 MAXSTR 3rd decoupler homo mode control extern char homo4 MAXSTR 4th decoupler homo mode control extern int xmsize Number of characters in xm extern int xmmsize Number of characters in xmm extern int dmsize Number of characters in dm extern int dmmsize Number of characters in dmm extern int dm2size Number of characters in dm2 extern int dmm2size Number of characters in dmm2 extern int dm3msize Number of characters in dm3 extern int dmm3msize Number of characters in dmm3 extern int dm4size Number of characters in dm4 extern int dmm4msize Number of characters in dmm4 extern int homosize Number of characters in homo extern int homo2size Number of characters in homo2 extern int homo3size Number of characters in homo3 extern int homo4size Number of characters in homo4 extern int hssize Number of characters in hs Table 23 Imaging Variables RF Pulses extern double p2 Pulse length extern double p3 Pulse length extern double p4 Pulse length extern double p5 Pulse length extern double pi Inversion pulse length extern double psat Saturation pulse length extern double pmt Magnetization transfer pulse length extern double pwx X nucleus pulse length extern double pwx2 X nucleus pulse length extern double ps1 Spin lock pulse length extern char pwpat MAXSTR Pattern for pw tpwr extern char pwlpat MAXSTR Pattern for pl tpwr1 extern char pw2pat MAXSTR Pattern for p2 tpwr2 extern char pw3pat MAXSTR Pattern f
247. chnique called the phase pulse described by Lallemand and co workers E Guittet D Piveteau M A Delsuc and J Y Lallemand J Magn Reson 62 336 339 1985 and also discovered independently at Varian D Iverson and S L Patt Varian Owners Conference April 1985 This method is applicable only to systems lacking hardware small angle phase shift which is the case on UNITY and VXR S spectrometers with type A or B rf This method involves shifting the frequency of the transmitter observe or decoupler for a brief time at a point in the pulse sequence when no pulse is required and then returning the frequency to its original value If this change of frequency can be accomplished with phase continuity the case on VNMR spectrometers the temporary shift of transmitter frequency has the effect of producing an apparent phase shift in the transmitter that is the product of the time during which the frequency was changed and the period of the difference frequency For example if the frequency is increased by 1000 Hz the phase will get VNMR 6 1C User Programming 01 999165 00 A0800 2 3 Spectrometer Control ahead at a rate of 360 in 1 ms If this frequency difference is left in effect for 100 us the phase shift is 360 1 ms x 100 us 36 Since the frequency difference and the time for this shift are under computer control tremendous flexibility is possible The larger the frequency shift the smaller the time for a partic
248. code in 3 axes 224 228 oblique shaped gradient with phase encode in 1 axis 225 229 oblique shaped gradient with phase encode in 2 axes 226 oblique shaped gradient with phase encode in 3 axes 226 230 oblique_gradient statement 155 218 oblique_shapedgradient statement 219 obs_mf parameter 95 obsblank statement 220 OBSch device 167 168 observe channel gating 251 observe transmitter modulation 243 01 999165 00 A0800 observe transmitter power 221 observe transmitter pulse 80 obsoffset statement 91 220 obspower statement 92 128 221 obsprgoff statement 144 221 obsprgon statement 95 136 144 221 obspulse statement 82 122 128 222 obspwrf statement 92 128 144 222 obsstepsize statement 87 222 obsunblank statement 223 off command 48 offset frequency 172 208 220 offset lists 167 offset macro 35 offset statement 90 123 128 144 223 offset table 272 on command 48 one pointer 99 operators 30 oph variable 87 99 130 order of precedence 30 orientation of image plane 197 outfields parameter 314 323 Output boards 72 73 133 160 output from commands and macros 28 output to various devices 41 output tools 40 overhead delays 155 overhead operations 103 override internal software AP bus delay 160 P pacemaker warning 19 pane design 341 pap command 307 par2d macro 148 par3d macro 148 par4d macro 148 paramedit command 300 304 paramet
249. cord Syntax Description Removes a macro from memory freeing extra memory space With no argument removes all macros loaded into memory by macrold Record keyboard entries as a macro record lt file off gt Records keyboard entries and stores the entries as a macro file in the user s maclib directory Miscellaneous Tools axis Syntax Description beepoff Description beepon Description bootup Syntax Description exec Syntax Description exists Syntax Description 46 VNMR 6 1C User Programming Provide axis labels and scaling factors axis fn fnl f n2 lt Saxis_label Sfrequency_scaling factor gt Returns axis labels the divisor to convert from Hz to units defined by the axis parameter with any scaling and a second scaling factor determined by any scalesw type of parameter The parameter fn fnl f n2 describes the Fourier number for the axis Turn beeper off Turns beeper sound off The default is beeper sound on Turn beeper on Turns beeper sound on The default is beeper sound on Macro executed automatically when VNMR is started bootup lt foreground gt Displays a message runs a user Login macro if it exists starts Acqgst at and acqi spectrometer only and displays the menu system bootup and login can be customized for each user login is preferred because boot up is overridden when a new VNMR release is installed foreground
250. cquisition mode 3D acquisition mode 4D acquisition mode d2 increment from 0 to ni 1 d3 increment from 0 to ni2 1 d4 increment from 0 to ni3 1 Programmable Decoupling Sequences extern char xseq MAXSTR extern char dseq MAXSTR extern char dseq2 MAXSTR extern char dseq3 MAXSTR extern char dseq4 MAXSTR extern double xres Digit resolution prg dec extern double dres Digit resolution prg dec extern double dres2 Digit resolution prg dec extern double dres3 Digit resolution prg dec extern double dres4 Digit resolution prg dec Status Control extern char xm MAXSTR Transmitter status control extern char xmm MAXSTR Transmitter modulation type control extern char dm MAXSTR 1st decoupler status control extern char dmm MAXSTR 1st decoupler modulation type control extern char dm2 MAXSTR 2nd decoupler status control 112 VNMR 6 1C User Programming 01 999165 00 A0800 2 6 Accessing Parameters Table 22 Global PSG Parameters continued extern char dmm2 MAXSTR 2nd decoupler modulation type control extern char dm3 MAXSTR 3rd decoupler status control extern char dmm3 MAXSTR 3rd decoupler modulation type control extern char dm4 MAXSTR 4th decoupler status control extern char dmm4 MAXSTR 4th decoupler modulation type control extern char homo MAXSTR 1st decoupler homo mode control extern char homo2 MAXSTR 2nd decoupler homo mode control extern
251. cquisition using the seqcon parameter Waveform Initialization Statements The waveform initialization statements init_rfpatternand init_gradpattern are available to all configurations and allow the user to calculate and create gradient and rf patterns in PSG Other Statements The init_vscan and vscan statements are used to provide a dynamic scan capability The sli and vs1i statements are used with the Synchronized Line Interface board which is a SIS specific hardware device used to support interfacing to external devices The sli and vs1i statements are not supported on UN YTNOVA UN YINOVA support for interfacing to an external device is included in the AP User interface 2 18 User Customized Pulse Sequence Generation The complete pulse sequence generation PSG source code is supplied in the VNMR system psg directory This code enables users to create their own libpsglib so PSG directory for link loading with the pulse sequence object file pulsesequence o The UNIX shell script set userpsg in the system directory creates the directory vnmrsys psg for a user if it does not already exist and initializes this user PSG directory with the appropriate object libraries from the system PSG directory The script setuserpsg should only have to be run once by each separate user setuserpsg places the file Libpsglib a in the user s psg directory The UNIX shell script psggen compiles files in the user PSG object directory and places the files
252. create command to create a new parameter or to use the paramvi and paramedit commands to edit a parameter and its attributes requires knowledge of the format of a stored parameter If an error in the format is made the parameter may not load This section describes the format in detail The format of stored parameters changed somewhat starting with version 4 2 of VNMR To make the changeover automatic parameters in the format prior to VNMR 4 2 are automatically updated when they are retrieved and saved in working with an experiment If you wish you can also use the macro parfix to manually update parameters For example the commands rtp mypars parfix svp mypars update a parameter set named mypars 01 999165 00 A0800 VNMR 6 1C User Programming 301 Chapter 5 Parameters and Data The stored format of a parameter is made up of three or more lines e Line 1 contains the attributes of the parameter and has the following fields given in same order as they appear in the file name is the parameter name which can be any valid string subtype is an integer value for the parameter type 0 undefined real 2 string 3 delay 4 flag 5 frequency 6 pulse 7 integer basictype is an integer value 0 undefined real 2 string maxva Lue is areal number for the maximum value that the parameter can contain or an index to a maximum value in the parameter parmax found in vnmr conpar Applies to both string and rea
253. csbebssdehad stacteegs besten EASE ERE E TEES 155 Oblique Gradient Statements srce irai enteo sobs ene ea E EE E EEE EEE EENEN EEEE EREE 155 Global List amd Position StAtemeniS seiiet Lancesiechs sheseaosedansvsstbasetscont sdicaseseenduemsonevosuaenvievvans 157 Looping SCAMS seprene nae TEE orae E EST REEE EEEE AE REEE EE EEEE EO EE E NEAS 157 Waveform Initialization Statements osis mensan eseas isee a Siea eioi iiaa 157 COMMS SMR NSE coer anaE E EE E EERE RE EEA R E O R AE 157 2 18 User Customized Pulse Sequence Generation sseessssesessereeseereresrestrresrertsrerrssretesreresreeerresrnrrssrereseet 157 Chapter 3 Pulse Sequence Statement Reference sssseeccessseeeeeseeeeeeeseseeeeeseseneeeeees 159 acquire Explicitly acquire data sssssssscsseiisicsersrereossersoisrsoisesstesissessssesssessvesses 159 add Add integer Valles usien EE S 160 apovrride Override internal software AP bus delay ssssseseeseeesseeseereerrerseeeeeee 160 apshaped_decpulse First decoupler pulse shaping via AP bus sssessesseeseeeerereerere 161 apshaped_dec2pulse Second decoupler pulse shaping via AP bus sssesssseeeseeeeseresrereerees 162 apshaped_pulse Observe transmitter pulse shaping via AP bus 00 0 0 eee eee eeeeeee 163 assign Assign integer VALVES sorena aior e aana 164 blankingoff Unblank amplifier channels and turn amplifiers on 0 0 eee 164 blankingon Blank amplifier channels and turn amplifiers Off es eceeeseeeeeeeee 164 blank
254. ctive is an integer value 0 not active 1 active intptr is not used generally set to 64 e Line 2 or the group of lines starting with line 2 list the values of the parameter The first field on line 2 is the number of values the parameter is set to The format of the rest of the fields on line 2 and subsequent lines if any depends on the value of basictype set on line 1 and the value entered in the first field on line 2 302 VNMR 6 1C User Programming 01 999165 00 A0800 5 4 Creating and Modifying Parameters If basictype is real and first value on line 2 is any number all parameter values are listed on line 2 starting in the second field Each value is separated by a space If basictype is 2 string and first value on line 2 is 1 the single string value of the parameter is listed in the second field of line 2 inside double quotes If basictype is 2 string and first value on line 2 is greater than 1 the first array element is listed in the second field on line 2 and each additional element is listed on subsequent lines one value per line Strings are surrounded by double quotes e Last line of a parameter file lists the enumerable values of a string or flag parameter This specifies the possible values the string parameter can be set to The first field is the number of enumerable values If this number is greater than 1 all of the values are listed on this line starting in the second field For example here is how a
255. ctr real time variable 99 102 ssval real time variable 99 102 standard data format 295 standard deviation of input 43 standard PSG variables 72 standard h file 73 120 start loop 212 starthardloop statement 126 258 status change 63 status entry 68 status of transmitter or decoupler 242 status statement 94 103 128 143 145 259 status window 322 status conf file 323 status conf file listing 323 statusdelay statement 95 103 steady state phase cycling 103 steady state pulses 102 step size decoupler 188 parameters 302 transmitter 222 steps in shaped pulse 139 stepsize statement 169 260 store array in AP table 107 stored format of a parameter 302 storing multiple traces 289 string command 32 string constant 30 string formatting for output 40 string length 47 string parameter value lookup 117 198 string parameters 32 string template 304 string variables 32 strings displayed in text window 40 string type parameter 298 300 style attribute 316 01 999165 00 A0800 Index sub statement 99 261 substr command 49 substring from a string 49 subtract AP table from second AP table 264 subtract integer from AP table elements 263 subtract integer values 261 sum of integer values 160 sum to memory error 76 Sun manuals 277 svfdf macro 294 svib macro 294 svsis macro 294 swapping rf channels 82 swept square wave modulation 243 synchronization of a pulse sequence
256. cusiceuscasnsouss scosucqssteavesoenss eacesasesagaaevensiecusebae 146 2 14 Multidimensional NMR ooo ee eeeeeeeecseeceecneessecscessecseessecsscessesneessvensesesccssseecaesnaesoesssesseessceneeseeneees 148 Elypercomplen WO tian tiichtaaidiah chitin nbdtn divi idea EEES EE aT TETEE EAE 148 Real Mode Phased 2D TEPPI csicsstastvecceisisissasesesyseps seuss EEEE EE EE EEEE EENE E EEE 150 2 15 Gradient Control for PFG and Imaging 0 eee eceesseeeeeecneceeeeeesecneceeesesecaecessscsaecaseesaesaseeserenaeeeeeees 150 Setting the Gradient Current Amplifier Level 2 cccicnacvietiin ee reesen ese Eeer ar Kae ra EKE ERSE 150 Generating a Gradient Pulse soiricsiiin neen n E A E E R E ee areeiat 151 Controline Lock CorecHon CUCUMTY ciscpescescessccscesseessceiesdiecstgensdscosseeecceecsoneesce EAEE R EENE EREE i 151 Programming Microimaging Pulse Sequences 5 i sccscecssesssscsessesesosassoceosesbescednsessaessbevecesesse 152 2 16 Programming the Performa XYZ PFG Module ou eee eee eeeeceeeeeseeeeeceeaeceaeesececeseseeeeseeeeseeeseeeeas 153 Creatine Gradient TADIGS s2isse tact siteshtesscaie secede teacvvas aces E E E E E ade Hates 153 Pulse Sequence Protamine oi cies sctescistves ys sehen bonsietbuvecs busi senp E R EErEE EE AS VETERES TEES ra 154 2 17 Imaging Related Statements oe eee ceecseecsecnseeecsseesececeseceeeesesenecsaecaetsaecaeesaecaessaesseesaseseeeseaeeees 155 Real time Gradient Statements osissa ise cosieeudestinededcevabve
257. d binary program file Neither is really suitable for display Fortunately the exists command has options to determine if a file is a directory or a text file The test for a directory is to include the statement exists n directory Se and display an error message if the return argument e is nonzero To test for an ASCII file include exists n ascii e and display an error message if Se is zero Files that make it through the macro without an error message can be considered suitable for display So our second version might be the following filesinfo number f n if f 1 then filesinfo name Sn exists n directory e if e lt gt 0 then write error 3 is a directory and cannot be displayed n abort endif exists n ascii e if e 0 then write error Ss is not an ASCII file n abort endif cat n else write error You must select on lement abort endif Now we would like to display the text file in that directory if it turns out that if the user selected a FID or an experiment directory Programming this extra capability is simple filesinfo number f n 1 if Sf 1 then filesinfo name Sn exists n directory e if e lt gt 0 then exists n text file e if e lt gt 0 then cat n text else write error S s is a directory and cannot be displayed n abort endif exists n ascii e if e 0 then write error Ss
258. d but the error status is OK 1401 Reserved RF monitor trip A occurred 1402 Reserved RF monitor trip B occurred 1404 Excessive reflected power at quad hybrid 1405 STOP button pressed at operator station 1406 Power for RF Monitor board RFM failed 1407 Attenuator control or read back failed 1408 Quad reflected power monitor bypassed 1409 Power supply monitor for RF Monitor board RFM bypassed 1410 Ran out of memory to report RF monitor errors 1411 No communication with RF monitor system 1431 Reserved RF monitor trip Al occurred on observe channel 1432 Reserved RF monitor trip B1 occurred on observe channel 1433 Reserved RF monitor trip C1 occurred on observe channel 1434 RF Monitor board PALI TUSUPI missing on observe channel 1435 Excessive reflected power on observe channel 1436 RF amplifier gating disconnected on observe channel 1437 Excessive power detected by PALI on observe channel 1438 RF Monitor system TUSUPD heartbeat stopped on observe channel 1439 Power supply for PALI TUSUPI failed on observe channel 1440 PALI asserted REQ_ERROR on observe channel should never occur 1441 Excessive power detected by TUSUPI on observe channel 1442 RF power amp overdrive on observe channel 1443 RF power amp excessive pulse width on observe channel 1444 RF power amp maximum duty cycle exceeded on observe channel 1445 RF power amp overheated
259. d device control On the YNTYZNOVA each spare line changes from low to high when turned on e UNITYTNOVA has five spare lines available from the Breakout panel on the back of the left console cabinet e UNITYplus has two spare lines located on the front panel of the Pulse Sequence Controller board in the digital cardcage e UNITY and VXR S have two spare lines on the Interface board e GEMINI 2000 has one spare line splon sp5on sp off Turn off specified spare line Control spin lock on observe transmitter Systems with a waveform generator on the observe transmitter channel spinlock pattern 90_pulselength tipangle_resoln phase ncycles char pattern name of DEC text file double 90_pulselength 90 deg pulse length of channel double tipangle_resoln resolution of tip angle codeint phase phase of spin lock int ncylces number of cycles to execute Executes a waveform generator controlled spin lock on the observe transmitter Both the rf gating and the mixing delay are handled within this function Arguments can be variables which require the appropriate get val and get str statements to permit changes via parameters see the second example below pattern is the name of the text file in the shape1lib directory that stores the decoupling pattern leave off the DEC file extension 90_pulselength is the pulse duration for a 90 tip angle on the observe transmitter tipang
260. d from the default set for imaging 1im2 is automatically set to half the nv number of views where nv is usually the number of phase encode steps Pulse sequence generation aborts if the DACs on a particular gradient are overrun after the angles and amplitude have been resolved statl stat2 stat3 are values in gauss cm of the components for the static portion of the gradient in the logical reference frame step2 is the value in gauss cm of the component for the step size change in the variable portion of the gradient vmult2 is a real time math variable v1 to v14 ct zero one two three or reference to AP tables t 1 to t 60 whose associated values vary dynamically in a manner controlled by the user pe_gradient 0 0 sgpe nv 2 0 gss sgpe v6 phase_encode_gradient Oblique gradient with phase encode in 1 axis Oblique gradient with phase encode in two axes Not applicable on MERCURY VX MERCURY and GEMINI 2000 pe2_gradient statl stat2 stat3 step2 step3 vmult2 vmult3 double statl stat2 stat3 static gradient components double step2 step3 variable gradient stepsize codeint vmult2 vmult real time math variables Sets only two oblique phase encode gradients otherwise pe2_gradient is the same as pe3_gradient Pulse sequence generation aborts if the DACs on a particular gradient are overrun after the angles and amplitude have been resolved statl stat2 stat3 are values in gauss cm o
261. d of the longer pulse For UN TYINOVA the absolute difference in the two pulse widths must be greater than or equal to 0 2 us otherwise a timed event of less than the minimum value 0 1 us would be produced e if the difference is less than 0 1 us the pulses are made equally long e If the difference is from 0 1 to 0 2 us the difference is made 0 2 us e If the difference is larger than 0 2 us the difference is made as close as the timing resolution allows 0 0125 us For systems other than YN TYZNOVA the minimum time is 0 2 us thus the times are doubled the difference must be 0 4 us resolution is 0 025 us obswidth and decwidth are the duration in sec of the pulse on the observe transmitter and first decoupler respectively obsphase and decphase are the phase of the pulse on the observe transmitter and the first decoupler respectively Each must be a real time variable RG1 is the delay in seconds between gating the amplifier on and gating the first rf transmitter on all phase shifts occur at the beginning of this delay RG2 is the delay in seconds between gating the final rf transmitter off and gating the amplifier off simpulse pw pp vl v2 0 0 rof2 decpulse Pulse the decoupler transmitter decrgpulse Pulse decoupler transmitter with amplifier gating dps_show Draw delay or pulses in a sequence for graphical display rgpulse Pulse observe transmitter with amplifier gating sim3pulse Simultaneous pulse
262. dd integer values assign Assign integer values dbl Double an integer value decr Decrement an integer value divn Divide integer values hlv Half the value of an integer incr Increment an integer value mod4 Find integer value modulo 4 modn Find integer value modulo n mult Multiply integer values sub Subtract integer values Find integer value modulo 4 mod4 vi vj codeint vi variable for starting value codeint vj variable for result Sets the value of vj equal to vi modulo 4 01 999165 00 A0800 VNMR 6 1C User Programming 215 Chapter 3 Pulse Sequence Statement Reference Arguments Examples Related modn Syntax Description Arguments Examples Related msloop Applicability 216 Syntax Description Arguments Examples vi is the starting integer value and vj is the value of vi modulo 4 the remainder after vi is divided by 4 Both arguments must be real time variables v1 to v14 etc mod4 v3 v5 mod2 Find integer value modulo 2 modn Find integer value modulo n Find integer value modulo n modn vi vj vk codeint vi real time variable for starting value codeint vj real time variable for modulo number codeint vk real time variable for result Sets the value of vk equal to vi modulo vj vi is the starting integer value vj is the modulo value and vk is vi modulo vj the remainder after vi is divided by vj All arguments must be
263. dec2offset dec3offset dec4offset decon dec2on dec3on decphase dec2phase dec3phase dec4phase decpower dec2power dec3power dec4power decprgoff dec2prgoff dec3prgoff decprgon dec2prgon dec3prgon decpulse decpwr decpwrf dec2pwrf dec3pwrf decr decrgpulse dec2rgpulse dec3rgpulse dec4rgpulse decshaped_pulse dec2shaped_pulse dec3shaped_pulse decspinlock dec2spinlock dec3spinlock decstepsize dec2stepsize dec3stepsize decunblank dec2unblank dec3unblank delay dhpflag divn dps Off dps_on dps_show dps skip 10 VNMR 6 1C User Programming Turn on first decoupler to full power eee eeeeeceeeeeeteeeeeeeeeenaeteeeeeees 171 Turn Off first decOupler sesen ospis srna aenean Eo 172 Turn off second decoupler ssesseeseesesseeeerstsieesersteretsrrrrrersrnreersrsreree 172 Torn off thitd decoupler scseehieceesicassteessensetencecetenendoveraedeusessesoaes 172 Change offset frequency of first decoupler cee eeeeeeeeeeeseneeeeeees 172 Change offset frequency of second decoupler eeeeeeeeesseeeeeeeeee 172 Change offset frequency of third decoupler eee eeeeeeesseneeeeeeee 173 Change offset frequency of fourth decoupler 0 ce eeeeeeeeeeseeeeeeeeee 173 Turn on first decoupler oo ee eeeceeseeseesececseeecesecaeeeceecsaesereeceeeneeeeeaes 173 Turn n second de oupler wiscscsscsccssisccsssessssssbescssesevanstenssoonessapsonssnv ens 173 Turn On third decoupler s nescccisic
264. decoupler power lin amp sys pwrf Change transmitter or decoupler fine power rlpwrf Set transmitter or decoupler fine power Set transmitter or decoupler linear modulator power UNITYINOVA and UNITYplus systems rlpwrm power device double power new level for lin mod power int device OBSch DECch DEC2ch or DEC3ch Changes transmitter or decoupler linear modulator power the same as the pwrm statement but to avoid using real time variables rl pwrm uses a C variable of type double as the argument for the amount of change power is the linear modulation fine power desired device is OBSch observe transmitter DECch first decoupler DEC2ch second decoupler or DEC3ch third decoupler rlpwrm 4 0 OBSch ipwrm Change transmitter or decoupler lin mod power with IPA pwrm Change transmitter or decoupler linear modulator power Obtain rotor period of MAS rotor Systems with MAS magic angle spinning rotor synchronization hardware 240 VNMR 6 1C User Programming 01 999165 00 A0800 Syntax Description Arguments Examples Related rotorsync Applicability Syntax Description Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference rotorperiod period codeint period variable to hold rotor period Obtains the rotor period periodis a real time variable into which is placed the rotor period as an integer in units of 100
265. der of 0 so 8 mod 2 is 0 Similarly 9 mod 2 is 1 since 2 into 9 gives 4 with a 01 999165 00 A0800 VNMR 6 1C User Programming 99 Chapter 2 Pulse Sequence Programming remainder of 1 The modulus of a negative number is not defined in VNMR software and should not be used Each statement performs one calculation at a time For example hlv ct v1 takes half the current value of ct and places it in the variable v1 Before each transient ct has a given value e g 7 and after this calculation v1 has a certain value e g 3 if ct was 7 To visualize the action of a statement over the course of a number of transients pulse sequences typically document this action explicitly as part of their comments The comment v1 0 0 1 1 or v1 001122 means that v1 assumes a value of 0 during the first transient 0 during the second 1 during the third etc The following series of examples illustrates the action of integer mathematics statements and how comments are typically used hlv ct vl v1 0011223344 dbl vl1 v1l v1 0022446688 mod4 v1 v1 v1 0022002200 mod2 ct v2 w2 010101 dbl v2 v3 v3 020202 Xy v1 00112233 hlv v1 v2 vw2 00001111 7 dbl vl1 v1 w1 00224466 add vl1 v2 v3 v3 00225577 mod4 v3 oph oph 00221133 receiver phase cycle Note that the same variable can be used as the input and output of a particular statement
266. dgets The style attribute defines the type of widget used to select information Available input styles include info radio check xradio xcheck textentry xradiocustom and xcheckcustom The info style is used when information is presented to the user but the user cannot make a selection This style is not used in the default enter conf file but is used in two alternative interfaces that are commented out e The first on lines 31 to 36 changes how the sample location is presented In the default interface a user presses a button to select a tray number In the commented out interface the user is presented with a location number into which the sample must be placed e The second on lines 52 to 56 changes the way user identification is selected In the default interface a user presses a button to select a user name In this interface the user id is displayed for informational purposes but cannot be changed The radio and check styles are identical in function but different in appearance The radio style presents a button with a label inside of the button The check style presents a small box that can be checked and the label is printed along side For both radio and check styles multiple selections can be made The Sample Number and Experiment Selection window panes use the radio style Stylistically xradio and xcheck styles are the same as the radio and check styles respectively The difference is that xradio and xcheck provide
267. dir directoryname rm r directoryname ls directoryname 01 999165 00 A0800 List files in a directory long list Copy file s into a directory Move file s into a directory Print working current directory Change current directory Text Commands Edit a text file using vi editor Edit a text file using ed editor Edit a text file using text edit editor Display first part of a file Display last part of a file Concatenate and display files Compare two files Compare two files deferentially Print file s on line printer Search file s for a pattern Find spelling errors Other Commands Pattern scanning and processing Change file protection mode Display current date and time Summarize disk usage Report free disk space Kill a background process Sign onto system Send mail to other users Print out UNIX manual entry Process status Convert quantities to another scale Who is on the system System identification Special Characters Send output into named file Append output into named file Take input from named file Send output from first command to input of second command pipe 4 2 UNIX A Reference Guide ls 1 directoryname cp filenames directoryname mv filenames directoryname pwd cd newdirectoryname vi filename ed filename textedit filename head filename tail filename cat filenames cmp filenamel filename2 diff filenamel filename2 lp filenames grep expressio
268. dps_on are shown in the graphical display dps_off Turn off graphical display of statements dps_show Draw delay or pulses in a sequence for graphical display dps_skip Skip graphical display of next statement Draw delay or pulses in a sequence for graphical display 1 dps_show delay time double time delay in sec 2 dps_show pulse channel label width char channel obs dec dec2 or dec3 char label text label selected by user double width pulse length in sec 3 dps_show shape_pulse channel label width char channel obs dec dec2 or dec3 char label text label selected by user double width pulse length in sec 4 dps_show simpulse label_of_obs width_of_obs label_of_dec width_of_dec char label_of_obs text label selected by user double width_of_obs pulse length in sec char label_of_dec text label selected by user double width_of_dec pulse length in sec 5 dps_show simshaped_pulse label_of_obs width_of_obs label_of_dec width_of_dec char label_of_obs text label selected by user double width_of_obs pulse length in sec char label_of_dec text label selected by user double width_of_dec pulse length in sec 6 dps_show sim3pulse label_of_obs width_of_obs label_of_dec width_of_dec label_of_dec2 width_of_dec2 char label_of_obs
269. dtable Load AP table elements from table text file setautoincrement Set autoincrement attribute for an AP table setdivnfactor Set divn return attribute and divn factor for AP table setreceiver Associate the receiver phase cycle with an AP table settable Store an array of integers in a real time AP table getorientation Read image plane orientation Applicability Syntax Description Arguments Systems with imaging or PFG modules Not applicable to MERCURY VX MERCURY and GEMINI 2000 systems lt error_return gt getorientation amp charl amp char2 amp char3 search_string char charl char2 char3 program variable pointers char search_string pointer to search string Reads in and processes the value of a string parameter used typically for control of magnetic field gradients The source of the string value is typically a user created parameter available in the current parameters of the experiment used to initiate acquisition error_return can contain the following values e error_return is set to zero if getorientation was successful in finding the parameter given in search_string and reading in the value of that parameter e error_return is setto l if search_string was not empty but it did not contain the correct characters e error_return is set to a value greater than zero if the procedure failed or if the string value is made up of characters other than n x y and z charl char2 and char
270. e 0 02 32676 y 1 NOWAIT This statement is only available on the Perform II PFG module Controlling Lock Correction Circuitry On MERCURY VX MERCURY YINOVA and UNITYplus systems 1k_sample and 1k_hold are provided to control the lock correction circuitry If during the course 01 999165 00 A0800 VNMR 6 1C User Programming 151 Chapter 2 Pulse Sequence Programming 152 Table 36 Delays for Obliquing and Shaped Gradient Statements Delay us Pulse Sequence Statements UNITYTNOVA UNITYplus UNITY VXR S shapedgradient 0 5 5 75 10 75 shapedvgradient Lied 14 95 27695 shapedincgradient Tao 1265 23 65 incgradient gradtype p 4 0 gradtype q incgradient gradtype w 0 5 3 45 6 9 obl_gradient 12 0 20 70 38 70 oblique_gradient pe_gradient phase_encode_gradient gradtype p gradtype q obl_gradient Las 10 35 20 70 oblique_gradient pe_gradient phase_encode_gradient gradtype w pe2_gradient 12 0 phase_encode3_gradient gradtype p gradtype q pe2_gradient 15 10435 20 70 phase_encode3_gradient gradtype w obl_shapedgradient 1 5 17 25 32 25 oblique_shapedgradient pe_shapedgradient 4 5 44 85 83 85 phase_encode_shapedgradient pe2_shapedgradient 4 5 37 595 70 95 pe3_shapedgradient phase_encode3_shapedgradient of a pulse sequence the lock signal is disturbed for instance with a gradient pulse or pulses at the H frequency the lock circ
271. e patnew pwnew v2 t4 t5 rofl rof2 3 After newpul c is created in a shell window enter seqgen newpul The following lines are displayed during pulse sequence generation Beginning Pulse Sequence Generation Process Adding DPS extensions to Pulse Sequence Lint Check of Sequence Compiling Sequence Link Loading Done Pulse sequence newpul now ready to use 118 VNMR 6 1C User Programming 01 999165 00 A0800 2 6 Accessing Parameters 4 To use the pulse sequence in VNMR add new parameters starting from a known good parameter set e g s2pul par by entering from the VNMR command line s2pul seqfil newpul create dinew delay dlnew 1 create d2new delay d2new 001 create plnew pulse plnew 0 create pwnew pulse pwnew 40 create patnew string patnew square 5 The parameters need to be saved as newpul par in parlib so you can easily retrieve them the next time you run the pulse sequence Enter cd cd vnmrsys parlib svp newpul 6 To access the new parameters and pulse sequence create a macro by entering for example editmac newpul 7 Inthe pop up editor window type editmac newpul to enter the insert mode and add the line psgset newpul array dg dlnew d2new plnew pwnew patnew Save the macro and exit This macro requires the file newpul par to be present in parlib You can now enter newpu1 in the VNMR c
272. e real is any positive or negative value and can be positive or negative e string is composed of characters and can be limited to selected words by enumerating the possible values with the command setenumeral VNMR 6 1C User Programming 01 999165 00 A0800 5 4 Creating and Modifying Parameters e delay is a value between 0 and 8190 0 and 4095 on GEMINI 2000 in units of seconds e frequency is positive real number values e f lag is composed of characters similar to the string type but can be limited to selected characters by enumerating the possible values with the command setenumeral If enumerated values are not set the st ring and flag types are identical e pulse isa value between 0 and 8190 0 and 4095 on GEMINI 2000 in units of microseconds e integer is composed of integers 0 1 2 3 The four parameter tree types are current global processed and systemglobal the default is current Each type is described below e current contains the parameters that are adjusted to set up an experiment The parameters are from the file curpar in the current experiment e global contains user specific parameters from the file global inthe vnmrsys directory of the present UNIX user e processed contains the parameters with which the data was obtained These parameters are from the file procpar in the current experiment e systemglobal contains instrument specific parameters f
273. e Row extent value of the item probably needs to be increased 01 999165 00 A0800 VNMR 6 1C User Programming 33 7 Chapter 6 Customizing Graphics Windows length Length of the scale in the long direction The value is in arbitrary units width Width of the scale in the narrow direction The value is in arbitrary units The default is 10 Vnmr Variables List of VNMR parameters used in the following Vnmr Cmd and Tcl Cmd fields This can be zero or more parameter names Vnmr Cmd MAGICAL expression sent to VNMR whenever a mouse button is released in the scale item Any specified VNMR parameters can be used The variable VALUE is set to the value of the scale Tcl Cmd Tcl expression that is evaluated to determine the value of the scale Any legitimate Tcl expression is allowed To access the values of any VNMR parameters specified in the Vnmr Variables list prepend a dollar sign to the front of the parameter name The scale element is a useful mechanism to modify a numerical parameter It prevents errors in parameter entry Its weakness is that it takes up a fair amount of area and is not always easily manipulated by dragging the slider with the left mouse button to a new value However clicking anywhere in the slider trough with the middle mouse button sets the scale to that value Also clicking inside the trough on either side of the slider with the left mouse button changes the scale value by one resolution unit Th
274. e Statement Reference Arguments Examples Related from a gradient table to scale and set the values correctly mashapedgradient leaves the gradients at the given levels until they are turned off To turn off the gradients add another mashapedgradient statement with gradlv1 set to zero or include the zero_all_gradients statement mashapedgradpulse differs from mashapedgradient in that the gradients are turned off after gradt ime seconds mashapedgradient is used if there are actions to be performed while the gradients are on mashapedgradpulse is best when there are no other actions required while the gradients are on pattern is the name of a text file describing the shape of the gradient The text file is located in Svnmrsystem shapelib or in the user directory Svnmruser shapelib gradlv1 is the gradient amplitude in gauss cm gradtime is the gradient application time in seconds theta defines the angle in degrees from the z axis phi defines the angle of rotation in degrees about the xy plane loops is a value from 0 to 255 to loop the selected waveform Gradient waveforms on UN TYINOVA systems do not use this field and Loops is set to 0 on UNTYTNOVA systems wait is a keyword either WAIT or NOWAIT that selects whether or not a delay is inserted to wait until the gradient is completed before executing the next statement mashapedgradient ramp_hold 3 0 trise 0 NOWAIT pulse pw oph delay 0 001 pw 2
275. e Statements Phase and Sequence Control The count argument used with loop is a real time variable that specifies the number of times to execute the enclosed statements count can be any positive number including zero index is a real time variable used as a temporary counter to keep track of the number of times through the enclosed statements and must not be altered by any of the statements An example of using loop and endloop is the following r mod4 ct v5 times through loop v5 01230123 loop v5 v3 v3 is a dummy to keep track of count delay d3 variable delay depending on the ct endloop v3 Statements within the pulse sequence can be executed conditionally by being enclosed within ifzero vi elsenz vi and endif vi statements vi is a real time variable used as a test variable to be tested for either being zero or non zero The elsenz statement may be omitted if it is not desired It is also not necessary for any statements to appear between the i fzero and the el senz or the elsenz and the endif statements The following code is an example of a conditional construction mod2 ct vl v1 010101 ifzero v1 test if vl is zero pulse pw v2 execute these statements delay d3 if vl is zero elsenz v1 test if vl is non zero pulse 2 0 pw v2 execute these statements delay d3 2 0 if vl is non zero endif v1 A syntactical difference exists
276. e autoincrement feature cannot be accessed within a hardware loop table is the name of the table t 1 to t 60 setautoincrement t9 getelem Retrieve an element from an AP table loadtable Load AP table elements from table text file setdivnfactor Set divn return attribute and divn factor for AP table setreceiver Associate the receiver phase cycle with an AP table settable Store an array of integers in a real time AP table 241 VNMR 6 1C User Programming Chapter 3 Pulse Sequence Statement Reference setdivnfactor Set divn return attribute and divn factor for AP table Applicability Syntax Description Arguments Examples Related setreceiver Applicability Syntax Description Arguments Examples Related setstatus Applicability Syntax Description All systems except the GEMINI 2000 setdivnfactor table divn_factor codeint table real time table variable int divn_factor number to compress by Sets the divn return attribute and divn factor for an AP table The actual index into the table is now set to index divn factor 0 1 2 is therefore translated by the acquisition processor not by PSG pulse sequence generation into 0 0 1 1 The divn return attribute results in a divn factor fold compression of the AP table at the level of the acquisition processor table specifies the name of the table t 1 to t 60 divn_factor specifies the divn factor for the table
277. e axis Oblique shaped gradient with phase encode in two axes Oblique shaped gradient with phase encode in three axes Phase EnC0de LOOP seseisissrecs sie Sevusied sti cteee Siva cebu eh theives Oblique gradient with phase encode in one axis 0 ee eee eee eee Oblique gradient with phase encode in three axes Oblique shaped gradient with PE in one axis Oblique shaped gradient with PE in three axes 0 0 eee ee eeeeeeeee Set phase pulse technique rf type A or B Set frequency based on position eeeeeeeeeseeseeseeseceeeecsaeeeeeeceeeeenees Set frequency from position list tees eeeseeseeeeceeeeeseeeeeeeeeeeesees Set frequency based on position ee eeeeeeeeseeseeseeeeceteeceseeeeeeeeeeeenees Set frequency from position list eee eeeseseeseeseceeeeceseseeeeceeeeenees Change power level linear amplifier systems 0 0 0 cess seeeeeeseeeeeeeee Pulse observe transmitter with amplifier gating 0 ee eeeeeeeeeeee Change transmitter or decoupler fine power 0 0 00 essseeeeeeeeseeeeeeeeee Change transmitter or decoupler linear modulator power Turn off receiver gate and amplifier blanking gate Turn on receiver gate and amplifier blanking gate cesses Read input from user AP register cecescceeceseeeeceeeeerceeeeeeeeseeeeeees Turn off receiver gate only eee ce eeeeesectecneeeeeseceeeeeeseeaeeeseecaeeeeeeaes Turn on receiver gate ONLY oo eee cee cseeceeceseeeceseeseeeeeeeeseseeeeeeas
278. e following example provides adjustment of the temperature Label of element temp Width of element 3 Scale Tcl pars to 100 from 0 tickinterval 20 length 180 Vnmr Variables temp Vnmr Cmd temp SVALUE Tcl Cmd Stemp If you wanted the scale value to move with the slider the value of Width of element field could be set to 0 and a showvalue 1 option could be added to the Scale Tcl pars field Scroll Element The scroll element adjusts a parameter with a up down buttons A label and the current value of the scale can be displayed to the left of the scroll buttons The scroll can be used for any list of items In contrast to a menu2 item you can only see the current value with a scroll element The available characteristics are the following Label of element Text string to be displayed to the left of the scroll buttons This field is optional Choices Set of text strings to be scrolled through If the text for a given choice is more than one word it must be enclosed in double quotes It must be filled in with at least two choices Width of element Amount of space reserved to display the value of the scroll If the width is 0 the value is not displayed If the center justification is selected the label and value are aligned along the left edge and the scroll is aligned along the right edge of the grid rectangle Vnmr Variables List of VNMR parameters to be used in the following Vnmr Cmd and Tcl Cmd fields This c
279. e g dbl v1 v1 is fine so it is not necessary to use db1 v1 v2 Note also that although the mod4 statement is used in several cases it is never necessary to include it even if appropriate because an implicit modulo 4 is always performed on all phases except when setting small angle phase shifts The division provided by the divn statement is integer division thus remainders are ignored vj in each case must be a real time variable and not a real number like 6 0 or even an integer constant like 6 To perform for example a modulo 6 operation something like the following is required initval 6 0 v1 modn v2 vl v7 v7 is v2 modulo 6 Controlling a Sequence Using Real Time Variables In addition to being used for phase calculations real time variables can also be used for pulse sequence control Table 18 lists pulse sequence control statements Table 18 Pulse Sequence Control Statements elsenz vi Execute succeeding statements if argument is nonzero endif vi End ifzero statement endloop index End loop ifzero vi Execute succeeding statements if argument is zero initval realnumber vi Initialize a real time variable to specified value loop count index Start loop By placing pulse sequence statements between a loop count index statement and an endloop index statement the enclosed statements can be executed repeatedly 100 VNMR 6 1C User Programming 01 999165 00 A0800 2 4 Pulse Sequenc
280. e magic angle by the correct combination of the Z gradient and the X gradient Variations on the vagradpulse statement include the capability of shaping the gradient waveform with the vashapedgradient and the vashapedgradpulse statements For more information about these statements see their descriptions in Chapter 3 VNMR 6 1C User Programming 01 999165 00 A0800 2 17 Imaging Related Statements In addition the magradpulse statement produces equal and simultaneous gradients on all three axes in order to produce an effective gradient at the magic angle Variations on the magradpulse statement include the capability of shaping the gradient waveform with the mashapedgradient andthe mashapedgradpulse statements Again for more information refer to Chapter 3 2 17 Imaging Related Statements Table 38 summarizes the PSG statements related to imaging In VNMR 5 1 most of these statements could only be used with the system configured as an imaging spectrometer With VNMR 5 3 and later software however the PSG imaging statements are used whenever their functionality is needed provided your system does not have a 63 step output board Statements related to imaging can be grouped as follows e Real time gradient statements e Oblique gradient statements e Global list and position statements e Looping statements e Waveform initialization statements e Other statements These statements were developed to support oblique imaging using standard un
281. e mouse button the slider moves to that position Clicking in the trough with the left mouse button alters the slider in that direction by one unit We have not used a slider in the sample panes but an application could be setting phase parameters Scrolls Scrolls are distinguished by two small boxes side by side one with an up arrow and the other with a down arrow A scroll has three fields a text string the current value and two arrows You cannot see the set of choices that a scroll offers only the currently selected value Each click with the left mouse button on one of the arrows moves the selected value in the appropriate direction A typical example of a scroll is in the selection of Fourier Number 01 999165 00 A0800 VNMR 6 1C User Programming 327 Chapter 6 Customizing Graphics Windows 328 Selecting the New Interface The primary program is named dg and resides in the tcl bin directory of the vnmr system directory This interface is selected by setting the UNIX environmental variable vnmrtext to the full path of the dg program A typical setting would be setenv vnmrtext Svnmrsystem tcl bin dg This line is in the login file distributed with the software Deselecting the New Interface You can run the noninteractive dg window by inserting a character in front of the vnmrtext line Window Configuration Files When the new interface is started a dg conf file specifies the general layout of the window see Figure
282. e on four channels 0 0 ceeeeseeseceeeeceseneeeeceeeseenees 252 simshaped_pulse Perform simultaneous two pulse shaped pulse eeeeeeeeeeseeeeeeees 253 sim3shaped_pulse Perform a simultaneous three pulse shaped pulse es eeeeeeeeeeee 254 li Set SLL JINGS ssessesdisscesscecteeceesiessacvdeh dvetassbeveascashses ERE EN EEEE EENES E a 255 sp off Turn off specified spare line 00 eeeeeeecseceeeseeeeceeeeeeseeaeeeseeesaeeeeeees 256 sp on Turn on specified spare Line oo eee eeeeesecseeseeseceeeeceseeaeeeeeecaeseeeeaes 257 spinlock Control spin lock on observe transmitter 0 eee ee cece eeeeeeeeeee 257 starthardloop Start hardware LOOP sscscsiteseibscstvensscevsconabevecsseansesicsodassteaevesp senscesdeusans 258 status Change status of decoupler and homospoil cesesseeeeeeeseeeeeeeees 259 statusdelay Execute the status statement with a given delay time ee 259 stepsize Set small angle phase step size rf type C or D oo eeeeeeeeeeeeees 260 sub Subtract integer valles si ssc cesevsaidcavecssshessesntansssiesdansneeddesspsstvsesvestveas 261 tsadd Add an integer to AP table elements 00 0 eee ceeeeeceeeeeeeeeeeeeeeee 261 tsdiv Divide an integer into AP table elements 0 eee eee eeeeeeeeeeeeeee 262 tsmult Multiply an integer with AP table elements 0 0 0 eeeeeeeeeees 262 tssub Subtract an integer from AP table elements 0 0 0 0 cesses eeeeeeeeneeeees 263 ttadd Add an AP table to a second table 00 0 eeseee
283. e or no improvement is achieved with more With a single 63 dB attenuator then a Gaussian pulse with 33 dB dynamic range can be superimposed on a level ranging from 0 to 30 dB more with a 79 dB attenuator e Overall power level of the shape A Gaussian pulse has an effective power approximately 8 dB lower than a rectangular pulse with an identical peak power This means that given a full power rectangular pulse of say 25 kHz a Gaussian pulse with the same peak power has approximately a 10 kHz strength Using instead a Gaussian pulse with only 33 dB dynamic range and a peak power 30 dB lower results in a shaped pulse of approximately 312 Hz which is useful for some applications like exciting the NH region of a spectrum but too strong for others To increase the dynamic range and decrease the strength of the shaped pulse further we can use one of three approaches e Replace the 63 dB attenuator with a 79 dB unit This adds 16 dB of dynamic range producing shaped pulses in the range of 50 Hz suitable for multiplet excitation e Add an additional 63 dB attenuator in series with the first If you use the entire 63 dB of the second attenuator to control the level of the pulse and use the first attenuator only for the shape you still produce a pulse whose power is for a Gaussian 71 dB 63 8 below that of the hard pulse This would produce a 7 Hz pulse about as weak a pulse as one ever needs and which could be reduced 30 dB furthe
284. e sequence and a homonuclear J resolved experiment as examples of using AP tables Two Pulse Sequence Listing 7 is the contents of the files home vnmr1 vnmrsys psglib t2pul cand home vnmrl vnmrsys tablib t2pul associated with a hypothetical two pulse sequence T2PUL Notice that t 2 and t 3 are identical The pulse sequence could have used just one phase for both the observe pulse and the receiver but using two separate phases in this way provides more flexibility for allowing run time modification of all phases independently e g a cancellation experiment can be run by changing line 2 in the tab1lib file to t2 0 or by changing line 3 to t3 0 VNMR 6 1C User Programming 01 999165 00 A0800 2 5 Real Time AP Tables Listing 7 Two Pulse Sequence t2pul c with Phase Tables include lt standard h gt tl 0 0000 pulsesequence t2 021 3 J 0213 loadtable t2pul t3 021 3 status A 0213 hsdelay d1 status B pulse p1 t1 hsdelay d2 status C pulse pw t2 setreceiver t3 Homonuclear J Resolved Experiment Listing 8 lists files home vnmr1 vnmrsys psglib hom2djt c and home vnmrl vnmrsys tablib hom2djt associated with a hypothetical homonuclear J resolved sequence HOM2DST Listing 8 Homonuclear J Resolved Sequence hom2djt c with Phase Tables status A hsdelay d1 status B pulse pw tl1 delay d2 2 pulse pl t2 delay d2 2 status C setrece
285. e sequences exist that implement this feature several contributions to the user library provide excellent examples of how to do this The statements shaped_pulse decshaped_pulse and dec2shaped_pulse provide fine grained waveform generator type pulse shaping through the AP bus If an rf channel does not have a waveform generator configured this is the same type of pulse shaping that statements apshaped_pulse apshaped_decpulse and apshaped_dec2pulse provide and is a simpler implementation This type of pulse shaping is available only on YNTYZNOVA and UNITYplus systems They use the standard pulse shape files such as gauss RF for the waveform generator MERCURY VX and MERCURY systems support these statements however only power level is controlled not phase making gauss RF the only shape currently provided The apshaped_pulse apshaped_decpulse and apshaped_dec2pulse pulse statements use table variables to define the amplitude and phase tables whereas the standard shaped_pulse decshaped_pulse and dec2shaped_pulse statements create and use these tables on the fly Both types of AP bus waveshaping statements use real time variables v12 and v13 to control execution of the shape Table 31 summarizes the statements described in this section Table 31 Statements for Pulse Shaping Through the AP Bus apshaped_decpulse First decoupler pulse shaping via the AP bus apshaped_dec2pulse Second decoupler pulse shaping via the AP b
286. e statement decshaped_pulse The decshaped_pul1se statement calls apshaped_decpulse without table variables if a waveform generator is not configured on the decoupler channel decshaped_pulse creates AP tables on the fly for amplitude and phase and does not use the AP tables allocated for users It still uses real time variables v12 and v13 shape is a shape file without the RF extension in vnmr shapelib or in vnmrsys shapelib The amplitude and phase fields of the shape file are used The relative duration field field 3 should be left at the default value of 1 0 or at least small numbers and the gate field field 4 is currently not used because the transmitter is switched on throughout the shape On MERCURY VX and MERCURY systems no phase is changed or set pulse_width is the total pulse width in seconds excluding the amplifier gating delays around the pulse pulse_phase is the 90 phase shift of the pulse For small angle phase shifting note that apshaped_decpulse sets the phase step size to the minimum on the one channel that is used power_table and phase_table are two table variables t 1 to t 60 used as intermediate storage addresses for the amplitude and phase tables respectively If apshaped_decpulse is called more than once different table names should be used in each call RG1 is the amplifier gating time in seconds before the pulse RG2 is the amplifier gating time in seconds after the pulse apshap
287. e user s vnmrsys templates dg default directory which contains experiment independent configuration files 3 Inthe system s user_templates dg directory if an Experiment Specific configuration file exists in a directory named after the value of seqfil 4 Inthe system s user_templates dg default directory which contains experiment independent configuration files Editing the Configuration Files While the configuration files are simple text files editing the files by hand is not recommended A configuration tool is provided to construct the files To activate the tool hold down the Control key and click the left mouse button on the currently selected tab Two windows appear The first window see Figure 14 as a matrix of buttons labeled 1 1 1 2 1 3 etc The name of the active configuration file is displayed in the title bar This matrix VNMR 6 1C User Programming 01 999165 00 A0800 6 3 Customizing the Interactive dg Window Listing 16 Text of dg conf File oOo MAA anA OF WN EF WWWWWWNNNNNNNNDND DW OPP WNHFRF OW WAATADAAHBWNEF OO 36 ITs 38 CODIAAGRWNHHRO set dgLocal title 1 Acquisition set dgLocal file 1 dg acq set dgLocal output 1 0 set dgLocal title 2 Pre FT set dgLocal file 2 dg processi set dgLocal output 2 0 set dgLocal title 3 FT amp Post FT set dgLocal file 3 dg process2 set dgLocal output 3 0 set dgLocal title 4 Text set dgLocal file
288. e user from infields If you uncomment the following 51 this mode will be selected 52 53 set user id user 54 set user label User identification is J9 set user style info 56 set user output USER 57 set user value env USER 312 VNMR 6 1C User Programming 01 999165 00 A0800 6 1 Customizing the Sample Entry Listing 14 Text of enter conf File continued Form Window 58 59 60 61 62 63 64 65 66 67 68 69 70 gae Ta WSs 74 TDs 76 77 78 T9 80 81 82 83 84 85 86 87 88 89 90 91 92 93u 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 set solvent id solvent set solvent label Solvent Selection set solvent menulabel Solvent Selection is set solvent style xradio set solvent file solvents set solvent numPerLine 4 set solvent required 1 set solvent output SOLVENT set exp id exp set exp label Experiment Selection set exp menulabel Experiment Selection is set exp style radio set exp file experiments set exp numPerLine 6 set exp required 1 set exp output MACRO The following three lines allow customization of experiments set exp style xradiocustom set exp label2 Selected Experiment set exp col 40 set textfield id textfield set textfield label Text t
289. e word it must be enclosed in double quotes It must be filled in with at least two labels Value of choices List of values the variable VALUE accessed as VALUE will be set to The number of values must match the number of labels If a value is more than a single word it must be enclosed in double quotes Vnmr Variables List of VNMR parameters used in the following Vnmr Cmd and Tcl Cmd fields This can be zero or more parameter names Vnmr Cmd MAGICAL expression sent to VNMR whenever one of the radio boxes is selected Any specified VNMR parameters can be used The variable VALUE is set to the value in the Value of choices list of the selected choice Tcl Cmd Tcl expression that is evaluated to determine which radio selection should be identified The return value of the expression must match one of the choices in the Value of choices list The radio buttons are useful when making exclusive choices among more than two items If the choice is between two items the check box is more appropriate A prototype example for using radio buttons is the following which selects one of three alternatives for temperature error handling Label of element Tgnore errors Warn on error Abort on error Value of choices nwy Vnmr Variables tin Vnmr Cmd tin SVALUE Tcl Cmd Stin Note the single quotes around VALUE in the Vnmr Cmd field This is standard MAGICAL syntax for setting string parameters The single quotes are not part of
290. each list created See the example for the create_delay_list statement create_delay_list Create table of delays create_offset_list Create table of frequency offsets getarray Retrieves all values of an arrayed parameter delay Delay for a specified time vfreq Select frequency from table create_offset_list Create table of frequency offsets Applicability Syntax Description Not applicable on MERCURY VX MERCURY and GEMINI 2000 create_offset_list list nvals device list_number double list pointer to list of frequency offsets int nvals number of values in list int device OBSch DECch DEC2ch or DEC3ch int list_number number 0 255 for each list Stores global lists of frequencies that can be accessed with a real time variable or table element for dynamic setting of frequency offsets Offset lists define lists of frequency offsets in Hz such as from tof dof Imaging pulse sequences typically use offset lists not frequency lists The lists need to be created in order starting from 0 using the 1ist_number argument or by setting the list_number argument to 1 which makes the software allocate and create the next free list and give the list number as a return value Each list must have a unique and sequential 1ist_number There can be a maximum of 256 lists depending on the size of the lists The lists are stored in data memory and compete for space with the acquisition data for eac
291. eal time variable RG1 is the time in seconds the amplifier is gated on prior to the start of the pulse 210 VNMR 6 1C User Programming 01 999165 00 A0800 Examples Chapter 3 Pulse Sequence Statement Reference RG2 is the time in seconds the amplifier is gated off after the end of the pulse label1 is the short character string to be given to the slider when displayed in the Acquisition window acqi program irgpulse pw v3 rofl rof2 rgpul irgpulse pw v7 rofl rof2 pw Related xrgpulse Pulse observe transmitter with amplifier gating 1k_hold Set lock correction circuitry to hold correction Applicability UN YINOVA MERCURY VX MERCURY and UNITYplus systems only Syntax 1k_hold Description Makes the lock correction circuitry hold the correction to the z0 constant thereby ignoring any influence on the lock signal such as gradient or pulses at 2H frequency The correction remains in effect until the statement 1k_sample is called or until the end of an experiment If an acquisition is aborted the lock correction circuitry will be reset to sample the lock signal Related 1k_sample Set lock correction circuitry to sample lock signal 1k_sample Set lock correction circuitry to sample lock signal Applicability UN TYINOVA MERCURY VX MERCURY and UNITYplus systems only Syntax 1k_sample Description Makes the lock correction circuitry continuously sample the lock signal and correct z0 with the time consta
292. eate a user macro without using a text editor crcom file actions Creates a user macro file in the user s macro directory The act ions string is the contents of the new macro Delete a user macro delcom file Deletes a user macro file in the user s macro directory The act ions string is the contents of the new macro Execute macro instead of command with same name hidecommand command_name lt new_name gt hidecommand Renames a built in VNMR command so that a macro with the same name as the built in command is executed instead of the built in command command_name is the name of the command to be renamed displays a list of renamed built in commands Display a user macro on the text window macrocat filel lt file2 gt lt gt Displays one or more user macro files where filel file2 are names of macros in the user macro directory Copy a user macro file macrocp from_file to_file Makes a copy of an existing user macro List user macros Lists names of user macros Edit a user macro with user selectable editor macroedit file 01 999165 00 A0800 Description macrold Syntax Description macrorm Syntax Description macrosyscat Syntax Description macrosyscp Syntax Description macrosysdir Description macrosysrm Syntax Description macrovi Syntax Description mstat Syntax Description purge Syntax 01 999165
293. ec2shaped_pulse provide pulse shaping through the linear attenuator and the small angle phase shifter on the AP bus This type of pulse shaping is available only on YN YINOVA and UNITYplus systems AP tables for the attenuation and phase values are created on the fly and the real time variables v12 and v13 are used to control the execution of the shape On previous versions of VNMR this pulse shaping through the AP bus was exclusively controlled by the statements apshaped_pulse apshaped_decpulse and apshaped_dec2pulse For shaped pulses under waveform generator control the minimum pulse length is 0 2 us The overhead at the beginning and end of the shaped pulse varies with the system and the type of acquisition controller board e OnNITYINOVA 0 95 us at start O at end e On UNITYplus 6 19 us at start 0 at end e On systems with an Acquisition Controller board 10 75 us at start 4 3 us at end e On systems with an Output board 10 95 us at start 4 5 us at end If the length is less than 0 2 us the pulse is not executed and there is no overhead The decshaped_pulse dec2shaped_pulse and dec3shaped_pulse statements allow a shaped pulse to be performed on the first second and third decoupler respectively The arguments and overhead used for each is the same as shaped_pulse except they apply to the decoupler controlled by the statement Simultaneous Two Pulse Shaped Pulse simshaped_pulse obsshape decshape obswidth decwidth
294. ec3rgpulse Applicability 182 Syntax Description Arguments idecpulse Pulse first decoupler transmitter with IPA idecrgpulse Pulse first decoupler with amplifier gating and IPA irgpulse Pulse observe transmitter with IPA rgpulse Pulse observe transmitter with amplifier gating simpulse Pulse observe decoupler channels simultaneously sim3pulse Simultaneous pulse on 2 or 3 rf channels Pulse second decoupler with amplifier gating Systems with a second decoupler dec2rgpulse width phase RG1 RG2 double width width of pulse in sec codeint phase real time variable for phase double RG1 gating delay before pulse in sec double RG2 gating delay after pulse in sec GI Performs an explicit amplifier gated pulse on the second decoupler DO2DEV width is the duration in seconds of the pulse phase is the phase of the pulse It must be a real time variable v1 to v1 4 etc or a real time constant zero one etc RG1 is the delay in seconds between gating the amplifier on and gating the rf transmitter on the phaseshift occurs at the beginning of this delay RG1 is important for amplifier stabilization under the same conditions as described for decrgpulse RG2 is the delay in seconds between gating the rf transmitter off and gating the amplifier off homo has no effect on the gating on the second decoupler board On TYINOVA and UNITYplus homo2 controls gating of second decoupl
295. eceseeeeeeeeeeeeeeeeeeeeee 263 biaiy Divide an AP table into a second table 0 eee ee cece eeeeeeeeeeeeeeeee 263 ttmult Multiply an AP table by a second table 00 eee eeteeteeeeeeeeeeeees 264 ttsub Subtract an AP table from a second table 0 eee eeeceseeeeeeeeeneenees 264 txphase Set quadrature phase of observe transmitter eee eeeeeeeeneeees 265 vagradient Variable anple eradient s s ssesacssscssssstenevesseaseeencasssevarnsasstensasssaesbaces ain 265 vagradpulse Variable angle gradient pulse oe cee ceeceseeeeceseeeeeeeeeeeeeseeeeeeee 266 vashapedgradient Variable angle shaped gradient 00 0 eee cece cee ceseeeeceseeeeeeeeeeeeeeeeeeeeee 266 vashapedgradpulse Variable angle shaped gradient pulse 000 lees cesses ceeeeeeeeeeeeeeeee 268 vdelay Set delay with fixed timebase and real time count 0 0 0 eee 268 vdelay_list Get delay value from delay list with real time index eee 269 vfreq Select frequency from table oo eee eeeeeeseeseeeeeseeseceteeceacseeeeeeeeeenees 270 vgradient Set gradient to a level determined by real time math 270 voffset Select frequency offset from table eee eeeeeeecseceeeeceseceeeeeeeeneeeees 272 vscan Provide dynamic variable scan 0 eee eeeeseceeceseeeeceseeeeseeeeeeeeeeeeeeeee 272 vsetuserap Set user AP register using real time variable 00 eee eee eeee 273 vsli Set SLI lines from real time variable 00 eee eeeeeceseceeeeeeeeneeeees 273 xgate Gate pulse sequence from an external ev
296. ecoupler dec3shaped_pulse Perform shaped pulse on third decoupler shaped_pulse Perform shaped pulse on observe transmitter simshaped_pulse Perform simultaneous two pulse shaped pulse sim3shaped_pulse Perform a simultaneous three pulse shaped pulse decshaped_pulse shape width phase RG1 RG2 dec2shaped_pulse shape width phase RG1 RG2 dec3shaped_pulse shape width phase RG1 RG2 simshaped_pulse obsshape decshape obswidth decwidth obsphase decphase RG1 RG2 sim3shaped_pulse obsshape decshape dec2shape obswidth decwidth dec2width obsphase decphase dec2phase RG1 RG2 134 VNMR 6 1C User Programming 01 999165 00 A0800 2 10 Pulse Shaping Shaped Pulse on Observe Transmitter or Decouplers To perform a shaped pulse on the observe transmitter under waveform generator control use shaped_pulse shape width phase RG1 RG2 where shape is the name of a text file in shapelib that stores the rf pattern leave off the RF file extension width is the duration of the pulse phase is the phase of the pulse it must be a real time variable RG1 is the delay between unblanking the amplifier and gating on the transmitter the phase shift occurs at the beginning of this delay and RG2 is the delay between gating off the transmitter and blanking the amplifier e g shaped_pulse gauss pw vl rofl rof2 If arf channel does not have a waveform generator the statements shaped_pulse decshaped_pulse and d
297. ecoupling but can be significant in certain experiments statusdelay allows the user to specify a defined period of time for the status statement to execute If the amount of time given as an argument is not long enough to account for the overhead delays of status the pulse sequence will still run but a warning message will be generated to let the user know of the discrepancy The following table lists the maximum amount of time per channel for the status statement to execute System Without programmable With programmable decoupling us decoupling us UNITY NOVA 2 5 2 5 UNITYplus 5 75 10 35 UNITY 2 15 12 9 VXR S 0 10 75 state specifies the status mode as A B C Z time specifies the delay time in seconds statusdelay A dl statusdelay B 0 000010 status Change status of decoupler and homospoil Set small angle phase step size rf type C or D Systems with rf type C or D and MERCURY VX and MERCURY This statement is due to be eliminated in future versions of VNMR software Although it is still functional you should not write any pulse sequences using it and should replace it in existing sequences with obsstepsize decstepsize dec2stepsize or dec3stepsize as appropriate stepsize step_size device double step_size step size of phase shifter int device OBSch DECch DEC2ch or DEC3ch Sets the step size of the small angle phase increment for a particular device T
298. ecuted The other type of loop is the repeat loop which has the form VNMR 6 1C User Programming 01 999165 00 A0800 1 2 Programming with MAGICAL repeat until booleanexpression This loop repeats statements between repeat and until untilbooleanexpression becomes TRUE if booleanexpression is TRUE at the start the statements are executed once The essential difference between repeat and while loops is that the repeat type always performs the statements at least once while the while type may never perform the statements The following macro is an example of using the repeat loop maxpk first last Find tallest peak in a series of spectra S first 1 repeat select 1 peak Sht if 1 first then maxht Sht else if Sht gt maxht then Smaxht Sht endif endif 1 1 1 until 1 gt 2 Both types of loops are often preceded by n 1 then have a statement like n n 1 inside the loop to increment some looping condition Beware of endless loops Macro Length and Termination Macros have no restriction on length Execution of a macro is terminated when the command return is encountered This is usually inserted into the macro after testing some condition as shown in the example below plotif Plot a spectrum if tallest peak less than 200 mm peak ht if ht gt 200 then return else pl endif The syntax return expression1 expression2 allows the macro to return values to another calling macro just as do commands Th
299. ed attenuators but without the T R switch preamplifiers The combination of these elements means that the capability for performing shaped pulse experiments is inherent in the systems and does not require the more sophisticated waveform generation capability of the optional waveform generators VNMR 6 1C User Programming 01 999165 00 A0800 2 11 Shaped Pulses Using Attenuators Hardware differences must be considered between systems with and without the waveform generators The attenuators have more limited dynamic range slower switching time and fewer pulse programming steps available Nonetheless the capability still allows significant experiments using only attenuators Two custom non standard configurations also exist on UNITY systems A third or fourth 0 dB to 63 dB attenuator can be added e One or both of the standard attenuators can be replaced with an 79 dB attenuator whose values run from 16 to 63 for consistency with the 63 dB attenuator Three issues affect all shaped pulses but particularly attenuator based pulses e Number of steps The more steps used the closer the shape approximates a continuous shape At what level does this become overkill For the most common shape Gaussian as few as 19 steps have been shown to be completely acceptable e Dynamic range How much dynamic range is required within a shape for proper results For a Gaussian shape it has been shown that 33 dB is a useful limit littl
300. ed dof 74 7 wtfile ss O dm nnn proc Ft pw 23 0 dmm c fn not used pl 0 dmf 200 math i di 0 dhp 0 d2 O dlp 20 werr logain tof 1100 0 homo n wexp nt 16 wbs ct 0 wnt Figure 7 Single String Display Template with Output 304 VNMR 6 1C User Programming 01 999165 00 A0800 5 5 Modifying Parameter Displays in VNMR In a single string template the string always starts with a double quote and then repeats the following information for each column in the display e Column number e g 2 e Condition for display of column optional e g 4 ni see below e Colon e Column title e g 2D ACQUISITION e Colon e Parameters to appear in column separated by commas for notation see below e Semicolon At the end of the string is another double quote Spaces cannot appear anywhere in the string template except as part of a column title Column titles are often in upper case but need not be and are limited to 19 characters More than one title can appear in the same column such as shown above SAMPLE and DECOUPLING are both in column 2 Parameters listed in plain form e g tn date math are printed either as strings or in a form in which the number of decimal places displayed varies depending on the value of the parameter To display a specific number of digits past the decimal place the desired number is placed following a colon e g sfrq 3 at 3 sw 0 Extra commas can be inserted to skip rows within a col
301. ed_decpulse gauss pw vl rofl rof2 apshaped_dec2pulse Second decoupler pulse shaping via the AP bus apshaped_pulse Observe transmitter pulse shaping via the AP bus 01 999165 00 A0800 VNMR 6 1C User Programming 161 Chapter 3 Pulse Sequence Statement Reference dcplrphase Set small angle phase of first decoupler rf type C or D decshaped_puls Perform shaped pulse on first decoupler apshaped_dec2pulse Second decoupler pulse shaping via AP bus Applicability 162 Syntax Description Arguments Examples Related UNITYINOVA and UNITYplus systems apshaped_dec2pulse shape pulse_width pulse_phase power_table phase_table RG1 RG2 char shape name of RF shape file double pulse_width pulse width in sec codeint pulse_phase real time phase of pulse codeint power_table table variable to store power codeint phase_table table variable to store phase double RG1 gating time before pulse in sec double RG2 gating time after pulse in sec Provides second decoupler fine grained waveform generator type pulse shaping through the AP bus A pulse shape file for the waveform generator vnmr shapelib RF is used Note that the real time variables v12 and v13 are used by this statement apshaped_dec2pulse overrides any existing small angle phase shifting i e a preceding dcp1r2phase and step size setting on the second decoupler channel Afte
302. eeeesecaeeeeesesaesereeeaeseeeeeaes autoscale Resume autoscaling after limits set by scalelimits 0 cee 42 expfit Least squares fit to exponential or polynomial curve UNIX 42 expl Display exponential or polynomial curves pexpl Plot exponential or polynomial curves 0 0 0 0 ce eeeeceseeeeceeeeeeeeeeeeeeeee polyo Display mean of the data in the file regression inp 0 0 0 eeeeeeeeeeeeee 42 rinput Input data for a regression analysis sseeesesecseeeceseeeeeeseeeeaeeeeeeeees 42 scalelimits Set limits for scales in regression eee sees eeeesecseeeceeeeeeeeeeeeaeeeeeeees 42 Mathematical Functions 2si c duis aiaeiciasnisnianicwaes abs Find absolute value of a number acos Find arc cosine Of a number 0 0 ee eeeeeeneeeeceecaeeeeesecaeeeeeeceaeeeseeeeeens asin Find arc sine Of a number 20 elec cee ceee cee ceeeeeceseeeeeeeeeeeeeaeeeeeeas atan Find arc tangent of a number oo eee eee eeee cee cnee cee eeeeeeeeeeeeeneees atan2 Find arc tangent of two numbers 000 ee eee ceeceee ce ceeeeeeeeeeeeeeees 43 averag Calculate average and standard deviation of input 0 0 ee 43 cos Find cosine value of an angle ossec exp Find exponential value of a number in Find natural logarithm of a number sin Find sine value of an angle ssseeeseseseseeeisrsrsrerssrsierersrrrrrrersrrerssrsreree tan Find tangent value of an angle 0 ee eeseeecnecseeeeesecaeeeeeeceaeeeseeeeeens Creating Modifying and Displaying Macros ssie si
303. ei se E EEE ESEE AS VEEE EESE ra R 298 5 4 Creating and Modifying Parameters 00 eesecssecesesseeeeseesecseeseesecnecaeesessecaecessesaecesseesassaeeeseeesasseeeees 298 Parameter Types and TICES cc siiescheesstesnsdctiea ris ets e riere eTEN ERE A E EE EEES ES VEE EEEE EErEE 298 Tools for Working with Patameter TIGOS cc secisseschvssszesscebasssusses eo ureien eE E E E EE E eE 299 Format ofa Stored Parameter ce cee saiciatsciesshShsaucs scheeb E reene EErEE EE EEEE EEE E EEEE REEE 301 5 5 Modifying Parameter Displays in VNMR ou ce eeesceeeseeseesecseeeeseeaecessecsaeneeseesecneeseesesaecaeeecsaeaeeaseeseaees 304 Display Vem plane cc cieii scsi ee raged vas E Mi ack idecier E E E ene 304 Default Displey Templates cs 0355cecese cacesetsecescassizecs dacveignatcasdgetsnessasencoetaoisescanesuingecoiauenie teasestedsnsene 305 Conditional and Arrayed Displays sinised aroei eE E E E aE awe dated 306 Omote E T E E adi gucesauesaguveesenatecesete 307 5 6 User Written Weighting FUNCIONS 0 eee eee csecsseeseceseesecesceseceseeeeeseeeecaeescecaeesaecaecsaessessaseeseeseseeees 307 Writns Wei pti PUGH OM cosis isce vs ce heu beavis edsensabubesied aedvscebeedenbesssabasevbseh EASES Vn eTa ES 308 Compiling the Weizhting Function ciccsccisisesszeesscsssbsceuscebiassaancvausies tess EE EEEE EEEE studs vedas E 309 Def User Written FID Biles scscstieviecsss Aisi cckcaes rie ee oreson eee EE EE eE OE REEE dive EEE ONSE NERE edad saeveadeayielbes 310 Chapt
304. eiig erre neres Ee Ere EEEE En ri I T EEE a a rara EREE TETEE ERE EREET EE 35 Conditonal STALSMIENIS cieisesiisiaedaccinltiat abate nae S EEE EE EREE A REE E EASES ASE AEE TESES TEE nret 36 DB DE E E E A A E 36 Macro Length amd Termination 2 63 5i x secks ofeeicaseiesestca seta cdesnenct E E E EE E E RR 37 Commandand Mocro Tracing sc ciacsssdecedicsescedcesgevscesnsssenesesdecvagscsusecunpeviesccdsssuoeecesaqusecs sdevisntedasecesats 37 1 3 Relevant VNMR Commands iscti eesi nk iio gceittincrsetasciedsdi Gathers ilies ales dade die aed 38 Special Analysis TOOLS soanen O EEEE EE EEA E SEARE NEEE T E 38 dres Measure linewidth and digital resolution 0 0 eee eee eects eeeeeeeeeee 38 dsn Measure signal to noise 0 0 eee cseeee cee ceseceeceseeeeceseeeeeeeeeeeeeseeeaeens 38 dsnmax Calculate maximum signal to noise 2 0 cece cess ceseeeeceeeeeeeeeeeeeeens 38 getll Get line frequency and intensity from line list wee eeeeeeteeeeeeeeee 38 getreg Get frequency limits of a specified region eeeeeeseereeeeeteeeeeeeees 38 integ Find largest integral in specified region 00 0 eee ee eeeeeeeeeeeeeeee tees 39 mark Determine intensity of the spectrum at a point sessen 39 mir Find line frequencies and intensities seseseeeeeeeeeeeeesreeerersrrerersrsrer 39 numreg Return the number of regions in a spectrum 0 0 cee eeeeeeteteteeeeee 39 peak Find tallest peak in specified region 0 0 eee ee eeeeeseeeeeeeeeeeeeeeeeeeene 39 select Selec
305. el 1 RF Amp duty cycle limit exceeded 1537 Channel 1 RF Amp temperature limit exceeded 1538 Channel 1 RF Amp pulse width limit exceeded 1539 Channel 1 RF Power Monitoring BYPASSED 1540 Channel 1 RF Amp errors BYPASSED 1551 Channel 2 RF power exceeds 10s SAR limit 1552 Channel 2 RF power exceeds 5 min SAR limit 1553 Channel 2 peak RF power exceeds limit 1554 Channel 2 RF Amp control cable error 1555 Channel 2 RF Amp reflected power too high 1556 Channel 2 RF Amp duty cycle limit exceeded 1557 Channel 2 RF Amp temperature limit exceeded 1558 Channel 2 RF Amp pulse width limit exceeded 1559 Channel 2 RF Power Monitoring BYPASSED 1560 Channel 2 RF Amp errors BYPASSED 2 3 Spectrometer Control More than 200 pulse sequence statements are available for pulse sequence generation PSG This section starts the discussion of each statement by covering statements intended primarily for spectrometer control For discussion purposes the statements in this section are divided into categories delay related observe transmitter pulse related decoupler transmitter pulse related simultaneous pulses transmitter phase control small angle phase shift frequency control power control and gating control Creating a Time Delay The statements related to time delays are delay hsdelay idelay vdelay initdelay and incdelay Table 6 summarizes these statements Table 6 Delay Related Statements
306. elective phase cycling 88 colon notation 28 command entry 278 command interpreter 26 command output to variables 28 command tracing 37 comments 31 in macros 26 comparing two files UNIX 279 compilation error messages 71 compiling a pulse sequence 66 compiling source code 70 completed transient counter 98 complex pair of FID data 287 compressed acquisitions 155 compressed data format 295 compressed files 291 compressed loop 216 227 Compressed compressed data format 295 compressed compressed image sequences 272 concatenate and display files UNIX 279 concatenate strings 31 conditional execution 194 202 conditional statements 26 36 config command 299 confirm command 40 confirm message with mouse 40 confirmer window 41 conpar file 299 302 constant delay time for changing the status 103 constant phases 99 constant strings 27 constants 30 continuous decoupling caution 92 continuous wave CW modulation 83 243 conventions used in manual 23 conversion of files between systems 283 conversion units 49 copying files UNIX 278 279 copying macros 44 cos command 43 01 999165 00 A0800 Index cosine value of an angle 43 COSY NOESY sequence 130 cp command UNIX 278 279 cp parameter 99 cr parameter 38 crcom command 44 create command 299 301 create_delay_list statement 157 165 create_freq_list statement 157 166 create_offset_list statement 157 167 creategtable macro
307. elete mstring i input Enter of Experiment to Delete exp delexp exp e ds automatically brings up the menu ds_1 when started e inset automatically brings up the menu inset when started A user or system administrator wishing to change the opening menu displayed when one of these commands is executed must edit the menu1ib file listed above for the command Similarly all the menus available for each program can be modified For further information see Programming Menus page 55 In order not to redraw the display after every menu selection these menus generally involve special calls to the program in question For example entering ds thresh activates the display of a horizontal threshold on the ds display For 1D displays df ds any change in a display parameter e g vs causes the display to be updated whereas for 2D displays dconi the display must be deliberately reactivated either by dconi restart which reactivates the display without redrawing it or by dconi again which redraws the display with any parameter changes in effect 1 6 Customizing the Files Menus 58 The Files program in VNMR provides an interface with the UNIX file system You can use the menus in the program to create delete copy and rename files or to select a data set or parameter set to load into your experiment Because the Files program relies on the standard menu and help file mechanism the special p
308. ement followed by dec2off e Likewise explicit gating of the third decoupler in the pulse sequence is provided by dec3o0ff and dec3on Third decoupler gating is handled automatically by dec3pulse dec3rgpulse dec3shaped_pulse and dec3spinlock The dec3prgon function should generally be enabled with an explicit dec3con statement followed by dec3of f On the GEMINI 2000 all amplifier types are handled internally in declvlon and declvloff No explicit declaration is needed as described above declvlon and declvloff have no effect on MERCURY VX and MERCURY systems The variable 01 999165 00 A0800 VNMR 6 1C User Programming 95 Chapter 2 Pulse Sequence Programming declvlflag is added to GEMINI 2000 MERCURY VX and MERCURY pulse sequence programming to distinguish between the two within a pulse sequence declvlflag is TRUE for GEMINI 2000 and FALSE for MERCURY VX and MERCURY See dept c for an example On UNITY and VXR S systems with class C amplifiers to switch from low power to high power decoupling insert the statement dhpf1lag TRUE or the statement dhpflag FALSE in a pulse sequence just before a status statement correct use of upper and lower case letters is necessary dhpflag TRUE switches the system to high power decoupling and dhpf1lag FALSE switches to low power decoupling Receiver Gating Explicit receiver gating in the pulse sequence is provided by the rcvroff rcvron recoff and
309. ement in table_modand the result is stored in t able_dest The number of elements in table_dest must be greater than or equal to the number of elements in table_mod moduloval is the modulo value taken on the result of the operation if moduloval is greater than 0 ttmult t28 t42 6 ttadd Add an AP table to a second table Etaivy Divide an AP table into a second table ttsub Subtract an AP table from a second table Subtract an AP table from a second table All systems except the GEMINI 2000 ttsub table_dest table_mod moduloval codeint table_dest real time table variable codeint table_mod real time table variable int moduloval modulo value of result A run time vector operation that subtracts one AP table from a second table table_dest is the name of the destination table t 1 to t 60 table_modis the name of the table t 1 to t 60 that modifies table_dest Each element in table_dest is modified by the corresponding element in table_modand the result is stored in t able_dest The number of elements in table_dest must be greater than or equal to the number of elements in table_mod moduloval is the modulo value taken on the result of the operation if moduloval is greater than 0 264 VNMR 6 1C User Programming 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference Examples ttsub t28 t42 6 Related ttadd Add an AP table to a second
310. en gating the rf transmitter off and gating the amplifier off homo has no effect on the gating on the third decoupler board On UWNITYTNOVA and UNITYplus homo3 controls gating of third decoupler rf dec3rgpulse pl v10 rofl rof2 decpulse Pulse first decoupler with amplifier gating decrgpulse Pulse first decoupler with amplifier gating idecpulse Pulse first decoupler with IPA rgpulse Pulse observe transmitter with amplifier gating simpulse Pulse observe decoupler channels simultaneously sim3pulse Simultaneous pulse on 2 or 3 rf channels Pulse fourth decoupler with amplifier gating UNITYINOVA systems with a deuterium decoupler channel as the fourth decoupler dec4rgpulse width phase RG1 RG2 double width width of pulse in sec codeint phase real time variable for phase double RG1 gating delay before pulse in sec double RG2 gating delay after pulse in sec Performs an explicit amplifier gated pulse on the fourth decoupler DO4DEV width is the duration in seconds of the pulse phase is the phase of the pulse It must be a real time variable v1 to v14 etc or a real time constant zero one etc RG1 is the delay in seconds between gating the amplifier on and gating the rf transmitter on the phaseshift occurs at the beginning of this delay RG1 is important for amplifier stabilization under the same conditions as described for decrgpulse RG2 is the delay in seconds between gating t
311. end These values hold regardless of the values for ooswidth decwidth and dec2width By setting one of the pulse lengths to the value 0 0 sim3shaped_pulse can also perform a simultaneous two pulse shaped pulse on any combination of three rf channels e g to perform simultaneous shaped pulses on the first decoupler and second decoupler but not the observe transmitter set the obswidth argument to 0 0 If any of the shape names are set to the null string a hard pulse occurs on the channel with the null shape name If either the pulse width is zero or the shape name is the null string a waveform generator is not required on that channel Programmable Transmitter Control Statements related to programmable transmitter control on YNITYZNOVA UNITYplus and UNITY systems with optional waveform generators are obsprgoff and obsprgon for the observe transmitter decprgoff and decprgon for the first decoupler dec2prgoff and dec2prgon for the second decoupler and dec3prgof fand dec3prgon for the third decoupler Table 28 provides a summary of these statements Programmable Control of Observe Transmitter Use obsprgon name 90_pulselength tipangle_resoln to set programmable phase and amplitude control of the observe transmitter name is the name of the file in shapelib that stores the decoupling pattern 90_pulselength is the pulse duration for a 90 tip angle and tipangle_resoln is the resolution in tip angle degrees to which the deco
312. ength of about 100 us For the Data Acquisition Controller Pulse Sequence Controller Acquisition Controller and MERCURY VX and MERCURY STM Output boards there are no timing restrictions between multiple back to back hard loops There is one subtle restriction placed on the actual duration of a hard loop if back to back hard loops are encountered the duration of the ith hard loop must be N i 1 0 4 us where N i 1 is the number of events occurring in the i 1 th hard loop VNMR 6 1C User Programming 01 999165 00 A0800 Arguments Examples Related status Syntax Description Arguments Examples Related statusdelay Applicability Chapter 3 Pulse Sequence Statement Reference vloop is the number of hardware loop repetitions It must be a real time variable v1 to v14 ct etc and not an integer a real number or a regular variable starthardloop v2 acquire Explicitly acquire data endhardloop End hardware loop Change status of decoupler and homospoil status state int state index A B Cy iesp A Controls decoupler and homospoil gating homospoil not available on the GEMINI 2000 Parameters controlled by status are dm first decoupler mode dmm first decoupler modulation mode and hs homospoil For systems with a third rf channel dm2 second decoupler mode dm3 third decoupler mode dmm2 second decoupler modulation mode and dmm3 third decoupler modulation mode are a
313. ent 0 0 0 eeeteeeeeeeeeteeeeeee 275 xmtroff Turn off observe transmitter 0 cesses cseeseeseceeeeceseeaeeeseecsaeseeeeees 275 xmt ron Turn on observe transmitter oo eee cee ceeeceeceseeeeceseeeeeeeeeeeeeeeeeeeee 275 xmtrphase Set transmitter small angle phase rf type C D wee eee eeeeeeeees 275 zero_all_gradients Zero all SrACSMiScvsesesscecsseesssvesssessyeaynecenckedvenvecsccs En e EE EE ES Ss 276 zgradpulse Create a gradient pulse on the z channel ssssseesseesseeeseeeeerrerereeesee 276 Chapter 4 UNIX Level Programming cccceseeeeceesseeeeeesseeneeeeseeneeesenseeeeeesnseeeeeensenneeeeees 277 41 UNIX a d VNMR i550 cssaecsesdeiennsnokd cl dereden decals a E a arse dade sua Ran EEEa e eaaa a toak iaaea 277 Hoo UNIX A Reference Guide ciiisean E cheese sed sdb eo anaE EAE ir Aar aa E Aaroa ESEESE 278 Corman EDY pioen i ope ae eE T EE AE A AEA RERE EA TEONE 278 File Names senorning torero a AE E E E E ESE A Maden 278 Fie Mandine Commands sos os sc vee cin aanere ro EE E EEEN E AE 278 Directory Names seasainn E E ieee O ain ain aa 278 Directory Mondine Commands oiera ei goscie rione p ea eE E E EEEO EE E AE EO EE 278 TERPCGMMANGS poiense irae a a E E EE E E EE E RS 279 01 999165 00 A0800 VNMR 6 1C User Programming 13 Table of Contents Other Commands 65 ccc citi Ae cence labia EET sade oad OEE eel E TTR 279 Speci l CUACACELS csscacisscssstsesiavevsesesbsvsasiapass Eee oes EESE E RE Ep e R APERAR bas OE
314. ent The default element number is 1 The program writes two values per line the first is the value from the X or real channel and the second is the value from the Y or imaginary channel 310 VNMR 6 1C User Programming 01 999165 00 A0800 Chapter 6 Customizing Graphics Windows Sections in this chapter e 6 1 Customizing the Sample Entry Form Window this page e 6 2 Customizing the status Window page 322 e 6 3 Customizing the Interactive dg Window page 324 Almost every aspect of VNMR graphics windows can be customized for local use Many of these windows are written in the scripting language Tcl Tk tool command language tool kit This language allows considerable customizing by users of the windows and their functions To find out more about Tcl Tk refer to books such as Tcl and the Tk Toolkit by J K Ousterhout Addison Wesley 1994 and Effective Tcl Tk Programming by M Harrison and M McLennan Addison Wesley 1998 For those who do not wish to learn Tcl Tk Varian has further simplified much of this customization through the use of conf files 6 1 Customizing the Sample Entry Form Window The Sample Entry Form window is the interface to the enter program The enter program is used to define experiments for an automation run The Sample Entry Form window is covered from the user s viewpoint in the manuals Getting Started User Guide Liquids and Walkup NMR Using GLIDE In this section we cover cust
315. ent an integer value 200 VNMR 6 1C User Programming 01 999165 00 A0800 hsdelay Syntax Description Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference mod2 Find integer value modulo 2 mod4 Find integer value modulo 4 modn Find integer value modulo n mult Multiply integer values sub Subtract integer values Delay specified time with possible homospoil pulse hsdelay time double time delay in sec Sets a delay for a specified number of seconds If the homospoil parameter hs is set appropriately see the definition of status hsdelay inserts a homospoil pulse of length hst sec at the beginning of the delay Although the GEMINI 2000 does not support homospoil GEMINI 2000 systems support hsdelay for compatibility with other systems time specifies the length of the delay in seconds hsdelay dl hsdelay 1 5e 3 delay Delay for a specified time idelay Delay for a specified time with IPA incdelay Real time incremental delay initdelay Initialize incremental delay vdelay Delay with fixed timebase and real time count idecpulse Applicability Syntax Description Arguments Examples Related Pulse first decoupler transmitter with IPA All systems except MERCURY VX MERCURY and GEMINI 2000 idecpulse width phase label double width pulse width in sec codeint phase real time variable for phase char label slider label in acqi
316. ent rf channels The overhead at the start and end of the shaped pulse varies e UNITYTNOVA 1 95 us start 0 end e UNITYplus 17 25 us 0 e Systems with an Acquisition Controller board 32 25 us 12 9 us e Systems with an Output board 32 45 us 13 1 us These values hold regardless of the values of the arguments obswidth decwidth and dec2width sim3shaped_pulse can also be used to perform a simultaneous two pulse shaped pulse on any combination of three rf channels This can be achieved by setting one of the pulse lengths to the value 0 0 see the second example below for an illustration of how this is done If any of the shape names are set to the null string then a hard pulse occurs on the channel with the null shape name If either the pulse width is zero or the shape name is the null string then a waveform generator is not required on that channel obsshape is the name of the text file in the shapelib directory that contains the rf pattern to be executed on the observe transmitter decshape is the name of the text file in the shapelib directory that contains the rf pattern to be executed on the first decoupler dec2shape is the name of the text file in the shapelib directory that contains the rf pattern to be executed on the second decoupler obswidth is the length of the pulse in seconds on the observe transmitter decwidth is the length of the pulse in seconds on the first decoupler 254 VNMR 6 1C
317. enter program to exit e The prioritySamp1e button submits the currently defined experiment to the front of the queue of an automation run and then exits the enter program e The quit button deletes the temporary file and then exits In the default case the user can create a lot of experiments with the addExp button but not actually add them to the entero file until the saveAndExit button is pressed As an alternative a two button exit scheme might be preferred by some In this case an addSaveAndExit button and a quit button would be present The addSaveAndExit button writes the experiments to a temporary file appends the temporary file to the enterQ output file deletes the temporary file and then exits In effect it is the combination of the addExp button and the saveAndExit button A third alternative is to use the saveExp and quit buttons In this case the only way to exit from the enter program is with the quit button After pressing the saveExp button there is no way to cancel those experiments Figure 1 shows this alternative The cnt rls parameter on line 107 specifies the buttons and their order The names are important in this case The alternate scheme is selected by removing the comment symbol in line 109 The second alternative scheme is selected by removing the in line 112 The only other attribute that is configurable is the label for each button rtoutput and rtoutoput2 Attributes B
318. ents Examples Chapter 3 Pulse Sequence Statement Reference timebase is one of the four defined time bases NSEC see note below USEC microseconds MSEC milliseconds or SEC seconds count is a real time variable v1 to v14 For predictable acquisition the real time variable should have a value of 2 or more If timebase is set to NSEC the delay depends on which acquisition controller board is used on the system see the description section of the acquire statement for further information about these boards e On systems with a Data Acquisition Controller board the minimum delay isa count of 0 100 ns and a count of n corresponds to a delay of 100 12 5 n ns For example vdelay NSEC v1 when v1 4 gives a delay of 100 12 5 4 ns or 150 ns e On systems with a Pulse Sequence Controller board or an Acquisition Controller board the minimum delay is a count of 2 200 ns A count greater than 2 is the minimum delay plus the resolution 25 ns of the board For example vdelay NSEC v1 when v1 4 gives a delay of 200 25 ns or 225 ns e On systems with Output boards the minimum delay is a count of 2 200 ns A count greater than 2 is the minimum delay plus the resolution 100 ns of the board For example vdelay NSEC v1 when v1 4 gives a delay of 200 100 ns or 300 ns vdelay USEC v3 create_delay_list Create table of delays delay Delay for a specified time
319. ents the vagradpulse gradlvl gradtime theta phi statement can be used and to produce three equal and simultaneous gradients such that an effective gradient is produced at the magic angle the magradpulse gradlvl gradtime statement is available The statements vagradpulse and magradpulse are structured so that the software does all of the calculations to produce the effective gradient desired Both statements take the argument for the gradient level grad1v1 in gauss cm This is distinctly different from the rgradient and zgradpulse statements which take the argument for the gradient level value in DAC With these statements the gcoil and sysgcoil parameters are required for the software to calculate the correct DAC value for each channel in order to produce the requested effective gradient After the gradients have each been calibrated and a gradtable has been constructed with the creategt able macro as described above then the sysgcoil parameter can be set to that coil name used The updt gcoil macro can then update the local gcoil parameter from the global sysgcoil parameter The vagradpulse statement uses the theta and phi angles to produce an effective gradient at any arbitrary angle For example using vagradpulse with theta 54 7 and phi 0 0 an effective gradient is produced at the magic angle by the correct combination of the Z gradient and the Y gradient Whereas if thet a 54 7 and phi 90 an effective gradient is produced at th
320. enus These menus can make many operations easier and faster than using the command line All menu buttons are user programmable through menu files which is covered below Table 3 lists the commands and parameters connected with programming menus The manual Getting Started covers menus from the user viewpoint Table 3 Menu Related Commands and Parameters Commands clear lt window_number gt Clear a window glide Toggle on and off the GLIDE interface help Display the current help file menu lt menu_name off gt Change status of menu system menuvi menu_name Edit a menu with vi text editor newmenu menu lt current_menu gt Select menu without activation Parameters helppath absolute path Path to user s help directory lastmenu menu name Menu to display if Return clicked menulibpath absolute path Path to user s menu directory mlabel string Menu label mstring command string Menu string Customizing the Permanent Menu The Permanent menu is the upper fixed row of buttons This menu provides easy user access to the most important functions of the system Start Delay Pulse DecPulse Status Other Finish The Permanent menu is fixed in the sense that the labels must be defined when VNMR starts however you can customize the labels and functions of the buttons by editing a text file When VNMR is started if the variable vnmrmenu is present in the UNIX environment it is used as the path to t
321. ept in special cases data acquisition begins at the end of the pulse sequence iobspulse Pulse observe transmitter with IPA ipulse Pulse observe transmitter with IPA irgpulse Pulse observe transmitter with IPA pulse Pulse observe transmitter with amplifier gating rgpulse Pulse observe transmitter with amplifier gating simpulse Pulse observe decoupler channels simultaneously sim3pulse Simultaneous pulse on 2 or 3 rf channels Set observe transmitter fine power Systems with fine power control Not available on MERCURY VX MERCURY and GEMINI 2000 systems obspwrf power double power new fine power level for OBSch Changes observe transmitter fine power This statement is functionally the same as rlpwrf value OBSch value is the fine power desired obspwrf 4 0 decpwrf Set first decoupler fine power dec2pwrf Set second decoupler fine power dec3pwrf Set third decoupler fine power rlpwrf Set transmitter or decoupler fine power Set step size for observe transmitter All systems except the GEMINI 2000 obsstepsize step_size double step_size small angl phase step size Sets the step size of the observe transmitter This statement is functionally the same as stepsize base OBSch step_size is the phase step size desired and is a real number or a variable 01 999165 00 A0800 Examples Related obsunblank Syntax Description Related offset Applicability Syntax De
322. equence initval 4 0 v9 divn ct v9 v8 status A hsdelay dl status B add zero v8 vl pulse pw v1 delay d2 2 0 mod4 ct v1 add v1 v8 v1 pulse pl vl delay d2 2 0 status C mod2 ct oph dbl oph oph add oph v8 oph The user psglib is stored in the user s private directory system e g for user vnmr 1 in export home vnmr1 vnmrsys psglib All pulse sequence files stored in these directories are given the extension c to indicate that the file contains C language source code For instance the homonuclear 2D J sequence that you may have written as an 01 999165 00 A0800 VNMR 6 1C User Programming 69 Chapter 2 Pulse Sequence Programming 70 example was automatically stored in your private pulse sequence directory and thus has a name like export home vnmrl vnmrsys psglib hom2dj c You may find that a pulse sequence you need is already available Numerous sequences are in the standard Varian supplied directory vnmr psg1lib and in the user library directory vnmr userlib psglib or you can program a sequence using the menu system or write a sequence using any of the standard text editors such as vi or textedit Once a pulse sequence exists it can subsequently be modified as desired again using one of a number of text editors Compiling the New Pulse Sequence After a pulse sequence is written the source code is compiled by one of these methods e By click
323. equence events during the gradient pulse Because oblique_shapedgradient talks to the x y and z gradient axes NOWAIT cannot be used to produce simultaneous oblique gradient pulses even if they are orthogonal In the following example oblique_shapedgradient patx tdelta gdiff 0 0 0 0 0 0 0 0 0 0 1 NOWAIT oblique_shapedgradient paty tdelta 0 0 gdiff 0 0 0 0 0 0 0 0 1 NOWAIT oblique_shapedgradient patz tdelta 0 0 0 0 gdiff 0 0 0 0 0 0 1 WAIT 01 999165 00 A0800 VNMR 6 1C User Programming 219 Chapter 3 Pulse Sequence Statement Reference the first two function calls set up all three gradients In both cases after a few microseconds the gradient hardware is reset by the third function call which is the only call fully executed Even though the third call is executed expect negative side effects from the first two suppressed calls Examples oblique_shapedgradient ramp_hold trise gvox1 0 0 vpsi vphi vtheta 1 NOWAIT Related obl_shapedgradient Execute a shaped oblique gradient obsblank Blank amplifier associated with observe transmitter Syntax obsblank Description Disables the amplifier for the observe transmitter This statement is generally used after a call to obsunblank Related decunblank Unblank amplifier associated with first decoupler obsunblank Unblank amplifier associated with observe transmitter revroft Turn off receiver revion Turn on receiv
324. er double power new power level for DODEV Changes the first decoupler power It is functionally the same as rlpower value DODEV power Sets the power level by assuming values from 0 minimum power to 63 maximum power on channels with a 63 dB attenuator or from 16 minimum power to 63 maximum power on channels with a 79 dB attenuator On systems with linear amplifiers be careful when using values of decpower greater than 49 about 2 watts Performing continuous decoupling or long pulses at power levels greater than this can result in damage to the probe Use config to set a safety maximum for parameters tpwr dpwr dpwr2 and dpwrs dec2power Change second decoupler power linear amplifier systems dec3power Change third decoupler power linear amplifier systems obspower Change observe transmitter power linear amplifier systems rlpower Change power level linear amplifier systems Change second decoupler power level linear amp systems Systems with a second decoupler dec2power power new power level for DO2DEV double power Changes the second decoupler power It is functionally the same as rlpower value DO2DEV 175 VNMR 6 1C User Programming Chapter 3 Pulse Sequence Statement Reference Arguments Related dec3power Applicability Syntax Description Arguments Related dec4power Applicability Syntax Description Arguments Related
325. er attributes 302 create new parameter 299 enumerable values 303 maximum value 302 minimum value 302 table 72 template 304 trees 298 typical parameter file 303 values 302 parameters accessing the value 299 arrayed parameter values 196 as global variables 32 as variables 26 categories 110 change type 300 conditional display 306 display field width 307 display formats 307 display values in text window 40 editing attributes 300 01 999165 00 A0800 Index existence test 46 get value 299 global PSG parameters 111 look up value 117 plotting automatically 40 protection bit 27 protection bits 300 set up for pulse sequence 41 spectroscopy imaging sequences 207 step size 302 types 298 user created 117 parameters retrieved from a parameter file 48 paramvi command 300 301 304 parent directory UNIX 278 parentheses notation 34 parfix macro 301 parlib directory 41 parmax parameter 302 parmin parameter 302 parsing macros 28 parstep parameter 302 pattern scanning and processing UNIX 279 pe_gradient statement 155 224 pe_shapedgradient statement 225 pe2_gradient statement 224 pe2_shapedgradient statement 226 pe3_gradient statement 225 pe3_shapedgradient statement 226 peak command 26 28 39 peak width of solvent resonances 48 peloop statement 157 227 Performa XYZ PFG module 153 Permanent menu 52 53 pexpl command 42 PFG pulsed field gradient 153 phase angle
326. er obsoffset Change offset frequency of observe transmitter Syntax obsoffset frequency double frequency offset frequency Description Changes the offset frequency in Hz of the observe transmitter parameter tof It is functionally the same as offset frequency OBSch For systems with rf types A or B the frequency typically changes between 10 to 30 us but 100 us is automatically inserted into the sequence by the offset statement so that the time duration of of f set is constant and not frequency dependent e For systems with rf type C which necessarily have PTS frequency synthesizers the frequency shift time is 15 05 us for standard non latching synthesizers and 21 5 us for the latching synthesizers with the overrange under range option e For systems with rf type D UNITYplus the frequency shift time is 14 95 us latching with or without over range No 100 us delay is inserted into the sequence by the of fset statement Offset frequencies are not returned automatically to their normal values before acquisition this must be done explicitly as in the example below e For the UN TYINOVA the frequency shift is 4 us e For the MERCURY VX and MERCURY this statement inserts a 86 4 us delay although the actual switching of the frequency takes 1 us e For the GEMINI 2000 rf types F or E on broadband systems only the decoupler can be shifted 8 6 us on H Bc systems observe 6 48 us decoupler 8 6 u
327. er 6 Customizing Graphics WiNdOWS ccssseecessseeeeeeeseeneeeeeeeeneeseneeeeneeseneeneeeeees 311 6 1 Customizing the Sample Entry Form Window sesssssesessereessreerssreresresrsrrsrerrerertnsrernsrernsrrerstrererrererreseet 311 Window Conmilpuranom Piles cial cick ctce costae ed vseasesvievine EOE E EEEE E E A vised ea donned eeaviaesente 311 Setting Which Selections Are Displayed siseses sariin oone E ERE E EASE 314 14 VNMR 6 1C User Programming 01 999165 00 A0800 Table of Contents Setting the Content or the Output Fue c c6c ae scsceisi ces chs setessehebiacssstdscanscntee oduehabevscnsbadhevaeebesdens 314 DSTI S Name A MTDUESS crest sch cere vases cas rere tr ea oe ape aE pede ER ERE EEE KRE E ESEE ERE O RTE IE ETAR EE RE S 315 Bettie the Types Of Widgets siiicar sei aise ai Aaa a aet 316 PAM ee UA Ua CA SS AA E E E E E eee epacenetne 316 Pile Atm bute anann npn teil ache E eect Ai een Ginna 317 Button DenmUSNS eean eaae ee ee NE E EE e E Eea O EN EEEE a ENA iSS 319 Sample Entity Control x cccseckdes seek esazstletexsevs cece ei e a ia a EEEE ER eie E aa aasi 321 POU al New Field ireccio ieu orae nnn Eo RERE EE EEEn EE RAE AREE 322 6 2 Customizing the status Window ou sees csecsecseceseeseceseeseceeceeceeeeseeeaeseeecaessuecaeesaecaecsaeseecaseaeseeseseeegs 322 Window Conigutauonm Fil sercis tnea bs deesucssunesdev ses sereen EEE EE EE EEE bined E AE TESE EEE 323 Defining Buttons and Window AtMIDUIES scisssrisiso
328. er controllable lines coinciding with two 8 bit AP bus registers All four of the AP bus registers are writeable but only one register is readable Table 16 shows the mapping of the Table 16 Mapping of User AP Lines user AP lines On both connectors lines 17 to 25 are ground lines Register Connector Lines Function User in lines allow gt 0 18213 9to16 output synchronous access by users to 1 18213 ee P external services while running a pulse sequence The statements 2 J8212 9to16 output setuserap value reg 3 J8212 1to8 input output vsetuserap rtvar reg and readuserap rtvar provide access to these lines The setuserap and vsetuserap statements enable writing 8 bit information to one of four registers Each write takes one AP bus cycle which is 0 5 us for the YNITYYZNOVA The 01 999165 00 A0800 VNMR 6 1C User Programming 97 Chapter 2 Pulse Sequence Programming only difference between setuserap and vsetuserap is that vsetuserap uses a real time variable to set the value The readuserap statement lets you read 8 bit information from the register into a real time variable You can then act on this information using real time math and real time control statements while the pulse sequence is running however because the system has to wait for the data to be read before it can continue parsing and stuffing the FIFO a significant amount of overhead is involved in servicing the read and refilling the FIFO The readus
329. er defined command that can duplicate a long series of commands and parameter changes you would otherwise have to enter one by one To plot a spectrum a scale under the spectrum and parameters on the page would require a sequence of commands such as pl pscale hpa page It would be possible to define a macro say plot that would be the equivalent of these commands Or perhaps you routinely plot 2D spectra using certain parameters In this case you might define a macro plot_2d as equivalent to the following wc 160 sc 20 wc2 160 sc2 20 pcon 10 1 4 page But macros in the VNMR software are much more than this Macros are written in Varian s special high level NMR language MAGICAL IIM MAGnetics Instrument Control and Analysis Language version II usually just called MAGICAL in this chapter MAGICAL provides an entire series of programming tools such as if statements and loops that can be used as part of macros In addition MAGICAL provides other NMR related tools that allow macros to access NMR information like peak heights integrals and spectral regions Using these two sets of tools NMR algorithms are easily implemented with MAGICAL 01 999165 00 A0800 VNMR 6 1C User Programming 25 Chapter 1 MAGICAL II Programming 26 Writing a Macro Consider the following problem Find the largest peak in a spectrum in which the peaks may be positive or negative such as an APT spectrum and adjust the vertical s
330. er mathematical statements are provided that are fast enough to execute in real time add assign dbl decr divn hlv incr mod2 mod4 modn mult and sub These statements are summarized in Table 17 Table 17 Integer Mathematics Statements add vi vj vk Add integer values set vk equal to vi vj assign vi vj Assign integer values set vj equal to vi dbl vi vj Double an integer value set vj equal to 2evi decr vi Decrement an integer value set vi equal to vi 1 divn vi vj vk Divide integer values set vk equal to vi div vj hlv vi vj Find half the value of an integer set vj to integer part of 0 5evi incr vi Increment an integer value set vi equal to vi 1 mod2 vi vj Find integer value modulo 2 set vj equal to vi modulo 2 mod4 vi vj Find integer value modulo 4 set vj equal to vi modulo 4 modn vi vj vk Find integer value modulo n set vk equal to vi modulo vj mult vi vj vk Multiply integer values set vk equal to viev j sub vi vj vk Subtract integer values set vk equal to vi vj Remember that integer mathematics does not include fractions If a fraction appears in a result the value is truncated thus one half of 3 is 1 not 1 5 Integer statements also use the modulo which is the number that remains after the modulo number is divided into the original number For example the value of 8 modulo 2 often abbreviated 8 mod 2 is found by dividing 2 into 8 giving an answer of 4 with a remain
331. er pulses dec3unb1lank is generally followed by a call to dec3blank dec3blank Blank amplifier associated with third decoupler tevroff Turn off receiver revron Turn on receiver 01 999165 00 A0800 VNMR 6 1C User Programming 189 Chapter 3 Pulse Sequence Statement Reference delay Syntax Description Arguments Examples Related dhpflag Applicability Syntax Description Values Related divn Syntax Description Arguments Examples Related dps_off Syntax 190 Delay for a specified time delay time double time delay in sec Sets a delay for a specified number of seconds time specifies the delay in seconds delay dl delay d2 2 0 dps_show Draw delay or pulses in a sequence for graphical display hsdelay Delay specified time with possible homospoil pulse idelay Delay for a specified time with IPA incdelay Real time incremental delay initdelay Initialize incremental delay vdelay Delay with fixed timebase and real time count Switch decoupling from low power to high power On all systems with class C amplifiers except the GEMINI 2000 dhpflag Switches the system from low power to high power decoupling e g dhpflag TRUE correct use of upper and lower case letters is necessary TRUE switches the system to high power decoupling FALSE switches the system to low power decoupling status Draw delay or pulses in a sequence for graphical display Div
332. er rf dec2rgpulse pl v1l0 rofl rof2 decpulse Pulse first decoupler with amplifier gating decrgpulse Pulse first decoupler with amplifier gating idecpulse Pulse first decoupler with IPA rgpulse Pulse observe transmitter with amplifier gating simpulse Pulse observe decoupler channels simultaneously sim3pulse Simultaneous pulse on 2 or 3 rf channels Pulse third decoupler with amplifier gating UNITYTNOVA and UNITYplus systems with a third decoupler dec3rgpulse width phase RG1 RG2 double width width of pulse in sec codeint phase real time variable for phase double RG1 gating delay before pulse in sec double RG2 gating delay after pulse in sec Performs an explicit amplifier gated pulse on the third decoupler DO3DEV width is the duration in seconds of the pulse phase is the phase of the pulse It must be a real time variable v1 to v 14 etc or a real time constant zero one etc RG1 is the delay in seconds between gating the amplifier on and gating the rf transmitter on the phaseshift occurs at the beginning of this delay RG1 is important for amplifier stabilization under the same conditions as described for decrgpulse VNMR 6 1C User Programming 01 999165 00 A0800 Examples Related dec4rgpulse Applicability Syntax Description Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference RG2 is the delay in seconds betwe
333. er that tags this gradient statement from any other gradient statement used in the sequence Examples include standard h pulsesequence char gphase gread gslice amplitude int 0 5 ni gpe stat getorientation amp gread amp gphase amp gslice orient r initval 1 0 v1 initval nf v9 loop v9 Vv5 shapedvgradient hsine d3 amplitude igpe v5 gphase vl NOWAIT 1 endloop v5 Related incdelay Set real time incremental delay rgradient Set gradient to specified level shapedgradient Generate shaped gradient pulse 250 VNMR 6 1C User Programming 01 999165 00 A0800 simpulse Syntax Description Arguments Examples Related sim3pulse Applicability Syntax Chapter 3 Pulse Sequence Statement Reference shaped2Dgradient Generate arrayed shaped gradient pulse vgradient Generate dynamic variable gradient pulse Pulse observe and decouple channels simultaneously simpulse obswidth decwidth obsphase decphase RG1 RG2 double obswidth decwidth pulse lengths in sec codeint obsphase decphase variables for phase double RG1 gating delay before pulse double RG2 gating delay after pulse Gates the observe and decoupler channels The shorter of the two pulses is centered on the longer pulse while the amplifier gating occurs before the start of the longer pulse even if it is the decoupler pulse and after the en
334. erap statement takes 500 Us to execute The readuserap statement puts ina 500 us delay immediately after reading the user AP lines in order for the parser to parse and stuff more words into the FIFO before it underflows However this time may not be long enough and you may want to pad this time with a delay immediately following the readuserap statement to avoid FIFO underflow Depending on the actions in the pulse sequence your delay may need to be a number of milliseconds If there is an error in the read a warning message is sent to the host and a 1 is returned to the real time variable 2 4 Pulse Sequence Statements Phase and Sequence Control 98 As explained previously a series of internal variables named v1 v2 v1 4 are provided to perform calculations during real time while the pulse sequence is executing All real time variables are pointers to particular memory locations in the acquisition computer You do not change a real time variable rather you change the value in the memory location to which that real time variable points For example when we speak of v1 being set equal to 1 what we really means is that the value in the memory location pointed to by the real time variable v1 is 1 The actual value of v1 a pointer is not changed The two ideas are interchangeable as long as we recognize exactly what is happening at the level of the acquisition computer These internal real time variables can be used for a
335. ered If go is entered ipwrm is ignored by the pulse sequence use vlpwrm for this purpose Do not execute r1pwrm and ipwrm together as they cancel each other s effect value is the new linear modulator power level It can range from 0 0 to 4095 0 60 dB on YN TYTINOVA and UNITYplus about 6 dB on other systems device is OBSch observe transmitter or DECch first decoupler On the UNITYINOVA and UNITYplus only device can also be DEC2ch second decoupler or DEC3ch third decoupler label1 is the short character string to be given to the slider when displayed in the Acquisition window acqi program ipwrm power OBSch fpower ipwrm 2000 0 DECch dpwrm rlpwrm Set transmitter or decoupler linear modulator power Pulse observe transmitter with IPA All systems except MERCURY VX MERCURY and GEMINI 2000 irgpulse width phase RG1 RG2 label double width pulse length in sec codeint phase real time variable for phase double RG1 gating delay before pulse in sec double RG2 gating delay after pulse in sec char label slider label in acqi Functions the same as the rgpulse statement except that irgpulse generates interactive parameter adjustment IPA information when gf or go acqi is entered If go is entered irgpulse is the same as rgpulse width specifies the duration in seconds of the observe transmitter pulse phase sets the observe transmitter phase It must be a r
336. erly interpret ppm and label axes the identity of the nucleus in question and the corresponding nuclear 01 999165 00 A0800 VNMR 6 1C User Programming 293 Chapter 5 Parameters and Data 294 resonance frequency are needed These fields are related to the abscissa values ppm1 ppm2 and ppm3 in that the 1 2 and 3 are indices into the nucleus and nucfreq fields That is the nucleus for the axis with abscissa string ppm1 is the first entry in the nucleus field e nucleus is one entry H1 F19 same as VNMR tn parameter for each rf channel e g char nucleus H1 H1 e nucfreq is the nuclear frequency floating point used for each rf channel e g float nucfregq 200 067 200 067 Miscellaneous Fields e checksum is the checksum of the data Changes to the header do not affect the checksum The checksum is a 32 bit integer calculated by the gluer program e g int checksum 0787271376 e compression isa string with either the command needed to uncompress the data or a tag giving the compression method This field is not currently implemented End of Header A character specifies the end of the header If there is data it immediately follows this character The data should be aligned according to its data type For single precision floating point data the data is aligned on word boundaries Currently the end of header character is lt zero gt an ASCH NUL Transformations By editing so
337. ern double runtime User variable for total experiment time 01 999165 00 A0800 115 VNMR 6 1C User Programming Chapter 2 Pulse Sequence Programming Table 23 Imaging Variables continued Frequencies extern double resto Reference frequency offset extern double wsfrq Water suppression offset extern double chessfrq Chemical shift selection offset extern double satfrq Saturation offset extern double mtfrq Magnetization transfer offset Physical Sizes and Positions for slices voxels and FOV extern double pro FOV position in readout extern double ppe ppe2 ppe3 FOV position in phase encode extern double posl pos2 pos3 Voxel position extern double pss MAXSLICE Slice position array extern double lro Readout FOV extern double lpe lpe2 lpe3 Phase encode FOV extern double lss Dimension of multislice range extern double vox1 vox2 vox3 Voxel size extern double thk Slice or slab thickness extern double lpe lpe2 lpe3 Phase encode FOV extern double fovunit Dimensional conversion factor extern double thkunit Dimensional conversion factor Bandwidths extern double sw1 sw2 sw3 Phase encode bandwidths Counts and Flags extern double nD Experiment dimensionality extern double ns Number of slices extern double ne Number of echoes extern double ni Number of standard increments extern double nv nv2 nv3 Number phase encode views extern double ssc Compressed ss transients extern double tic
338. errrrrsreresre 48 shell St rt x UNIX shell i sessisdscosstevteaieascdbsbas stat cobsesavee lachabcvedbastsasesanevens 48 solppm Return ppm and peak width of solvent resonances cesses 48 substr Select a substring from a String 0 ee eeeeeeeseeceeseeeeceteeceseseeeeeeeeneenees 49 textis Return the current text display status 00 0 eles ceeeeeeceeeeeeeeeeeeeeeee 49 unit Define conversion UNIES 0 0 eee eseeeeesecseceeeecsecaeeeceeesaecereeceeeneeseeat 49 1 4 Using Dialog Boxes from a Macro o cceeccessessessseeseceseeseceseesecaseesecesceseeeeeseeececaeeeseeaeecaecaaecaecaeeeeneeeeensees 49 1 5 Customizing the Menu Systemi o s cccccccsccccescectesoceesecensvedeiecuicestsessbocseseseasossssncoodesbessedncecbaessdstscendevtess 52 Customizing the Permanent Menm oc i02 c lt ceskcsccisp esses sxc casnecesnosdasieds devsteqvissivs oz E Oa E RT sie 52 Customizing Meny Piles and Help Piles c cciauitia aii niadieiiadsiniiacdsien audiences 53 Controline MENiS sessin neess oeo arn neee E o E REEE REAR EEEE E ERNE ETAS 55 Programmi Men s s errorecrersee grrr ranean e ae Ea EEE E E RE EE EE eira E E EPT DC ESENE EErEE 55 User Proprammable Menus in Interactive Programs c scccccscesessecaccosseovesssseensasvesiivsspsnssesusoveeeesens 57 1 6 Customizing the Piles Men s wis ccasccsccscsescssescassscisscteaeescnevsanesdaieveanes nse earn te aroki anirai io ERR Ee Esi 58 PLACE ie Prorail sseni naetne Eeee e ci ee EE S Ed E EE ERASERS
339. erting some macrold commands into your login macro Macros are also loaded into memory when you use the macrovi or macroedit commands to edit the macro The only argument in each is the name of the macro file for example enter macrovi pa ormacroedit pa ifthe macro name is pa Which command you use depends on the type of macro and the text editor you want For a user macro from the UNIX vi editor use macrovi e For a user macro from an editor you select use macroedit e To edit a system macro copy the macro to your personal macro directory and edit it there with macrovi or macroedit To select the editor for macroedit set the UNIX variable vnmreditor to its name vnmreditor is set through the UNIX env command You must have also a script for VNMR 6 1C User Programming 01 999165 00 A0800 1 2 Programming with MAGICAL the editor in the bin subdirectory of the VNMR system directory For example you can select Emacs by setting vnmreditor emacs and having a script vnmr_emacs Several minor problems need to be considered in loading macros into memory e These macros consume a small amount of memory In memory critical situations you might want to remove one or more macros from memory This is done with the purge lt file gt command where file is the name of a macro file to be removed from memory Entering purge with no arguments removes all macros loaded into memory CAUTION The purge command with no arguments should
340. es 180 Decrement an integer vale ooo eee eee cee cee ese ceeeeeeceeeeeeteeeeeeeeeeeeeees 180 Pulse first decoupler with amplifier gating cece eeeeeeeneeeeeeee 181 Pulse second decoupler with amplifier gating 0 eee eeeeeseeeeeeeee 182 Pulse third decoupler with amplifier gating 0 0 ieee eeeeeseeteeeeeeee 182 Pulse fourth decoupler with amplifier gating 0 eee eeeeeeeeeeeeee 183 Perform shaped pulse on first decoupler csceeceeseeseeeeeeeeeeeeeeeees 183 Perform shaped pulse on second decoupler cssssesseeeeseeeeeeeees 184 Perform shaped pulse on third decoupler ceeeseseeseeeeeeeeeeeeees 185 Set spin lock waveform control on first decoupler 0 0 00 cesses 186 Set spin lock waveform control on second decoupler eeeee 187 Set spin lock waveform control on third decoupler 0 0 0 cesses 187 Set step size for first decoupler 00 eee eeeeeseeeeeseeseceeeeceseseeeeeeeeeenees 188 Set step size for second decoupler 0 ceeeeseceeseeseceeeeceeseeeeeeeeneenees 188 Set step size for third decouple ce eeeeseseeseeseceeeeceeeeeeeeeeeseenees 189 Unblank amplifier associated with first decoupler 00 cesses 189 Unblank amplifier associated with second decoupler eeee 189 Unblank amplifier associated with third decoupler 0 00 eee 189 Delay for a specified time oo eee eeeeeeectecseeseeseceeeeeeseaeeeseeeaeseeeeeaes 190 Switch decoupling from low power to high p
341. es N type connectors instead by BNC connectors on the magnet leg Valid values of Legrelay are the following e n means to use normal logic to set the magnet leg relay e h means to set the leg relay to high band e 1 means to set the leg relay to low broad band Any other value will result in an error message and PSG will abort The legrelay parameter normally does not exist but can be created with the command create legrelay string 01 999165 00 A0800 VNMR 6 1C User Programming 147 Chapter 2 Pulse Sequence Programming 2 14 Multidimensional NMR 148 A standard feature of all pulse sequences is the ability to array acquisition parameters and automatically acquire an array of the corresponding FIDs For example arraying the pw parameter and viewing the resulting array of spectra is one way to estimate the 90 degree pulse width This explicit array feature is automatic whenever a parameter is set to multiple values such as pw 5 6 7 8 9 10 A separate type of arrayed data set are the 2D 3D and 4D data sets The distinguishing feature of this type of data set is that the arrayed element has a uniform automatically calculated increment between values The ni parameter is set to the number of increments desired in the first indirect dimension of a multidimensional data set The inverse of the parameter sw1 defines the increment in successive values of the implicitly arrayed delay d2 For example if ni 8 an implicit d2 array
342. es with implicit acquisition the decoupler phase is set to 0 automatically within the test 4acq procedure in the module hwlooping c in vnmr psg so under most circumstances no problems are seen But if you are using explicit acquisition or if you are trying to perform WALTZ decoupling during a period other than acquisition you must use a decphase zero statement in the pulse sequence before the relevant time period Setting Small Angle Phase Shifts Setting the small angle phase of rf pulses is implemented by three different methods e Fixed 90 settings e Direct synthesis hardware control e Phase pulse phase shifting The statements related to these methods are summarized in Table 11 None of these statements apply to the GEMINI 2000 Table 11 Phase Shift Statements dcplrphase multiplier Set small angle phase of first decoupler rf type C or D dcplr2phase multiplier Set small angle phase of second decoupler rf type C or D dcplr3phase multiplier Set small angle phase of third decoupler rf type C or D decstepsize base Set step size of first decoupler dec2stepsize base Set step size of second decoupler dec3stepsize base Set step size of third decoupler obsstepsize base Set step size of observe transmitter phaseshift Set phase pulse technique rf type A or B stepsize base device Set small angle phase step size rf type C or D xmt rphase multiplier Set small angle phase of observe transmitter rf
343. eset various gate lines to turn on and off pulses phase shift lines etc but activate the timing circuitry in the same way Timing is accomplished as follows e The Data Acquisition Controller board uses one time base of 12 5 ns e Other acquisition controller boards use four time bases 1 s 1 ms 1 us and 0 1 us for Output boards or 25 ns for Acquisition Controller and Pulse Sequence Controller boards For each time base the counter can count from 2 to 4095 A maximum of two time bases is used to time any delay with the smallest time base possible being used e MERCURY VX and MERCURY uses two time bases 0 1 us and 1 ms As many events as needed are used Delays greater than 96 seconds use a hard loop For example consider a pulse of 35 us on an Output board This produces a count of 350 in the 0 1 us time base and generates a single event in a hardware loop On the other hand consider a delay of 542 4 us This time cannot be generated solely in the lowest time base so it generates two timed events a count of 542 in the 1 us time base and a count of 4 in the 0 1 us time base Thus 542 4 us generates two events in a hardware loop however a delay of 542 0 us generates only one event since it can be made fully with the 1 us time base The final point to understand is that some things that look like one event may actually be more Consider for example the statement rgpulse pw v1 rof1 rof2 Does this generate a single event No it
344. et to zero or insert a zero_all_gradients statement Note that vashapedgradient assumes the gradient pattern zeroes the gradients at its end and it does not explicitly zero the gradients vashapedgradient is used if there are actions to be performed while the gradients are on pattern is a text file that describes the shape of the gradient The text file is located in Svnmrsystem shapelib or in the users directory Svnmruser shapelib gradlv1 is the gradient amplitude in gauss cm gradt ime is the time in seconds to apply the gradient theta is the angle in degrees from the z axis phi is the angle of rotation in degrees about the xy plane loops is a value from 0 to 255 to loop the selected waveform Gradient waveforms on the Y TYTNOVA do not use this field and it should be set to 0 wait is a keyword either WAIT or NOWAIT that selects whether or not a delay is inserted to wait until the gradient is completed before executing the next statement vashapedgradient ramp_hold 3 0 trise 54 7 0 0 0 NOWAIT pulse pw oph delay 0 001 pw 2 trise vashapedgradient ramp_down 3 0 trise 54 7 0 0 0 NOWAIT magradient Simultaneous gradient at the magic angle magradpulse Simultaneous gradient pulse at the magic angle mashapedgradient Simultaneous shaped gradient at the magic angle mashapedgradpulse Simultaneous shaped gradient pulse at the magic angle vagradient Variable angle gradient vagradpulse Variable ang
345. eters supplied to it by go together with a series of instructions that form the pulse sequence 01 999165 00 A0800 VNMR 6 1C User Programming 101 Chapter 2 Pulse Sequence Programming The output of the pulse sequence program in seqlib isa table of numbers known as the code table generally referred to as Acodes or Acquisition codes which contains instructions for executing a pulse sequence in a special language The pulse sequence program sends a message to the acquisition computer to begin operation informing it where the code table is stored This code table is downloaded into the acquisition computer and processed by an interpreter which is executing in the acquisition computer and which controls operation during acquisition If after entering go or su etc the message that PSG aborted abnormally appears run the psg macro to help identify the problem A pulse sequence can intermix statements involving C such as d2 1 0 2 0 J with special statements such as hlv ct v2 These two statements are fundamentally different kinds of operations When you enter go all higher level expressions are evaluated once for each increment Thus in d2 1 0 2 0 J the value of J is looked up d2 is calculated as one divided by 2 J and the value of d2 is fixed Statements in this category are called run time since they are executed when go is run The h1v statement however is executed every transient Before each transient the system examines
346. eters used in the following Vnmr Cmd and Tcl Cmd fields This can be zero or more parameter names MAGICAL expression sent to VNMR Any specified VNMR parameters can be used Their value is accessed by prepending a dollar sign see example below One special variable is also available That is the value of the typed in entry The value is accessed by the keyword VALUE Tcl expression that is evaluated to determine the value displayed by this entry item Any legitimate Tcl expression is allowed VNMR 6 1C User Programming 333 Chapter 6 Customizing Graphics Windows 334 Show Condition Tcl expression that is evaluated to determine whether the value background should be grayed out If it evaluates to false the color specified in dg conf by dgLocal off is used To access the values of any VNMR parameters specified in the Vnmr Variables list prepend a dollar sign to the front of the parameter name The basic example for setting a Vnmr variable would be the following Vnmr Variables bs Vnmr Cmd bs VALUE Tcl Cmd Sbs Show Condition vnmrOn bs The Vnmr Variables field requests access to the VNMR parameter bs The Vnmr Cmd field constructs a MAGICAL expression where bs is set to the value entered into this entry widget The Tcl Cmd field states how the value displayed in the entry field is determined When a value is entered the field is updated according to the instructions in the Tcl Cmd field If a nonsense value
347. etween gating the first decoupler off and gating the amplifier off decshaped_pulse sinc pl v5 rofl rof2 apshaped_decpulse First decoupler pulse shaping via AP bus dec2shaped_puls Perform shaped pulse on second decoupler dec3shaped_puls Perform shaped pulse on third decoupler shaped_pulse Perform shaped pulse on observe transmitter simshaped_pulse Simultaneous two pulse shaped pulse sim3shaped_pulse Simultaneous three pulse shaped pulse dec2shaped_pulse Perform shaped pulse on second decoupler Applicability Syntax Description Systems with a waveform generator on rf channel for the second decoupler dec2shaped_pulse pattern width phase RG1 RG2 char pattern name of RF text file double width width of pulse in sec codeint phase real time variable for phase double RG1 gating delay before pulse in sec double RG2 gating delay after pulse in sec Performs a shaped pulse on the second decoupler If a waveform generator is configured on the channel it is used otherwise the linear attenuator and the 184 VNMR 6 1C User Programming 01 999165 00 A0800 Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference small angle phase shifter are used to effectively perform an apshaped_dec2pulse statement When using the waveform generator the shapes are downloaded into the waveshaper before the start of an experiment When dec2shaped_pulse is cal
348. example above is with the following Label of element Value of choices Vnmr Variables Vnmr Cmd Tcl Cmd Expl Exp2 Exp3 Exp4 Exp5 Exp6 Exp7 Exp8 Exp9 xpl exp2 exp3 exp4 exp5 exp6 exp7 exp8 exp9 curexp J SVALUE file tail S curexp Some might claim the second Tc1 Cmd expression is simpler Menu2 Element The menu2 element gives a number of choices in a drop down menu A label can be displayed to the left of the menu2 button and the current selection is displayed inside the menu2 button This button is distinguished from the button element by a second small rectangle imbedded in the button The available characteristics are the following Label of element Choices Value of choices Vnmr Variables Vnmr Cmd 336 VNMR 6 1C User Programming Text string to be displayed to the left of the menu box This field is optional Set of text strings to be displayed in the drop down menu If the text for a given choice is more than one word it must be enclosed in double quotes It must be filled in with at least one choice The label of the currently selected choice is displayed in the menu box List of values the variable VALUE accessed as SVALUE will be set to The number of values must match the number of choices If a value is more than a single word it must be enclosed in double quotes List of VNMR parameters to be used in the following Vnmr Cmd
349. extension If ile_inde x is not specified the return argument contains the number of files in the directory dot files are not included in the count Return the current graphics display status graphis command yes_no graphis display_command Determines what command currently controls the graphics window If no argument is supplied the name of the currently controlling command is returned Determine length of a string length string string_length Determines the length in characters of the given string Disable receipt of messages from send2Vnmr Deletes file Svnmruser talk disallowing UNIX command send2Vnmr to send commands to VNMR Enable receipt of messages from send2Vnmr Writes files with VNMR port number that UNIX command send2Vnmr needs to talk to VNMR The command then to send commands to VNMR is vomr bin send2Vnmr vnmruser talk command where command is any character string Commands macros or if statements normally typed into the VNMR input window User macro executed automatically when VNMR activated When VNMR starts the boot up macro executes and then if the login macro exists boot up executes the login macro By creating and 47 VNMR 6 1C User Programming Chapter 1 MAGICAL II Programming off Syntax Description on Syntax Description readlk Syntax Description rtv Syntax Description shell Syntax Description solppm Syntax Description 48 VNMR 6 1C User Programm
350. f Unblank amplifier channels and turn amplifiers on blankingon Blank amplifier channels and turn amplifiers off decblank Blank amplifier associated with the 1st decoupler dec2blank Blank amplifier associated with the 2nd decoupler dec3blank Blank amplifier associated with the 3rd decoupler decoff Turn off first decoupler dec2off Turn off second decoupler dec30ff Turn off third decoupler decon Turn on first decoupler dec2on Turn on second decoupler dec3on Turn on third decoupler decunblank Unblank amplifier associated with the 1st decoupler dec2unblank Unblank amplifier associated with the 2nd decoupler dec3unblank Unblank amplifier associated with the 3rd decoupler dhpflag TRUE FALSE Switch decoupling between high and low power levels initparms_sis Initialize parameters for spectroscopy imaging sequences obsblank Blank amplifier associated with observe transmitter obsunblank Explicitly enables the amplifier for the observe transmitter revroff Turn off receiver gate and amplifier blanking gate revron Turn on receiver gate and amplifier blanking gate recoff Turn off receiver gate only recon Turn on receiver gate only setstatus Set status of observe transmitter or decoupler transmitter status state Change status of decoupler and homospoil statusdelay state time Execute status statement with given delay time xmtroff Turn off observe transmitter xmtron Turn on observe trans
351. f statement gate DECUPLR2 TRUE bya dec2on statement gate DECUPLR2 FALSE byadec2off statement gate RXOFF TRUE bya rcvroff statement gate RXOFF FALSE bya rcvron statement XON FALSE bya xmtroff statement XON TRUE bya xmtron statement gate gate Get arrayed parameter values Not applicable on MERCURY VX MERCURY and GEMINI 2000 number getarray parname array char parname parameter name double array starting address of array Retrieves all values of an arrayed parameter from the parameter set It performs a sizeof on the array address to check for the maximum number of statements that the array can hold The number of statements in the arrayed parameter parname is determined and returned by get array as an integer This statement is very useful when reading in parameter values for a global list of PSG statements such as poffset_list and position_offset_list When creating an acquisition parameter array that will be treated as lists protection bit 8 256 is set if the parameter is not to be treated as an arrayed acquisition parameter An example of the pss parameter when compressing slice select portion of the acquisition is create pss real setprotect pss on 256 number is an integer return argument that holds the number of values in parname parname is a numeric parameter either arrayed or single value array is the starting address of an arra
352. f it is a standard VNMR command If the program is not a command the command interpreter then attempts to find a macro with the program name Unlike a built in VNMR command which VNMR 6 1C User Programming 01 999165 00 A0800 1 1 Working with Macros is a built in procedure containing code that normally cannot be changed by users the code inside a macro is text that is accessible and can be changed by users as needed If a VNMR command and a macro have the same name the VNMR command always takes precedence over a macro For example there is a built in VNMR command named wft If someone happens to write a macro also named wft the macro wft will never get executed because the VNMR command wft takes precedence To get around this restriction the hidecommand command can rename a command so that a macro with the same name as a command is executed instead of the built in command If the user who wrote the wft macro enters hidecommand wft the command is renamed to Wft first letter made upper case and the macro wft is now executable directly The new wft macro can access the hidden wft built in command by calling it with the name Wft To go back to executing the command wft first enter hidecommand Wft Macro files can reside in four separate locations 1 Inthe user s maclib directory 2 Inthe directory pointed to by the maclibpath parameter if maclibpath is defined in the user s global parameter file 3 In the directory pointed
353. f the components for the static portion of the gradient in the logical reference frame step2 step3 are values in gauss cm of the components for the step size change in the variable portion of the gradient vmult2 vmult3 are real time math variables v1 to v14 ct zero one two three or references to AP tables t 1 to t 60 whose associated values vary dynamically in a manner controlled by the user pe2_gradient gro sgpe nv 2 0 sgpe2 nv2 2 0 sgpe sgpe2 v6 v8 pe3_gradient Oblique gradient with phase encode in 3 axes Oblique gradient with phase encode in three axes Not applicable on MERCURY VX MERCURY and GEMINI 2000 224 VNMR 6 1C User Programming 01 999165 00 A0800 Syntax Description Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference pe3_gradient statl stat2 stat3 stepl step2 step3 vmultl1 vmult2 vmult3 double statl stat2 stat3 static gradient components double stepl step2 step3 gradient step sizes codeint vmultl vmult2 vmult3 real time variables Sets three oblique phase encode gradients This statement is the same as phase_encode3_gradient except the Euler angles are read from the default set for imaging lim1 lim2 and lim3 are set to nv 2 nv2 2 and nv3 2 respectively Pulse sequence generation aborts if the DACs on a particular gradient are overrun after the angles and amplitude have been resolved statl stat2 stat3 are va
354. fault2d display templates 306 defaultold2d display templates 306 delay create delays table 165 for synchronizing sample rotor 241 initialize 207 interincrement 103 intertransient 103 parameter type 299 real time incremental 203 routine 199 specified time 190 specified time with IPA 202 timebase fixed and real time count 268 with possible homospoil pulse 201 delay statement 79 124 128 190 delay related statements 79 delays initializing next for hardware shimming 200 delays entry 66 delcom command 44 deleting files UNIX 278 01 999165 00 A0800 deleting user macros 44 destroy command 301 destroygroup command 301 device gating 196 df command 57 dfid command 57 dg command 304 dg parameter 304 dg program 328 dg window 324 dg conf file 328 dg conf file listing 329 dg info file 328 dgl macro 304 dg2 macro 304 dg2 parameter 305 Dgroup attribut 342 Dgroup field 302 Dgroup of a parameter 301 dgs macro 304 dhp parameter 93 171 dhpflag statement 96 diagram of a pulse sequence 63 diff command UNIX 279 differentially compare files UNIX 279 diffusion analysis 42 digital resolution measurement 38 dimensioning statement 33 directory information 47 disk blocks 285 disk cache buffering 284 disk file errors 77 Display button 59 display command 301 display template 304 display templates 305 displaying confirmer window 41 controlling pulse sequence graphical display 1
355. fdfgluer program Use the syntax fdfgluer header_file lt data_file lt output_file gt gt from UNIX only VNMR 6 1C User Programming 01 999165 00 A0800 5 3 Reformatting Data for Processing This program takes aheader_file anda data_file and puts them together to form an FDF file It also calculates a checksum and inserts it into the header If the data_file argument is not present dfgluer assumes the data is input from the standard input and if the output_file name is not present fdfgluer puts the FDF file to the standard output Splitting FDF Files The dfsplit command takes an FDF file and splits it into its data and header parts The syntax is fdfsplit fdf_file data_file header_file from UNIX only If the header still has a checksum value that value should be removed 5 3 Reformatting Data for Processing Sometimes data acquired in an experiment has to be reformatted for processing This is especially true for in vivo imaging experiments where time is critical in getting the data so experiments are designed to acquire data quickly but not necessarily in the most desirable format for processing Reformatting data can also occur in other applications because of a particular experimental procedure The VNMR processing applications ft 2d and ft 3d can accept data in standard compressed or compressed compressed 3D data formats There are a number of routines that allow users to reformat their data into these formats for
356. file and compiles the pulse sequence Some messages appear in the text window and then the output is saved in the user pulse sequence directory If you have followed this procedure correctly a homonuclear 2D J pulse sequence is now ready to use You can view it graphically by entering dps in the input window Notice that you have just used a few keystrokes and the mouse to write a complete computer program in the C language Pulse Sequence Programming Menus By clicking the buttons Main Menu gt More gt Write Pulse Sequence many pulse sequence entry menus are available on your system to help you program pulse sequences including the following menus Pulse Sequence Entry Main Menu Pulse Sequence Entry Delay Menu D1 D2 0272 D3 MIX Other Allow Homospoil Return Pulse Sequence Entry Phases Menu SELECT PHASE Use Previous x Y x Y Fixed o More Pulse Sequence Entry Phases Secondary Menu Pulse Sequence Entry Pulses Menu Pul Pal 2Pul 2P1 Other Return Pulse Sequence Entry Decoupler Pulses Menu PP 2PP Other Return Pulse Sequence Entry Status Menu A B c D Revron Revroff Set Revr Phase Return The only tricky part is that the Pulse Sequence Entry Pulses Menu and Pulse Sequence Entry Decoupler Pulses Menu are not directly accessible from the Main Menu Instead any time a pulse is called for a phase menu appears for you to set phase and then the appropriate pulse menu appears for you to
357. flammable gases warning 20 FLASH pulse sequence 96 flashc command 296 flexible data format files See FDF files flip between graphics and text windows 40 flip command 40 floating constant 30 floating point 32 float type variables 74 flush command 284 288 fm fm modulation 243 fn parameter 288 focus command 47 format command 40 format of weighting function 308 formatting for output 40 forward slash notation UNIX 278 Fourier transform process 288 fourth attenuator 139 fourth decoupler offset frequency 173 power level 176 pulse with receiver gating 183 quadrature phase 175 fractions in integer mathematics 99 framework for pulse sequences 72 fread command 301 frequency control 90 create frequencies table 166 offsets table 167 set based on position 231 set from position list 232 set on position 232 table indexing 270 frequency and intensity from line list 38 01 999165 00 A0800 frequency limits of region 38 frequency lists 166 frequency offset lists 272 frequency offset routine 122 199 frequency type parameter 299 fsave command 284 301 ft command 288 ft3d command 284 function keys 52 G G_Delay general routine 120 123 199 G_Offset general routine 120 122 199 G_Power general routine 120 125 199 G_Pulse general routine 120 121 124 200 gap command 47 GARP modulation 243 gate pulse sequence from an external event 275 gate statement 196 gating control statemen
358. following dp n single precision 16 bit data dp y double precision 32 bit data 16 bit single precision 16 bit data 32 bit double precision 32 bit data If an FID file already exists format is the precision of data in that file Otherwise the default for format is 32 bits The number of points comes from the number of numeric values read from the file Remember it reads only two values per line If the current experiment already contains a FID you will not be able to change either the format or the number of points from that present in the FID file Use the command rm curexpt acqfil fid to remove the FID The makefid command does not look at parameter values when establishing the format of the data or the number of points in an element Thus if the FID file is not present it is possible for make fid to write a FID file with a header that does not match the value of dp or np Since the active value is in the processed tree you will need to use the set value command if any changes are needed Be aware that makefid can modify data returned to an experiment by the rt command To avoid this enter the following sequence of VNMR commands on the saved data before running makefid cp curexpt acqfil fid curexp acqfil fidtmp rm curexpt acqfil fid mv curexp acqfil fidtmp curexp acqfil fid The command writefid textfile lt element_number gt writes a text file using data from the selected FID elem
359. for exclusive selection of a choice That is if you press choice a and then choice b choice a is deselected The User identification and Solvent Selection window panes are examples of the xradio style If the style for the exp parameter is changed from radio to xradio then the user can only select a single experiment In the default setup a user can select multiple experiments on a single sample location A user can also select one or more experiments on a number of sample locations When multiple samples and experiments are selected then enterQ is ordered to minimize robot usage by finishing all experiments on a sample before putting the next sample into the magnet If the style of the Loc selection is changed from radio to xradio the user can select only a single location The Sample Location buttons use the right mouse button to facilitate selecting multiple locations The left mouse button selects and deselects an item just as it does for all the check boxes A single click of the right mouse button on one of the location check boxes selects that location and all preceding locations down to the next selected location For example a left mouse click on location 10 selects it A right mouse click on 14 selects locations 14 13 12 and 11 A double click of the right mouse button on a location deselects that location and all preceding locations down to the first deselected location Alternate Interfaces Figure 10 shows an interface in which
360. from bs to 1 during each block of transients After completing the last transient in the block bsctr is set back to a value of bs Thus if bs 8 bsctr has successive values of 8 7 6 5 4 3 2 1 8 7 oph Real time variable that controls the phase of the receiver in 90 increments 0 0 1 90 2 180 and 3 270 Prior to the execution of the pulse sequence itself oph is set to 0 if parameter cp is set to n or to the successive values 0 1 2 3 0 1 2 3 if cp is set to y The value of oph can be changed explicitly in the pulse sequence by any of the real time math statements described in the next section assign add etc and is also changed by the setreceiver statement zero one two Pointers to constants set to select constant phases of 0 90 180 three and 270 They cannot be replaced by numbers 0 1 2 and 3 ssval ssctr Real time variables described in Manipulating Acquisition bsval Variables page 102 id2 id3 id4 Pointers or indexes to constants identifying the current increment in multidimensional experiments id2 is the current d2 increment Its value ranges from 0 to the size of the d2 array minus 1 which is typically 0 to ni 1 id3 corresponds to current index of the d3 array in a 3D experiment Its range is 0 to ni2 1 id4 corresponds to the current index of the d4 array Its range is 0 to ni3 1 Calculating in Real Time Using Integer Mathematics A series of special integ
361. g Transmitter Quadrature Phase SMIS soni siceisiccsssctiosiesstheedbsesbtdarsscsudealensobecbssctsdaevens senveevys 85 Setting Small Amele PHASE Shifts s 5 ccs ccsccssenedascesvarsandaseosesvsseseapssensesinsceaesteacscopnesniaseaaevensiesvsesy 86 Controlling the Offset Frequency isisisi heidi iae Aedes a A aia aa 90 Controlling Observe and Decoupler Transmitter PoWer oo eeeeeecceeceseceeeeeeeeeeeeeecoeesaesnaeaeenees 91 Controlling Stans and Gang 2 2 03 tains tei astiia aida diane ti es ailerons 93 Interface to Extemal User Devices sei becsccdscscesesiecsctecstensneo at eovecees essouseatesescesageoraistiennsapentecseeesstes 97 2 4 Pulse Sequence Statements Phase and Sequence Control ooo cece eeeeeeseeeeeeeeseecaeeaecaeceaeeneeseeeeeesees 98 Real Time Variables arid Constants xc c cc oss casiece ced oises scvscnevs estes steeed sosstdovansancesebsnsanevssnstesuevbst svbsaoeds 98 Calculating in Real Time Using Integer Mathematics cece eeeeeseeeseeseceeceseeeeeeeeeeaeeeseaeeseeenees 99 Controlling a Sequence Using R al Time Variables ocesecsicscsassies cs eseseectsascossestssusvecnsvoedearicescete 100 Real Time vs Run Time When Do Things Happen s ccsicccccscsssscusescesssvusescisssetesseessvsaseeascesvaces 101 Manipulatins Acquisition Variables iocis enne ne EEEE E EECa E E EEEE EE EEEE ETE E KEA 102 Interttansient and Interincrement Delays i 5 c sssatveissspsdessdeerensessdesaiabenseecaseotaiesbuaensddavcsnesdisessante 103 Con
362. gate events rotorperiod Obtain rotor period of MAS rotor Gated pulse sequence delay from MAS rotor position rocorsync Turn off observe transmitter xmtroff Explicitly gates off the observe transmitter in the pulse sequence xmtron Turn on observe transmitter Turn on observe transmitter xmtron Explicitly gates on the observe transmitter in the pulse sequence Transmitter gating is handled automatically by the statements obspulse pulse rgpulse shaped_pulse simpulse sim3pulse simshaped_pulse sim3shaped_pulse and spinlock The obsprgon statement generally needs to be enabled with an explicit xmt ron statement and followed by a xmt rof f call xmtroft Turn on observe transmitter Set transmitter small angle phase rf type C D All systems except GEMINI 2000 xmtrphase multiplier codeint multiplier real time AP variable Sets the phase of transmitter in units set by the st epsize statement The small angle phaseshift is a product of mult iplier and the preset step size for the transmitter If st epsize has not been used the default step size is 90 If the product of the step size set by the stepsize statement and multiplier is greater than 90 the sub 90 part is set by xmt rphase Carryovers that are multiples of 90 are automatically saved and added in at the time of the next 90 phase selection such as at the time of the next pulse or decpulse 275 VNMR 6 1C User Programming Chapter 3
363. ge lower filename or lower inputfile outputfile esac In the first script only one form of input is allowed but in the second script not only is a second form of input allowed but a prompt explaining how to use lower appears if the user enters Lower without any arguments Notice that in both scripts a colon is used to identify lines containing comments and that each script is carefully commented 282 VNMR 6 1C User Programming 01 999165 00 A0800 Chapter 5 Parameters and Data Sections in this chapter e 5 1 VNMR Data Files this page e 5 2 FDF Flexible Data Format Files page 290 e 5 4 Creating and Modifying Parameters page 298 e 5 5 Modifying Parameter Displays in VNMR page 304 e 5 6 User Written Weighting Functions page 307 e 5 7 User Written FID Files page 310 5 1 VNMR Data Files Although a number of different files are used by VNMR to process data VNMR data files use only two basic formats e Binary format Stores FIDs and transformed spectra Binary files consist of a file header describing the details of the data stored in the file followed by the spectral data in integer or floating point format Because of the different representations of integer and floating point numbers on different computer systems binary files cannot be copied between VAX and Sun systems without a conversion step On Sun systems integers are 32 bits wide and are stored byte by byte with the mo
364. ge of transmitter power Therefore if you pulse at low power with a certain phase and later at high power with the same phase the two phases are the same to within 5 at any one power level the phase is constant to considerably better than 0 5 The time of the power change is specified in Table 32 On UNITY and VXR S systems the power change is somewhat discontinuous and it is advisable although not strictly necessary to change the power level at a time when the observe pulse is not turned on then to allow a minimum of 4 us before using a transmitter pulse On systems with an Output board only see page 72 for the types of acquisition controller board the power and associated statements are preceded internally by a 0 2 us delay by default see the apovrride pulse statement for more details CAUTION On systems with linear amplifiers be careful when using values of power obspower decpower dec2poser and dec3power greater than 49 about 2 watts Performing continuous decoupling or long pulses at power levels greater than this can result in damage to the probe Use config to set a safety maximum for the tpwr dpwr dpwr2 and dpwr3 parameters Fine Power Control To change the fine power of a transmitter or decoupler by adjusting the optional linear fine attenuators use pwrf value device or pwrm value device The value argument is real time variable which means it cannot be placed directly in the pwrf or pwrm stateme
365. gent of two numbers 43 argument number 35 arguments passed to commands and macros 27 array defined 32 arraydim parameter 148 289 arrayed experiment 289 arrayed parameter values 196 arrayed shaped gradient generation 246 arrayed string variables 34 arrayed variables 31 33 arraying acquisition parameters 148 ASCII format 283 asin command 43 asm directory 311 assign integer values 164 assign statement 99 164 asterisk character 279 307 asynchronous decoupling 243 at parameter 117 atan command 43 atan2 command 43 attenuators based shaped pulses 138 attributes of parameter 302 attributes of variables 32 auto file 284 auto conf fuke 311 Autogain see automatic gain autogo command 315 autoincrement attribute 105 106 107 241 Autolock see automatic lock automatic execution of macros 302 automatic gain errors 76 automatic lock 346 VNMR 6 1C User Programming errors 76 automatic macro execution 28 automatic teller machine ATM cards caution 21 automatic variables 32 automation control window 322 automation file 284 automation run 311 autoSample button 319 autoSampleNoExit button 319 autoscale command 42 autoscaling 42 average command 43 average value of input 43 awc parameter 308 awk command UNIX 279 axis command 46 axis labels 46 axis parameter 46 B background process UNIX 279 background processing 281 backslash notation 30 backslash single quote
366. ger values assign Assign integer values dbl Double an integer value decr Decrement an integer value divn Divide integer values hlv Half the value of an integer mod2 Find integer value modulo 2 mod4 Find integer value modulo 4 modn Find integer value modulo n mult Multiply integer values sub Subtract integer values indirect Set indirect detection Applicability No longer useful to any system using VNMR 5 2 or later Syntax indirect Description Starting with VNMR 5 2 if tn is H1 and dn is not H1 the software init_rfpattern Applicability Syntax automatically uses the decoupler as the observe channel and the broadband channel as the decoupler channel Create rf pattern file Not applicable on MERCURY VX MERCURY and GEMINI 2000 init_rfpattern pattern rfpat_struct nsteps char pattern RFpattern rfpat_struct int nsteps typedef struct _RFpattern double phase a double amp JR double time name of RF text file pointer to struct RFpattern number of steps in pattern phase of pattern step amplitude of pattern step length of pattern step in sec Description Arguments Examples 01 999165 00 A0800 RFpattern Creates and defines rf patterns within a pulse sequence The patterns can be created by any algorithm as long as each pattern step is correctly put into the rfpat_struct argument The number of steps in the pattern also has to be furnished as an argument
367. getval parametername Look up value of numeric parameter Parameters are defined by the user in particular experiment files exp1 exp2 etc in which the operation is occurring These parameters are not the same as the parameters that are accessible to the pulse sequence during its execution although they are at least potentially the same Categories of Parameters Parameters can be divided into three categories e Parameters used in a pulse sequence exactly as in the parameter set in other words the name of the parameter d1 for example is the same in both places Thus a statement like delay d1 is legitimate Table 22 lists VNMR parameter names and corresponding pulse sequence generation PSG variable names and types Table 23 summarizes VNMR parameter names used primarily for imaging Not available on the GEMINI 2000 are d3 d4 dfrq2 dfrq3 dm2 dm3 dm4 dmf2 dmf3 dmm2 dmm3 dmm4 dof2 dof3 dof4 dpwr2 dpwr3 dowr4 dres dres2 dres3 dres4 dseq dseq2 dseq3 homo homo2 homo3 inc2D inc3D inc4D nf phase2 phase3 pwx satdly satpwr and satmode VNMR 6 1C User Programming 01 999165 00 A0800 2 6 Accessing Parameters Table 22 Global PSG Parameters Acquisition extern char il MAXSTR interleaved acquisition parameter y n o extern double inc2D tl dwell time in a 3D 4D experiment extern double inc3D t2 dwell time in a 3D 4D experiment extern double sw Sweep width extern dou
368. gradient elements used in the sequence These tags are used for variable amplitude pulses oblique_gradient oblique_shapedgradient pe_shapedgradient phase_ ncode3_shapedgradient Execute an oblique gradient Execute a shaped oblique gradient Oblique sh gradient with PE in 1 axis Oblique sh gradient with PE on 3 axes phase_encode3_shapedgradient Oblique shaped gradient with PE in three axes Not applicable on MERCURY VX MERCURY and GEMINI 2000 phase_encode3_shapedgradient pattern width statl stat2 stat3 stepl step2 step3 vmultl vmult2 vmult3 liml lim2 lim3 angl ang2 ang3 loops wait Applicability Syntax Description Arguments 230 char pattern double width double statl stat2 stat3 double stepl step2 step3 codeint vmultl vmult2 vmult3 double liml 1lim2 1im3 double angl ang2 ang3 int loops Le int wait name of gradient shape file width of gradient in sec static gradient components var gradient step sizes real time variables max gradient value steps Euler angles in degrees number of times to loop WAIT or NOWAIT Sets three oblique phase encode shaped gradient Note that this statement has a loops argument that is an integer as opposed to the vloops argument in phase_ ncode_shapedgradient It has no return value Pulse sequence generation aborts if the DACs on a particular gradient are over
369. guments At the end of the pulse the gradient is set to 0 value is the amplitude of the pulse It is a real number between 32768 and 32767 delay is any delay parameter such as d2 zgradpulse 1234 0 d2 dps_show Draw delay or pulses for graphical display of a sequence rgradient Set gradient to specified level vgradient Set gradient to level determined by real time math 2 6 VNMR 6 1C User Programming 01 999165 00 A0800 Chapter 4 UNIX Level Programming Sections in this chapter e 4 1 UNIX and VNMR this page e 4 2 UNIX A Reference Guide page 278 4 3 UNIX Commands Accessible from VNMR page 280 e 4 4 Background VNMR page 280 e 4 5 Shell Programming page 282 UNIX is among the most popular operating systems in the world today with hundreds of books written on every aspect of UNIX at every level This manual does not attempt to replace that material but attempts instead to provide a glimpse of the subject and then to guide you to resources that can paint a fuller picture 4 1 UNIX and VNMR Many VNMR software users do not need to have any contact with UNIX whatsoever Although the UNIX operating system is running the workstation at all times a user who wants to use only the Varian VNMR software package can do just that In some installations the system operator starts VNMR and different users simply sit down at the instrument and use the NMR software just as in the earlier generation
370. h an exceptionally responsive user programming environment that allows customizing the system software and the operator interface This manual explains how to use these capabilities Chapter 1 MAGICAL II Programming describes MAGICAL II MAGnetics Instrument Control and Analysis Language a powerful software application that enables full automation of spectrometer operation and data analysis using macros Chapter 2 Pulse Sequence Programming covers pulse sequence programming via menus as well as user written programs using Varian s powerful and extensive set of pulse sequence statements Chapter 3 Pulse Sequence Statement Reference is an alphabetical reference to each pulse sequence statement in VNMR Chapter 4 UNIX Level Programming is a short overview of UNIX the operating system used with VNMR Chapter 5 Parameters and Data covers manipulating parameters using data files modifying parameter displays and writing user defined weighting functions Chapter 6 Customizing Graphics Windows describes how to customize the interactive graphics display windows for the enter status and dg programs Notational Conventions The following notational conventions are used throughout all VNMR manuals Typewriter like characters identify VNMR and UNIX commands parameters directories and file names in the text of the manual For example The shutdown command is in the etc directory Typewr
371. h array element If a list is created the return value is the number of the list 0 to 255 if an error occurs the return value is negative create_offset_list creates what is called a global list Global lists are different from AP tables in that the lists are sent down to the acquisition console when the experiment starts up and are accessible until the experiment completes In working with arrayed experiments be careful when using a 1 in the 1ist_number argument because a list will be created for each array 01 999165 00 A0800 VNMR 6 1C User Programming 167 Chapter 3 Pulse Sequence Statement Reference element In this case a list parameter can be created as an arrayed parameter with protection bit 8 256 set To read in the values of this type of parameter use the get array statement To ensure that the list is only created once check the global array counter variable ix and only call create_offset_list to create the list when it equals 1 An example is shown in the entry for the create_delay_list statement Arguments list is a pointer to a list of frequency offsets nvals is the number of values in the list device is OBSch observe transmitter or DECch first decoupler For the UNITYINOVA and UNITYplus only device can also be DEC2ch second decoupler or DEC3ch third decoupler list_number is 1 or a unique number from 0 to 255 for each list created Examples See the example for the create_delay_list statement
372. h as 10 us on a GEMINI 2000 H 3C system about 1 us on a MERCURY VX MERCURY or GEMINI 2000 broadband system about 400 ns for rf type C less than 200 ns for rf type D used on UNITYplus and longer for types A and B you may wish to preset the transmitter phase at the beginning of a delay that precedes a particular pulse The normal pulse sequences use an rof 1 time preceding the pulse to change the transmitter phase and do not need to preset the phase The phase change will occur at the start of the next event in the pulse sequence The other phase control statements are variations of txphase e To set the decoupler phase use decphase phase The decphase statement is syntactically and functionally equivalent to txphase decphase is useful for a decoupler pulse in all cases where t xphase is useful for a transmitter pulse To set the quadrature phase of the second decoupler rf or third decoupler rf use dec2phase phase or dec3phase phase respectively On N YTINOVA MERCURY VX MERCURY GEMINI 2000 and UNITYplus the hardware WALTZ decoupling lines are XORed with the decoupler phase control The performance of the WALTZ decoupling should not be affected by the decoupler phase setting On UNITY and VXR S systems however the hardware WALTZ decoupling lines are ORed with the decoupler phase control As a consequence the decoupler phase must be set to 0 for WALTZ to function properly When using pulse sequenc
373. h many programming languages MAGICAL provides two classes of variables e Global variables also called external that retain their values on a permanent or semi permanent basis e Local variables also called temporary and automatic that are created for the time it takes to execute the macro in question after which the variables no longer exist Global and local variables can be of two types real and string Global real variables are stored as double precision 64 bit floating point numbers The real variable command creates a real variable without a value where variable is the name of the variable to be created Although global real variables have potential limits from 1e308 to 1e 308 when such variables are created they are given default maximum and minimum values of 1e18 and 1e18 these can subsequently be changed with the set 1imit command For example setlimit rl 1e99 1e99 0 sets variable r1 to limits of 1e99 and 1e99 Local real variables have limits slightly less than 1e18 9 999999843067e17 to be precise and cannot be changed String variables can have any number of characters including a null string that has no characters The command string variable where variable is the name of the variable to be created creates a string variable without a value Both real and string variables can have either a single value or a series of values also called an array Global and local variables have the following set
374. h the dps extensions fails the pulse sequence is recompiled without the dps extensions If the executable pulse sequence code is successfully produced it is stored in the user seqlib directory e g export home vnmril vnmrsys seqlib If the user does not have a seql ib directory it is automatically created Like psg1lib different seqlib directories exist including the system directory and each user s directory The user s vnmrsys directory should have directories psglib and seqlib Whenever a user attempts to run a pulse sequence the software looks first in the user s personal directory for a pulse sequence by that name then in the system directory A number of sequences are supplied in vnmr seqlib compiled and ready to use The source code for each of these sequences is found in vnmr psglib To compile one of these sequences or to modify a sequence in vnmr psglib copy the sequence into the user s psglib make any desired modifications then compile the sequence using seqgen seqgen will not compile sequences directly in vnmr psglib All sequences in vnmr psglib have an appropriate macro to use them VNMR 6 1C User Programming 01 999165 00 A0800 2 2 Overview of Pulse Sequence Programming Troubleshooting the New Pulse Sequence During the process of pulse sequence generation PSG with the seqgen command the user written C procedure is passed through a utility to identify incorrect C syntax or to hint at potential cod
375. hape file must be at least 10 us long and 2 the time for every element must be a multiple of 50 ns If the width of the pulse is less than 10 us times the number of steps in the shape a warning message is generated The shaped gradient software rounds each element to a multiple of 50 ns If the requested width differs from the actual width by more than 2 a warning message is displayed amp is a value that scales the amplitude of the pulse Only the integer portion of the value is used and it ranges from 32767 to 32767 where 32767 is full scale and 32767 is negative full scale channel selects the gradient coil channel desired and should evaluate to the characters x y or z Be sure not to confuse the characters x y or z with the strings x y or z Loops is a value from 1 to 255 that allows the user to loop the selected waveform Note that the given value is the number of loops to be executed and that the values 0 and 1 cause the pattern to execute once wait is a keyword either WAIT or NOWAIT that selects whether or not a delay is inserted to wait until the gradient is completed before executing the next statement The total time it will wait is width loops If loops is supplied as 0 it will be counted as 1 when determining its total time Examples shapedgradient hsine 0 02 32767 y 1 NOWAIT include standard h define POVR 1 2e 5 shaped pulse overhead 12 us pulsese
376. has nothing of interest in its pane The tab labeled Text is the text window of older versions of VNMR It is here that commands such as d11 display output Commands dg dgs etc still work and display their traditional output on this pane As soon as the text displayed is greater than the size of the pane a vertical scroll bar appear as an aide to navigation Menus A menu consists of either one or two elements Used on its own a menu may have a character string label element and a choice bar Used in conjunction with an Entry only VNMR 6 1C User Programming 01 999165 00 A0800 6 3 Customizing the Interactive dg Window the choice bar is seen The choice bar has a small rectangle embedded in it The choice bar also shows the current choice The left mouse button drops down the menu of choices when depressed while the mouse is on the choice bar Keep the button depressed and move the mouse to highlight the desired choice Release the mouse button and this will make the choice Buttons A button differs from a menu in a several ways First it has only one element a bar with a text string in it Second when clicked on with the mouse a button causes an action to occur in VNMR An example is the button in the FT amp Post FT pane marked Transform When pressed an Ft is performed Titles are often buttons You can tell if this is the case as inactive titles have no border Check Boxes A check box can have one o
377. he phase information into statements decpulse decrgpulse dec2rgpulse dec3rgpulse pulse rgpulse and simpulse is still expressed in units of 90 step_size is areal number or a variable for the phase step size desired device is OBSch observe transmitter or DECch first decoupler For the UNITYTNOVA and UNITYplus only device can also be DEC2ch second VNMR 6 1C User Programming 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference decoupler or DEC3ch third decoupler The step_size phase shift selected is active only for the xmt rphase statement if device is OBSch only for the dcplrphase statement if device is DECch only for the dcplr2phase statement if device is DEC2ch or only for the dcplr3phase statement if the device is DEC3ch Examples stepsize 30 0 OBSch stepsize step DEC2ch Related dcplrphase Set small angle phase of first decoupler rf type C or D dcplr2phase Set small angle phase of second decoupler rf type C or D dcplr3phase Set small angle phase of third decoupler rf type C or D decstepsize Set step size of first decoupler dec2stepsize Set step size of second decoupler dec3stepsize Set step size of third decoupler obsstepsize Set step size of observe transmitter xmtrphase Set small angle phase of observe transmitter rf type C sub Subtract integer values Syntax sub vi vj vk codeint vi real time variable for minuend codeint vj real time variable for subt
378. he given levels until they are turned off To turn off the gradients add another magradient statement with gradlv1 set to zero or insert the statement zero_all_gradients Arguments gradlv1 is the gradient amplitude in gauss cm 212 VNMR 6 1C User Programming 01 999165 00 A0800 Examples Related magradpulse Applicability Syntax Description Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference magradient 3 0 pulse pw oph delay 0 001 pw zero_all_gradients magradpulse Simultaneous gradient pulse at the magic angle mashapedgradient Simultaneous shaped gradient at the magic angle mashapedgradpulse Simultaneous shaped gradient pulse at the magic angle vagradient Variable angle gradient vagradpulse Variable angle gradient pulse vashapedgradient Variable angle shaped gradient vashapedgradpulse Variable angle shaped gradient pulse zero_all_gradients Zero all gradients Gradient pulse at the magic angle Not applicable on MERCURY VX MERCURY and GEMINI 2000 magradpulse gradlvl gradtime double gradlvl gradient amplitude in G cm double gradtime gradient time in sec Applies a simultaneous gradient pulse on the x y and z axes at the magic angle to Bo Information from a gradient table is used to scale and set values correctly magradpulse differs from magradient in that the gradients are turned off after gradt ime seconds Use magradpulse if there are n
379. he rf transmitter off and gating the amplifier off dec4rgpulse pl v10 rofl rof2 decpulse Pulse first decoupler with amplifier gating decrgpulse Pulse first decoupler with amplifier gating idecpulse Pulse first decoupler with IPA rgpulse Pulse observe transmitter with amplifier gating simpulse Pulse observe decoupler channels simultaneously sim3pulse Simultaneous pulse on 2 or 3 rf channels decshaped_pulse Perform shaped pulse on first decoupler Applicability Syntax Description UNITYINOVA and UNITY plus systems or systems with waveform generator on rf channel for the first decoupler decshaped_pulse pattern width phase RG1 RG2 char pattern name of RF text file double width width of pulse in sec codeint phase real time variable for phase double RG1 gating delay before pulse in sec double RG2 gating delay after pulse in sec Performs a shaped pulse on the first decoupler If a waveform generator is configured on the channel it is used otherwise the linear attenuator and the 01 999165 00 A0800 VNMR 6 1C User Programming 183 Chapter 3 Pulse Sequence Statement Reference Arguments Examples Related small angle phase shifter are used to effectively perform an apshaped_decpulse statement When using the waveform generator the shapes are downloaded into the waveshaper before the start of an experiment When decshaped_pulse is called the shape is add
380. he text file defining the menu buttons you can display this environment by entering the command env from UNIX For example if the GLIDE option is installed the vnmrmenu variable displayed by env is set to a file named vnmrmenu in the glide subdirectory VNMR 6 1C User Programming 01 999165 00 A0800 1 5 Customizing the Menu System If the vnmrmenu variable does not exist the default text file defining the menu is still named vnmrmenu but is instead located in the VNMR system directory The definition text file is a list of up to eight button descriptions Each menu button is defined with three fields e The first field is the word Function The second is the action to be performed when that button is pressed The available actions are the following abort Abort acquisition cancel Cancel the current VNMR command glide Toggle the GLIDE interface menu Select the current menu mainmenu Select the main menu flip Hide and show the text window resize Toggle the graphics window between large and small size help Display help file for the current menu exit Exit from VNMR usermacrol to Call user defined macros usermacrol usermacro8 usermacro2 usermacros8 The third field which starts one character after the second field and extends to the end of the line is the label displayed for the button The default Permanent menu definition found in the vnmrmenu file includes the following definitions Function abort Abort Acq F
381. head nbheaders 2 have the following structure data file header header for block 1 second header for block 1 data of block 1 header for block 2 second header for block 2 data of block 2 All data in this file is contiguous The byte following the 32nd byte in the file is expected to be the first byte of the first data block header If more than one block is stored in a file the first byte following the last byte of data is expected to be the first byte of the second data block header Note that these data blocks are not disk blocks rather they are a complete data group such as an individual trace in a experiment For non arrayed 1D experiments only one block will be present in the file Details of the data structures and constants involved can be found in the file data h which is provided as part of the VNMR source code license The C specification of the file header is the following struct datafilehead Used at start of each data file FIDs spectra 2D long nblocks number of blocks in file long ntraces number of traces per block long np number of elements per trace long ebytes number of bytes per element long tbytes number of bytes per trace long bbytes number of bytes per block short vers_id software version file_id status bits short status status of whole file long nbheaders number of block headers per block The variables in datafilehead
382. hem to the different modes of imaging and include the capabilities of multislice and multiecho imaging Many of the spectroscopic preparation pulse sequences can be linked to the standard imaging sequences to limit the spin population type that is imaged to provide greater contrast in the image or to remove artifacts from the image For UNITYplus UNITY and VXR S systems configuring the system as an imaging spectrometer has a number of PSG implications See the next section for more information on the implications relative to PSG and see the software installation manual for system configuration procedures 2 16 Programming the Performa XYZ PFG Module The Performa XYZ pulsed field gradient PFG module adds new capabilities to high resolution liquids experiments on Varian spectrometers The module applies gradients in Bo along three distinct axes at different times during the course of the pulse sequence These gradients can perform many functions including solvent suppression and coherence pathway selection This section describes pulse sequence programming of the module Creating Gradient Tables In order for the software to have the necessary information on all three axes to convert between gauss cm and DAC values the XYZ PFG probe and amplifier combination can be calibrated using the creategt able macro and a gradient table made in vnmr imaging gradtables The macro first prompts the user to see if the gradient axes are set to the sa
383. here mback is a keyword entered exactly as shown n sets that processing will occur in experiment e g n2 sets experiment 2 and command_stringisaVNMR command or macro If n is omitted processing occurs in experiment 1 If more than one command is to be executed place double quote marks around the command string e g printon dg printoff UNIX background operation amp is possible as in Vnmr mback wft2da amp Usually it is a good idea to use redirection gt or gt gt with background processing Vnmr mback n3 wft2da gt vnmroutput amp The UNIX shell script vbg see below is also available to run VNMR processing in the background All text output both normal text window output and the typical two letter prompts that appear in the upper right FT PH etc are directed to the UNIX output window Note the following characteristics of the Vnmr command e Full multiuser protection is implemented If user vnmr1 is logged in and using experiment 1 and another person logs in as vnmr1 from another terminal and tries to use the background Vnmnr the second vnmr1 receives the message experiment 1 locked if that person tries to use experiment 1 The second user can use other experiments however e Pressing Control C does not work if you type the UNIX command shown you cannot abort it with Control C e Operation within VNMR is possible using the she 11 command e g shell Vnmr m
384. here are five classes of tokens in MAGICAL identifiers reserved words constants operators and separators Identifiers An identifier is the name of a command macro parameter or variable and is a sequence of letters digits and the characters _ The underline _ counts as a letter Upper and lower case letters are different The first letter of identifiers except temporary variable identifiers must be a letter Temporary variable identifiers start with the dollar sign character Identifiers can be any length but be reasonable Examples of identifiers are pcon _pw or height 01 999165 00 A0800 VNMR 6 1C User Programming 29 Chapter 1 MAGICAL II Programming 30 Reserved Words The identifiers listed in Table 1 are reserved words and may not be used otherwise Reserved words are recognized in both upper and lower case formats e g do not use either and or AND except as a reserved word Table 1 Reserved Words in MAGICAL abort else or typeof abortoff endif repeat then aborton endwhile return until and if size while break mod sqrt do not trunc Constants Constants can be either floating or string e A floating constant consists of an integer part a decimal point a fractional part the letter E or e and optionally a signed integer exponent The integer and fraction parts both consist of a sequence of digits Either the integer part or the fraction part but not both may be missing similarly ei
385. hes to pplv1 high from dpwr low or on GEMINI 2000 1H 3 systems to full pulse power from dhp If declvlon is used make sure declvloff is used prior to time periods in which normal controllable power levels are desired such as prior to acquisition Use full decoupler power only for decoupler pulses or for solids applications declvloff Return first decoupler back to normal power power Change transmitter or decoupler power lin amp sys pwrf Change transmitter or decoupler fine power rlpower Change transmitter or decoupler power lin amp sys rlpwrf Set transmitter or decoupler fine power 01 999165 00 A0800 VNMR 6 1C User Programming 171 Chapter 3 Pulse Sequence Statement Reference decoff Syntax Description Related dec2off Applicability Syntax Description Related dec30ff Applicability Syntax Description Related decoffset Syntax Description Arguments Examples Related dec2offset Syntax Description Arguments Examples Related 172 VNMR 6 1C User Programming Turn off first decoupler decoff Explicitly gates off the first decoupler in the pulse sequence decon Turn on first decoupler dec2off Turn off second decoupler dec30ff Turn off third decoupler Turn off second decoupler Systems with a second decoupler dec2off Explicitly gates off the second decoupler in the pulse sequence dec2on Turn on second decoupler
386. his include the round off of fn entries to powers of two limitation of various parameters to be positive only etc Boolean Expressions Boolean expressions have a value of either TRUE or FALSE Booleans are represented internally as 0 0 for FALSE and 1 0 for TRUE although in a Boolean expression any number other than zero is interpreted as TRUE Boolean expressions can only compare quantities of the same type real numbers with real numbers or strings with strings Some examples of Boolean expressions include pw 10 sw gt 10000 at 2 lt 0 05 and pw lt 5 or pw gt 10 The explicit use of the words TRUE and FALSE is not allowed All Boolean expressions are implicit they are evaluated when used and given a value of TRUE or FALSE for the purpose of some decision Input Arguments Arguments passed to a macro are referenced by n where n is the argument number An unlimited number of arguments 1 2 and so on can be passed The name of the macro itself may be accessed using the special name 0 For example if the macro test1 is running 0 is given the value test 1 A second special variable contains the number of arguments passed and can be used for routines having a variable number of arguments Arguments can be either real or string types as with all parameters An example of using an input arguments such as 1 vysmult multiplier Multiply vertical scale vs by input argument vs l vs Another example
387. ht h in the directory vnmr bin 5 Compiles the user written weighting function which is stored in the wt lib directory link loads it with usrwt o and places the executable program in the same directory Any compilation and or link loading errors are placed in the file errmsg in wt lib 6 Removes the soft links to usrwt o andweight h inthe bin subdirectory of the VNMR system directory The name of the executable program is the same as that for the source file without a file extension For example testwt c is the source file for the executable file test wt 01 999165 00 A0800 VNMR 6 1C User Programming 309 Chapter 5 Parameters and Data 5 7 User Written FID Files You can introduce computed data into your experiment by using the command makefid input_file lt element_number format gt The input_file argument which is required is the name of a file containing numeric values two per line The first value is assigned to the X or real channel the second value on the line is assigned to the Y or imaginary channel Arguments specifying the element number and the format are optional and may be entered in either order The argument element_number is any integer larger than 0 If this element already exists in your FID file the program will overwrite the old data If not entered the default is the first element or FID format is a character string with the precision of the resulting FID file and can be specified by one of the
388. hy gl ete int sync TRUE synchronous or FALSE double mod_freq modulation frequency Sets the status of a transmitter independent of the status statement thus overriding decoupler parameters such as dm and dmm Since the set status statement is part of the pulse sequence it has no effect when only an su 242 VNMR 6 1C User Programming 01 999165 00 A0800 Arguments Examples Related settable Applicability Syntax Description Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference command is executed It is the only way the observe transmitter can be modulated on UN TYINOVA and UNITYplus systems channel is OBSch observe transmitter DECch first decoupler DEC2ch second decoupler or DEC3ch third decoupler on is TRUE turn on decoupler or FALSE turn off decoupler mode is one of the following values for a decoupler mode for further information on decoupler modes refer to the description of the dmm parameter in the manual VNMR Command and Parameter Reference e c sets continuous wave CW modulation e f sets fm fm modulation swept square wave e g sets GARP modulation e m sets MLEV 16 modulation e n sets noise modulation e p sets programmable pulse modulation i e waveform generation e r sets square wave modulation e u sets user supplied modulation from external hardware e w sets WALTZ 16 modulatio
389. ich sets the vertical scale as simple variables in our macro This line accomplishes the task of calculating a new value of vs that will make the height of the tallest peak equal to 180 mm Part of the power of the MAGICAL macro language is its ability to build on itself For example we can create first level macros out of existing commands second level macros out of first level macros and commands and so on Suppose we created a macro plot for example we might also create a macro set uph another macro acquireh and yet another macro processh Now we might create a higher level macro H1 which is equivalent to setuph acquireh processh plot Perhaps we have created two more similar macros C13 and APT Now we might create yet another higher level macro HCAPT equivalent to H1 C13 APT At every step of the way the power of the macro increases but without increasing the complexity Many macros are part of the standard VNMR software These macros are discussed in the relevant chapters of the manual Getting Started processing macros are discussed along with processing commands acquisition setup macros along with acquisition setup commands etc Refer to the VWMR Command and Parameter Reference for a concise description of standard macros The examples used here are instructive examples and do not necessarily represent standard Varian software Executing a Macro When any program is executed the command interpreter first checks to see i
390. ich the autoincrement feature is set AP index the second argument to getelem is ignored and can be set to any AP variable name each element in such a table is by definition always accessed sequentially The setautoincrement tablename statement sets the autoincrement attribute for an AP table tablename specifies the name of the table t 1 to t 60 The index into the table is set to O at the start of an FID acquisition and is incremented after each access into the table Tables using the autoincrement feature cannot be accessed within a hardware loop 01 999165 00 A0800 VNMR 6 1C User Programming 107 Chapter 2 Pulse Sequence Programming 108 The setdivnfactor tablename divnfactor statement sets the divn return attribute and the divn factor for an AP table tablename specifies the name of the table t 1 to t 60 The actual index into the table is now set to index divnfactor 0 1 2 is therefore translated by the acquisition processor not by pulse sequence generation PSG into 0 O 1 1 The divn return attribute results in a divn factor fold compression of the AP table at the level of the acquisition processor The setreceiver tablename statement assigns the ct th element of the AP table tablename to the receiver variable oph If multiple set receiver statements are used in a pulse sequence or if the value of oph is changed by real time math statements such as assign add etc the last value of oph prior to the acquisition of d
391. ide integer values divn vi vj vk codeint vi codeint vj codeint vk real time variable for dividend real time variable for divisor real time variable for quotient VNMR 6 1C User Programming Sets the integer value vk equal to vi divided by vj Any remainder is ignored vi is the dividend vj is the divisor and vk is the quotient All three are real time variables v1 to v14 oph etc divn v2 v3 v4 add Add integer values assign Assign integer values dbl Double an integer value decr Decrement an integer value hlv Half the value of an integer inct Increment an integer value mod2 Find integer value modulo 2 mod4 Find integer value modulo 4 modn Find integer value modulo n mult Multiply integer values sub Subtract integer values Turn off graphical display of statements dps_off 01 999165 00 A0800 Examples Related dps_on Syntax Description Related dps_show Syntax Syntax Syntax Syntax Syntax Syntax Syntax Chapter 3 Pulse Sequence Statement Reference Turns off dps display of statements Pulse statements following dps_off are not shown in the graphical display dps_on Turn on graphical display of statements dps_show Draw delay or pulses in a sequence for graphical display dps_skip Skip graphical display of next statement Turn on graphical display of statements dps_on Turns on dps display of statements Pulse statements following
392. ider is changed in acqi the amount that the actual pulse width changes is determined by the product of the slider change and the respective multiplicative factors specified by the attribute SLIDER_UNITS For example if the slider increased by 3 units the first pulse width would by increased by 3 1 0e 6 seconds and the second pulse would be increased by 3 2 0e 6 seconds In this way the initial 1 to 2 ratio in pulse widths is maintained while the slider is changed VNMR 6 1C User Programming 01 999165 00 A0800 2 8 Hardware Looping and Explicit Acquisition Fine Power Subroutine The G_Power subroutine is used on systems with the optional linear fine attenuators It has the following syntax G_Power POWER_VALUE tpwrf POWER_DEVICE TODEV SLIDER_LABEL NULL SLIDER_SCALE i SLIDER_MAX 4095 SLIDER_MIN 0 SLIDER_UNITS 1 0 0 The following table describes the attributes used with G_Power Attribute Type Default Description POWER_VALUE double tpwrf As specified in parameter set POWER_DEVICE int TODEV TODEV for transmitter channel or DODEV for decoupler channel On UNITYplus also DO2DEV and DO3DEV for 2nd and 3rd decoupler channels SLIDER_LABEL char NULL Label 1 to 6 characters for acqi or NULL for no output to acqi SLIDER_SCALE int 1 Decimal places 0 to 3 on slider SLIDER_MAX
393. ient phase_encode3_shapedgradient phaseshift poffset poffset list position offset position offset list power pulse pwrf pwrm revroLT rcevron readuserap recofft recon rgpulse rgradient rlpower rlpwrf rlpwrm rotorperiod rotorsync setautoincrement setdivnfactor setreceiver setstatus settable setuserap shapedpulse shaped_pulse shapedgradient shaped2Dgradient 12 VNMR 6 1C User Programming Execute a shaped oblique gradient 00 0 eee eee cee ceecseeeeeeseeeeeneees 218 Execute a shaped oblique gradient 0 0 0 ee eee cee ceeceeeeneeeseeeeeeeees 219 Blank amplifier associated with observe transmitter 0 00 eee 220 Change offset frequency of observe transmitter 10 0 eeeeeeeeeeeee 220 Change observe transmitter power level lin amp systems End programmable control of observe transmitter cesses Start programmable control of observe transmitter Pulse observe transmitter with amplifier gating 0 eee eeeeeeeeeee Set observe transmitter fine POWEeT ceeeeseseeseeseceeeeeseteeeeceeeeenees Set step size for observe transmitter eee eeeeeeceeeeeeeeceeeeeeeeneeeees Unblank amplifier associated with observe transmitter Change offset frequency of transmitter or decouplert Oblique gradient with phase encode in one axis Oblique gradient with phase encode in two axes Oblique gradient with phase encode in three axes Oblique shaped gradient with phase encode in on
394. ient pulse at the magic angle vagradient Variable angle gradient vashapedgradient Variable angle shaped gradient vashapedgradpulse Variable angle gradient pulse zero_all_gradients Zero all gradients vashapedgradient Variable angle shaped gradient Applicability Not applicable on MERCURY VX MERCURY and GEMINI 2000 266 VNMR 6 1C User Programming 01 999165 00 A0800 Syntax Description Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference vashapedgradient pattern gradlvl gradtime theta phi loops wait char pattern name of gradient shape text file double gradlvl gradient amplitude in G cm double gradtime time to apply gradient in sec double theta angle from z axis in degrees double phi angle of rotation in degrees int loops number of waveform loops int wait WAIT or NOWAIT Applies a gradient shape pattern with an amplitude gradlv1 at an angle theta from the z axis and rotated about the xy plane at an angle phi Information from a gradient table is used to scale and set the values correctly The amplitudes applied to each gradient axis are as follows x gradlvl sin phi sin theta y gradlvl cos phi sin theta z gradlvl cos theta vashapedgradient leaves the gradients at the given levels until they are turned off To turn off the gradients add another vashapedgradient statement with gradlv1 s
395. iew of Pulse Sequence Programming ou eeeeeessessesecseeeeeseeseeeesecesesceseesecaeeseeseaecaseecsaesaeeeeeeenaeaees 69 SE E BI CCS E E E indie edb n tide dade E 69 Pulse Sequence Generation DITSctory sssri ieres ear rop E E iae rE EE EEE EE EER EEE EERE EEE 69 Compiling the New Pulse Sequence ic csciasieed asain ee a EE E R EEEF 70 Troubleshooting the New Pulse Seguente iimissceiricierieoeotosooiiosipcenes sieo es N ET nEn Toenni 71 Types of Acquisition Controller Boards sosssnaiieineieiniie p e an En 72 Creating a Parameter Table for Pulse Sequence Object Code oo eeu eeesceeeseeeeeeeesecseeeeesecneeasenes 72 C Framework for Pulse Sequences 2osi0 cr diana aivainaal ind REEE ERE E EN 72 Whips hen ACUSAN seis ss escese Ses cecesendsdeeascevateocsanasocescssssoedessoes O AE EREE EEE EO AEREOS 74 ACOUISINOM Stas CODES lt 2255 sc cesccessecsielssesesansdasceshscetuansenasssavcebubeoastvbass soxesannboescsdantabenssaaacesvaasbretess 74 2 5 Spectrometer Control arnese ech ins cists cases ETER REEE E EE IEE EE EEE EEE TEE EEEE 79 Creatine a Time Delay escrire enarrant aee E ae E e a EEE a a ea EEE E Eea ERE EE e STE 79 Pulsinp the Observe TMansiMiti t siorino osoren ouer Ee EIE aE A E EEEE EA E EEEE TOTEE TOR EErEE 80 Pulsing the Decoupler Transtonttor svrsi eseuri retena iea Er E e EE A N EEEE 82 Pulsing Channels Simultaneously seriinin a sta E E adie E e EENT 84 01 999165 00 A0800 VNMR 6 1C User Programming 7 Table of Contents Settin
396. ifications for each kind of pattern are listed in the following table if a field is not specified the default given is used As an example an slightly modified excerpt from a file in the system directory shapel1ib is also shown RF Patterns Column Description Limits Default 1 Phase angle in degrees 0 5 resolution Required Phase limits No limit on magnitude 2 Amplitude 0 to scalable max max Relative duration 0 or 1 to 255 1 4 Transmitter gate 0 1 1 gate on For example the first 8 elements after the comment lines of the file sinc RF 0 000 0 000 1 000000 0 000 8 000 L 000000 0 000 16 000 L 000000 0 000 24 000 L 000000 0 000 32 000 L 000000 0 000 40 000 L 000000 0 000 48 000 L 000000 0 000 56 000 L 000000 VNMR 6 1C User Programming 01 999165 00 A0800 2 10 Pulse Shaping In using the RF patterns the actual values for the amplitude are treated as relative values not as absolute values All of the amplitudes in the rf shape file are divided by the largest amplitude in the shape file and then multiplied by 1023 0 The net result is that shapes with values of the amplitudes between 0 to 10 0 or between 0 to 1023 0 or between 0 to 100000 0 are effectively all the same shape To implement RF patterns with absolute values for amplitudes you can use a shape element with O duration to fix the scaling factor for the shape Here is a simple example A shape with elements 0 00 10 0 1 0
397. ile in the current experiment Without any arguments both display only the file header Using the same arguments as the ddf command ddf f and ddfp display a block header and part of the data of that block is displayed The mst at command displays statistics of memory usage by VNMR commands 5 2 FDF Flexible Data Format Files 290 The FDF file format was developed to support the ImageBrowser chemical shift imaging CSD and single voxel spectroscopy SVS applications When these applications were under development the current VNMR file formats for image data were not easily usable for the following reasons e The data and parameters describing the data were separated into two files If the files were ever separated there would be no way to use or understand the data e The data file had embedded headers that were not needed and provided no useful purpose e There was no support or structure for saving multislice data sets or a portion of a multislice data set as image files FDF was developed to make it similar to VNMR formats with parameters in an easy to manipulate ASCII format and a data header that is not fixed so that parameters can be added This format makes it easy for users and different applications to manipulate the headers and add needed parameters without affecting other applications File Structures and Naming Conventions Several file structure and naming conventions have been developed for more ease in using and i
398. imes from 1 to 255 to loop the waveform wait is a keyword either WAIT or NOWAIT that selects whether or not a delay is inserted to stop until the gradient has completed before executing the next statement obl_shapedgradient ramp_hold trise gro 0 0 0 0 1 NOWAIT oblique_shapedgradient Execute a shaped oblique gradient VNMR 6 1C User Programming 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference oblique_shapedgradient Execute a shaped oblique gradient Applicability Syntax Description Arguments Not applicable on MERCURY VX MERCURY or GEMINI 2000 oblique_shapedgradient patl pat2 pat3 width lvli lv12 1v13 psi phi theta loops wait char patl pat2 pat3 names of gradient shapes double width gradient length in sec double lvll1 lvl2 1vl13 gradient values in G cm double psi phi theta Euler angles in degrees int loops times to loop waveform int wait WAIT or NOWAIT Defines a shaped oblique gradient with respect to the magnet reference frame The gradient patterns pat 1 pat2 pat3 and the gradient amplitudes 1v11 1v12 1v13 are put through a coordinate transformation matrix using psi phi and theta to determine the actual x y and z gradient levels patil and 1v11 correspond to the logical read out axis pat2 and 1v12 correspond to the logical phase encode axis pat3 and 1v13 correspond to the logical slice select axis
399. in degrees with a range of 90 to 90 phi is an Euler angle in degrees with the range of 180 to 180 theta is an Euler angle in degrees with the range 90 to 90 oblique_gradient gvox1 0 0 vpsi vphi vtheta obl_gradient Execute an oblique gradient obl_shapedgradient Execute a shaped oblique gradient Applicability 218 Syntax Description Arguments Examples Related Not applicable on MERCURY VX MERCURY or GEMINI 2000 obl_shapedgradient patl pat2 pat3 width lvll 1lv12 1v13 loops wait char patl pat2 pat3 names of gradient shapes double width gradient length in sec double lvll1 lvl2 1vl13 gradient values in G cm int loops times to loop waveform int wait WAIT or NOWAIT Defines a shaped oblique gradient with respect to the magnet reference frame Itis basically the same as the oblique_shapedgradient statement except that ob1_shapedgradient uses the parameters psi phi and theta in the parameter set rather than setting them directly The pulse sequence generation aborts if the DACs on a particular gradient are overrun after the angles and amplitude have been resolved patil pat2 pat 3 are names of gradient shapes Note that the VNMR 5 1 and 5 2 software releases used only one pattern in the argument list width is the length of the gradient in seconds vell level2 level3 are gradient values in gauss cm loops is the number of t
400. include lt standard h gt pulsesequence Implement steady state phase cycling sub ct ssctr vl10 initval 16 0 v9 add v10 v9 v10 Phase calculation statements follow using v10 in place of ct as the starting point Actual pulse sequence goes here Intertransient and Interincrement Delays When running arrayed or multidimensional experiments using ni ni2 etc certain operations are done preceding and following the pulse sequence for every array element the same as there are operations preceding and following the pulse sequence for every transient These overhead operations take up time that may need to be accounted for when running a pulse sequence This might be especially important if the repetition time of a pulse sequence has to be maintained across every element and every scan during an arrayed or multidimensional experiment These overhead times between increments array elements and transients on UN TYTNOVA systems are deterministic i e both known and constant however the time between increments which we will call x is longer than the time between transients which we will call y Also the time between increments will change depending on the number of rf channels To maintain a constant repetition time for Y YZNOVA systems a parameter called d0 for d zero can be created so that x y d0 Because the interincrement overhead time will differ with different system configurations and to
401. ing customizing the Login macro a VNMR session can be tailored for an individual user The Login macro does not exist by default Make a parameter inactive off parameter n lt tree gt Makes a parameter inactive tree is current global processed or systemglobal Make a parameter active or test its state on parameter y lt tree gt lt Sactive gt Makes a parameter active or tests the active flag of a parameter t ree is current global processed or systemglobal Read current lock level readlk lt lock_level gt Returns the same information as would be displayed on the digital lock display using the manual shimming window It cannot be used during acquisition or manual shimming but can be used to develop automatic shimming methods such as shimming via grid searching Retrieve individual parameters rtv lt file parl lt indexl lt par2 index2 gt gt gt lt val gt Retrieves one or more parameters from a parameter file to the experiment s current tree If a return argument is added rt v instead returns values to macro variables which avoids creating additional parameters in the current tree For arrayed parameters array index arguments can specify which elements to return to the macro The default is the first element Start a UNIX shell shell lt command gt filel Sfile2 If no argument is given brings up a normal UNIX shell If a UNIX command entered as an argument she11 e
402. ing on the Finish button in the Pulse Sequence Entry Main Menu only if the sequence was created using the VNMR menu system e By entering seqgen file lt c gt within VNMR e By entering seqgen file lt c gt froma UNIX shell For example entering seqgen hom2dj compiles the hom2dj c sequence in VNMR andentering seqgen hom2dj does the same in UNIX Note that a full path such as seqgen export home vnmrl vnmrsys psglib hom2dj c oreven seqgen hom2d j c is not necessary or possible the seqgen command knows where to look to find the source code file and knows that it will have a c extension During compilation the system performs the following steps 1 Ifthe program dps_ps_gen is present in vnmr bin extensions are added to the pulse sequence to allow a graphical display of the sequence by entering the dps command Statements dps_off dps_on dps_skip and dps_show can be inserted in the pulse sequence to control the dps display 2 The source code is passed through the UNIX program lint to check for variable consistency correct usage of functions and other program details 3 The source code is converted into object code 4 If the conversion is successful the object code is combined with the necessary system psg object libraries Libparam so and libpsglib so ina procedure called link loading to produce the executable pulse sequence code This is actually done at run time If compilation of the pulse sequence wit
403. ing pattern is stored in the waveform generator phase is the phase of the spin lock It must be a real time variable v1 to v14 etc or a real time constant zero one etc ncycles is the number of times the spin lock pattern is to be executed decspinlock mlev16 p190 dres vl1 30 decspinlock spinlk pp90 dres vl cycles dec2spinlock Set spin lock waveform control on second decoupler dec3spinlock Set spin lock waveform control on third decoupler spinlock Set spin lock waveform control on obs transmitter Set spin lock waveform control on second decoupler Systems with a waveform generator on rf channel for the second decoupler dec2spinlock pattern 90_pulselength tipangle_resoln phase ncycles char pattern name of DEC text file double 90_pulselength 90 deg pulse length of channel double tipangle_resoln resolution of tip angle codeint phase phase of spin lock int ncylces number of cycles to execute Executes a waveform generator controlled spin lock on the second decoupler Both the rf gating and the mixing delay are handled within this function Arguments can be variables which require the appropriate get val and get str statements to permit changes via parameters see the second example below pattern is the name of the text file in the shape1lib directory that stores the decoupling pattern leave off the DEC file extension 90_pulselength is the pulse duratio
404. ing problems If an error occurs a number of messages usually are displayed Somewhere among them are these statements Pulse Sequence did not compile The following errors can also be found in the file home vnmrl1l vnmrsys psglib errmsg As a rule of thumb focus on the lines in the errmsg text file that begin with the name of the pulse sequence enclosed in double quotes followed by the line number and those that begin with a line number in parentheses In both cases a brief description of the problem is also displayed If the line of code looks correct often the preceding line of code is the culprit Note that a large number of error messages can be generated from the same coding error If a warning occurs the following message appears Pulse Sequence did compile but may not function properly The following comments can also be found in the file home vnmrl1l vnmrsys psglib errmsg This message means that although the pulse sequence has some inconsistent C code that may produce run time errors the pulse sequence did compile Three warnings to watch for are the following warning conversion from long may lose accuracy warning parameter_name may be used before set warning parameter_name redefinition hides earlier on The first warning may be generated by less than optimum usage of the ix variable conversion from long may lose accuracy An example can be found in a few of the earlier pulse sequences implementing TP
405. ingle element in an arrayed parameter the default is 1 01 999165 00 A0800 VNMR 6 1C User Programming 299 Chapter 5 Parameters and Data Table 40 Commands for Working with Parameter Trees Commands create parameter lt type lt tree gt gt Create a new parameter in parameter tree destroy parameter lt tree gt Destroy a parameter dest roygroup group lt tree gt Destroy parameters of a group in a tree display parameter lt tree gt Display parameters and their attributes fread file lt tree lt reset value gt gt Read in parameters from a file into a tree fsave file lt tree gt Save parameters from a tree to a file getvalue parameter lt index gt lt tree gt Get value of parameter in a tree groupcopy from_tree to_tree group Copy group parameters from tree to tree paramvi parameter lt tree gt Edit parameter and its attributes using vi prune file Prune extra parameters from current tree setdgroup parameter dgroup lt tree gt Set the Dgroup of a parameter in a tree setenumeral Set values of a string parameter in a tree setgroup parameter group lt tree gt Set group of a parameter in a tree setlimit Set limits of a parameter in a tree setprotect Set protection mode of a parameter settype parameter type lt tree gt Change type of a parameter setvalue Set value of any parameter in a tree setenumeral parameter N enuml enum2 enumN lt tree gt setlimit paramete
406. ingless and is consequently ignored On all systems with class C amplifiers except the GEMINI 2000 to switch from low power to high power decoupling insert dhpflag TRUE or dhpflag FALSE ina pulse sequence just before a status statement state sets the status mode to A B C or Z status A dhpflag Switch decoupling from low power to high power hsdelay Delay specified time with possible homospoil pulse setstatus Set status of observe transmitter or a decoupler transmitter statusdelay Execute the status statement with a given delay time Execute the status statement with a given delay time UNITYINOVA UNITYplus UNITY VXR S 01 999165 00 A0800 VNMR 6 1C User Programming 259 Chapter 3 Pulse Sequence Statement Reference Syntax Description Arguments Examples Related stepsize Applicability 260 Syntax Description Arguments statusdelay state time int state index A By C A double time delay time in sec Executes the status statement and delays for the time provided as an argument The current status statement takes a variable amount of time to execute which depends on the number of rf channels configured in the system the previous status state of each decoupler channel and the new status state of each decoupler channel This time is small on the order of a few microseconds without programmable decoupling to tens of microseconds with programmable d
407. ion 01 999165 00 A0800 VNMR 6 1C User Programming 55 Chapter 1 MAGICAL II Programming Listing 3 shows what a typical menu looks like this menu is somewhat simplified from the actual system menu In this menu the first three lines is a comment with the name of the menu Like regular macros comments are indicated by double quotation marks Listing 3 Typical Menu mlabel mstring mlabel 1 Plot mstring 1l pl mlabel 2 Scale mstring 2 pscale if plotter HP7550A or plotter HP7570A or plotter HP7570A_C or plotter HP7570A_D or plotter HP7475A then mlabel 3 HP Params mstring 3 hpa else mlabel 3 mstring 3 endif mlabel 4 Params mstring 4 ppa mlabel 5 All Params mstring 5 pap mlabel 6 Peaks mstring 6 ppf mlabel 7 Page mstring 7 page menu display_1D mlabel 8 Return mstring 8 menu display_1D In the first active line of the menu mlabel and mst ring are set to a null string This removes any trace of the previously active menu After that a series of assignments are made for each of up to eight values of mlabel i andmstring i The labels are just that button labels and hence can contain anything appropriate The strings on the other hand are themselves macros to be executed later and hence they must contain valid commands parameters macros and other MAGICAL language statements
408. ion Arguments Examples Related initdelay Applicability Syntax Description Arguments Examples Related initparms_sis Applicability Syntax Description Examples Chapter 3 Pulse Sequence Statement Reference Initialize real time variable for vscan statement Systems with imaging capability init_vscan vi number_points codeint vi variable to initialize double number_points number of points to acquire Initializes a real time AP math variable for use with the vscan statement init_vscan has no return value vi is an AP math variable v1 to v14 Its range is 1 to 32767 number_points is the number of points to acquire in the scan This is not limited to one acquisition but can be the sum of multiple acquires See the example used in the entry for vscan vscan Dynamic variable scan function Initialize incremental delay All systems except MERCURY VX MERCURY and GEMINI 2000 initdelay time_increment index double time_increment time increment in sec int index time increment DELAY1 etc Initializes a time increment delay and its associated delay index This statement must be executed before an incdelay statement can set an incremental delay A maximum of five incremental delays set by the index argument can be defined in one pulse sequence time_increment is the time increment in seconds that is multiplied by the count argument set in
409. ion and resetting the decoupler status dO does not take these delays into account The overhead operations preceding every array element are initializing the rf channel settings frequency power etc initializing the high speed HS lines initializing the DTM and if arrayed setting the receiver gain dO does not take into account arraying of decoupler status shims VT or spinning speed Controlling Pulse Sequence Graphical Display The dps_off dps_on dps_skip and dps_show statements summarized in Table 19 can be inserted into a pulse sequence to control the graphical display of the pulse sequence statements by the dps command To turn off dps display of statements insert dps_off into the sequence All pulse sequences following dps_off will not be shown e To turn on dps display of statements insert dps_on into the sequence All pulse sequences following dps_on will be shown e Toskip dps display of the next statement insert dps_skip into the sequence The next pulse sequence statement will not be displayed e To draw pulses for dps display insert dops_show options statements into the pulse sequence The pulses will appear in the graphical display of the sequence Many options to dps_show are available These options enable drawing a line to represent a delay drawing a pulse picture and displaying the channel name below the picture drawing shaped pulses with labels drawing observe and decoupler pulses at the
410. ions while the gradients are on vashapedgradient is used when there are actions to be performed while the gradients are on pattern is a text file that describes the shape of the gradient The text file is located in Svnmrsystem shapelib or in the user directory Svnmruser shapelib gradlv1 is the gradient amplitude in gauss cm gradt ime is the time in seconds to apply the gradient theta is the angle in degrees from the z axis phi is the angle of rotation in degrees about the xy plane vashapedgradpulse hsine 3 0 0 001 54 7 0 0 magradient Simultaneous gradient at the magic angle magradpulse Simultaneous gradient pulse at the magic angle mashapedgradient Simultaneous shaped gradient at the magic angle mashapedgradpulse Simultaneous shaped gradient pulse at the magic angle vagradient Variable angle gradient vagradpulse Variable angle gradient pulse vashapedgradient Variable angle shaped gradient zero_all_gradients Zero all gradients Set delay with fixed timebase and real time count All systems except MERCURY VX MERCURY and GEMINI 2000 vdelay timebase count int timebase NSEC USEC MSEC or SEC codeint count real time variable for count Sets a delay for a time period equal to the product of the specified timebase and the count 268 VNMR 6 1C User Programming 01 999165 00 A0800 Arguments Examples Related vdelay list Applicability Syntax Description Argum
411. ire statement may internally be done as a hardloop by itself However a construct like the following does not work initval np 2 0 v14 starthardloop v14 acquire 2 0 1 0 sw endhardloop A hardloop that consists of a single acquire call are not permitted but such constructs are not needed because a single statement can be used instead acquire np 1 0 sw This statement is not equivalent to the first construct because the acquire statement will sample more than just two points i e a complex data point per loop cycle thus allowing for np greater than 2 0 x maximum number of hardloop cycles Note that the hardloop uses a 16 bit loop counter Therefore the maximum number of cycles is 32767 the largest possible 16 bit number On the other hand a hardloop that contains acquire together with other pulse sequence events works fine as long as the number of complex points to be acquired plus the number of extra FIFO words per loop cycle does not exceed the total number of words in the loop FIFO 63 on Output boards 1024 on Acquisition Controller boards or 2048 on Pulse Sequence Controller boards initval np 2 0 v14 starthardloop v14 acquire 2 0 1 0 sw rofl pw rof2 rgpulse pw vl rofl rofr2 endhardloop Explicit hardloops with acquire calls are a standard feature in multipulse solids sequences Receiver Phase For Explicit Acquisitions Receiver phase can be changed for explicit acquisitions the
412. is 0 if VNMR is being run in foreground non zero otherwise Execute a VNMR command exec command_string Takes as an argument a character string constructed from a macro and executes the VNMR command given by command_string Determine if a parameter file or macro exists exists name type Sexists Checks for the existence of a parameter file or macro with the given name typeis parameter file maclib ascii or directory 01 999165 00 A0800 focus Description gap Syntax Description getfile Syntax Description graphis Syntax Description length Syntax Description listenoff Description listenon Description login Description 01 999165 00 A0800 1 3 Relevant VNMR Commands Send keyboard focus to VNMR input window Sends keyboard focus to the VNMR input window Find gap in the current spectrum gap gap height found powition width Looks for a gap between lines of the currently displayed spectrum where gap is the width of the desired gap and height is the starting height found is 1 is search is successful or 0 if unsuccessful Get information about directories and files getfile directory file_index Sfile file_extension get file directory Snumber_files If ile_inde x is specified the first return argument is the name of the file in the directory with the index file_index excluding any extension and the second return argument is the
413. is entered or if parameter recalculation occurs the displayed value should be redisplayed based on VNMR parameters not some internal state of that entry field If the Tcl Cmd field is left blank the entry field is cleared after the Vnmr Cmd is sent The Vnmr Cmdis sent if the Return key is pressed in the entry window or the mouse arrow is clicked on some other widget so that the focus leaves the entry window Check Element The check element selects and de selects some mode or state often as a yes or no selection It is presented as a small square box to the left of a label The box is depressed and colored if it is selected The available characteristics are the following Label of element Text string to be displayed to the right of the check box This field is optional Vnmr Variables List of VNMR parameters used in the following Vnmr Cmd Vnmr Cmd2 and Tcl Cmd fields This can be zero or more parameter names Vnmr Cmd MAGICAL expression sent to VNMR whenever the check box is selected Any specified VNMR variables can be used Vnmr Cmd2 MAGICAL expression sent to VNMR whenever the check box is deselected Any specified VNMR parameters can be used Tcl Cmd Tcl expression that is evaluated to determine whether or not the check box should be identified as selected or de selected The prototype example for using a check box would be the following which selects or de selects experiment interleaving Vnmr Variables il Vnmr Cmd
414. is format is rarely needed The field width and digit field options can be used to clean up the display The first number after the colon is the field width The next colon is the digit field For example 1 Sample Table Output pw 6 2 p1 6 2 d1 10 6 d2 10 6 Here the parameters pw and p1 are displayed in 6 columns with 2 places after the decimal point while d1 and d2 are displayed in 10 columns with 6 places after the decimal point Output Format For display each parameter and value occupies 20 characters of space e Characters 1 to 8 are the name of the parameter Parameters with names longer than 8 characters are permitted within VNMR itself but cannot be displayed or printed with dg or pap e Character 9 is always blank e Characters 10 to 18 are used for the parameter value Any parameter value exceeding 9 characters a file name is a common example is continued on the next line in this case character 19 is a tilde which is used to show continuation e Character 20 is always blank For printing with the pap command which uses the ap parameter template a da listing is printed starting in column 3 so that the template will typically specify only two columns of output ap can specify more than two columns but if any parameter is arrayed the listing of that parameter will overwrite the third column For printing the maximum number of lines in each column is 64 5 6 User Written Weighting Functions The pa
415. is information is captured by the calling macro using the format argument1 argument2 Here is an example of returning a value to the calling macro abs input output Take absolute value of input if 1 gt 0 then return 1 else return 1 endif In nested macros ret urn terminates the currently operating macro but not the macro that called the current macro To terminate the action of the calling macro and all higher levels of nesting the abort command is provided abort can be made to act like return at any particular level by using the abortoff command Consider the following sequence abortofft macrol macro2 If macrol contains an abort command and it is executed abort terminates macrol however macro2 still will be executed If the macro sequence did not contain the abortoff statement however execution of an abort command in macro1 would have prevented the operation of macro2 The aborton command nullifies the operation of abortoff and restores the normal functioning of abort Command and Macro Tracing The commands debug c and debug C turn on and off respectively VNMR command and macro tracing When tracing is on a list of each executed command and 01 999165 00 A0800 VNMR 6 1C User Programming 37 Chapter 1 MAGICAL II Programming macro is displayed in the Terminal in CDE or Command Tool in OpenWindows window from which VNMR was started Nesting of the calls is shown by indentation of the output
416. ission data acquisition In most pulse sequences the sequence of events consists of a series of pulses and delays followed at the very end by the acquisition of an FID the entire process is then repeated for the desired number of transients and then again for arrayed and nD experiments for subsequent elements of the arrayed or nD experiment In all these cases pulse sequences use implicit acquisition that is following the pulse sequence as written by the user an FID is automatically implicitly acquired This acquisition is preceded by a delay that combines the parameter alfa with a delay based on the type of filter and the filter bandwidth In addition the phase of all channels of the spectrometer except the receiver is set to zero at this time Some pulse sequences are not described by this simple model many solids NMR sequences are in this category for example These sequences use explicit acquisition in which the preacquisition and acquisition steps must be explicitly programmed by the user This method is described further in Hardware Looping and Explicit Acquisition page 125 Explicit acquisition is not available on the MERCURY and GEMINI 2000 Acquisition Status Codes Whenever wbs wnt wexp or werr processing occurs the acquisition condition that initiated that processing is available from the parameter acqstatus This acquisition condition is represented by two numbers a done code and an error code
417. iter like characters also show text displayed on the screen including the text echoed on the screen as you enter commands For example Self test completed successfully Text shown between angled brackets lt gt in a syntax entry is optional For example if the syntax is seqgen s2pul lt c gt entering the c suffix is optional and typing seqgen s2pul cor seqgen s2pul1 is functionally the same Lines of text containing command syntax examples of statements source code and similar material are often too long to fit the width of the page To show that a line of text had to be broken to fit into the manual the line is cut at a convenient point such as at a comma near the right edge of the column a backslash is inserted at the cut and the line is continued as the next line of text This notation will be familiar to C programmers Note that the backslash is not part of the line and except for C source code should not be typed when entering the line Because pressing the Return key is required at the end of almost every command or line of text you type on the keyboard use of the Return key will be mentioned only in cases where it is not used This convention avoids repeating the instruction press the Return key throughout most of this manual 01 999165 00 A0800 VNMR 6 1C User Programming 23 Introduction e Text with a change bar like this paragraph identifies material new to VNMR version 6 1C that was not in
418. ith IPA 209 full power 171 gate channel 251 gating 94 95 259 high power level 93 179 linear modulator power 235 240 linear modulator power with IPA 210 modes 94 modulation mode 94 normal power 171 offset frequency 90 91 172 223 pattern type 132 348 VNMR 6 1C User Programming phase 86 168 phase control 87 power adjustment 92 power level 93 96 175 233 239 power level switching 91 programmable decoupling 176 177 pulse shaping via AP bus 161 pulse with IPA 201 202 pulse with receiver gating 179 181 pulse related statements 82 quadrature phase 174 set status 242 shaped pulse 183 simultaneous pulses 84 small angle phase 169 small angle phase step size 260 spin lock waveform control 186 status 259 step size 188 turn off 172 turn on 173 two pulse shaped pulse 135 unblank amplifier 189 WALTZ decoupling 86 waveforms 133 decoupler mode 243 decoupler pulses entry 68 decoupling switching 190 decphase statement 86 128 174 decpower statement 92 128 144 175 decprgoff statement 134 137 144 176 decprgon statement 95 134 137 144 177 decpulse statement 83 128 147 179 decpwr statement 93 179 decpwrf statement 92 128 144 179 decr statement 99 180 decrement integer value 180 decrgpulse statement 83 128 181 decshaped_pulse statement 135 141 144 183 decspinlock statement 138 144 186 decstepsize statement 87 188 decunblank statement 96 97 189 de
419. its gauss cm to set the gradient values and to support the use of real time variables and loops when constructing imaging sequences Using real time variables and loops resulting in compressed acquisitions instead of standard acquisition arrays reduces the number of acodes sets needed to run the experiment cutting down significantly on the start up time of the experiment and removing any inter FID and intertransient overhead delays This is not really a problem on N YINOVA systems because its small overhead delays and d0 parameter make the inter FID and intertransient delays consistent but may make a difference in some applications Real time Gradient Statements Real time gradient statements consist of additions to the standard gradient and shapedgradient statements which provide real time variable control for the gradient amplitudes Real time statements include shapedvgradient which provides real time control on one axis incgradient and shapedincgradient which support real time control over three axes The vgradient statement also belongs to this group Oblique Gradient Statements To support oblique imaging and the imaging interface oblique gradient statements include oblique_gradient phase_encode_gradient pe_gradient and all of their variations The inputs to these statements are amplitudes and phases Amplitudes are expressed in gauss cm and correspond to the read out phase encode and slice select axis in the logica
420. itten to take advantage of the pop up dialog box Listing 1 is the array macro rewritten using dialog Note the following in this macro e Lines 1 7 are comments explaining what the macro does e Line 8 checks if none interactive or all arguments are supplied non interactive If only part of the arguments are supplied an error message Lines 9 11 is displayed e Line 12 forces Spar to a string type 01 999165 00 A0800 VNMR 6 1C User Programming 49 Chapter 1 MAGICAL II Programming Listing 1 The array Macro Rewritten Using the dialog Command OANA BWN HE dls 12 13 14 L533 16 ys 18 Lois 203 21 22 23 24 25s 26 218 28 29 3 30 31 322 33 34 35 36 Sh WK KKK KKK KKK KKK KKK KKK KKK KKK KK KKK KKK KKK KKK KR v w array macro for easy setup of arrays WKK KKK KKK KKK KKK KKK KKK KKK KEK KKK KKK KK KKK KARA u u usage array interactive mode array parameter_name steps start stsize 7 optional fifth argument avoids da uv v if S gt 1 and lt 4 then write error usage array lt parameter_name lt steps start stepsize gt gt return 1 endif Spar W exists tmp array file Se if Se gt 0 then shell rm tmp array endif dialog userdirt dialoglib array tmp array exists tmp array file Se if Se 0 then return endif lookup file tmp array lookup readli
421. iver t3 include lt standard h gt tl 0 16 pulsesequence 0000000000000000 t2 1 2 3 0 4 loadtable hom2djt 1230123012301230 ttadd t1 t4 4 t3 0 2 8 ttadd t2 t4 4 0202020202020202 ttadd t3 t4 4 t4 0 2 1 3 4 0000222211113333 This sequence uses conventional phase cycling completely different than the pulse cycling in the standard HOM2DJ sequence found in psg1ib The phase cycling contained here in t 4 is added to the phases by the pulse sequence itself with the series of three ttadd statements This can also be done in the table itself for example by replacing the t2 line in the tab1lib file with t2 1230301223010 1 2 3 which is the completely spelled out phase cycle for the second pulse When using a table to be referenced with a tt add statement you cannot compress the table by using t4 0 2 1 3 4 You must use square brackets which are exactly equivalent to the curly brackets but without achieving table compression at the level of the acquisition processor 01 999165 00 A0800 VNMR 6 1C User Programming 109 Chapter 2 Pulse Sequence Programming 2 6 Accessing Parameters 110 The get val and get str statement look up the value of parameters providing access to parameters Table 21 summarizes these statements Table 21 Parameter Value Lookup Statements getstr parametername internalname Look up value of string parameter internalname
422. iver only recon Turn on receiver only Turn on receiver gate and amplifier blanking gate rcevron On UN TYINOVA and GEMINI 2000 systems the receiver is normally off during the pulse sequence It is turned on only during acquisition On other systems rcvron provides explicit receiver gating in the pulse sequence The rcvron statement also blanks or disables the observe transmitter Receiver gating is normally controlled automatically by obspulse pulse and rgpulse on UNITYplus and UNITY systems and by decpulse decrgpulse dec2rgpulse and dec3rgpulse on UNITY systems At the end of each of these statements the receiver is automatically turned back on if and only if the receiver has not been previously turned off explicitly by a rcevroff statement In all cases the receiver is implicitly turned back on immediately prior to data acquisition revroff Turn off receiver gate and amplifier blanking gate recoff Turn off receiver gate only recon Turn on receiver gate only Read input from user AP register UNITYTNOVA systems readuserap vi codeint vi index to value read in user AP register Reads input from user AP bus register 3 to a real time variable The user can then act on this information using real time math and real time control statements while the pulse sequence is running Register 3 is lines to 8 of the USER AP connector J8212 on the Breakout panel on the rear of the left console cabinet This register interfaces t
423. keep the dO delay consistent across systems if d0 is set greater than the overhead delay the inter FID delay x is padded such that y d0 x d0 x y In other words dO is used to set a standard delay so the interincrement delay and the intertransient delay are the same when executing transient scans within an array element The delay is inserted at the beginning of each scan of a FID after the first scan has completed The d0 delay can be set by the user or computed by PSG if dO is set to n When dO does not exist no delay is inserted Another factor to consider when keeping a consistent timing in the pulse sequence is the status statement The timing of this statement varies depending on the number of channels and the type of decoupler modulation To keep this timing constant there is the pulse sequence statement st atusdelay that allows the user to set a constant delay time for changing the status For this to work the delay time has to be longer than the time it takes to set the status For timing and more information see the description of statusdelay in Chapter 3 The overhead operations preceding every transient are resetting the DTM data to memory control information The overhead operations following every transient are error 01 999165 00 A0800 VNMR 6 1C User Programming 103 Chapter 2 Pulse Sequence Programming detection for number of points and data overflow detection for blocksize end of scan and stop acquisit
424. ks External trigger counter extern char ir MAXSTR Inversion recovery flag extern char ws MAXSTR Water suppression flag extern char mt MAXSTR Magnetization flag extern char pilot MAXSTR Auto gradient balance flag extern char seqcon MAXSTR Acquisition loop control flag extern char petable MAXSTR Name for phase encode table extern char acqtype MAXSTR Example full or half echo extern char exptype MAXSTR Example se or fid in CSI extern char apptype MAXSTR Keyword for parameter init e g imaging extern char seqfile MAXSTR Pulse sequence name extern char rfspoil MAXSTR rf spoiling flag extern char satmode MAXSTR Presentation mode 116 VNMR 6 1C User Programming 01 999165 00 A0800 2 6 Accessing Parameters Table 23 Imaging Variables continued extern char verbose MAXSTR Verbose mode for sequences and psg Miscellaneous extern double rfphase rf phase shift extern double BO Static magnetic field level extern double slcto Slice selection offset extern double delto Slice spacing frequency extern double tox Transmitter offset extern double toy Transmitter offset extern double toz Transmitter offset extern double griserate Gradient rise rate e Parameters used in the pulse sequence derived from those in the parameter set e Parameters unknown to the pulse sequence This includes parameters created by the user for a particular pulse sequence such as J or mix as well as a fe
425. l frame Phase angles correspond to Euler angles psi phi and theta and describe the coordinate rotation applied to the input amplitudes For more information on use see the manual User Guide Imaging 01 999165 00 A0800 VNMR 6 1C User Programming 155 Chapter 2 Pulse Sequence Programming Table 38 Imaging Related Statements create_delay_list create_freq_list create offset list endmsloop endpeloop getarray getorientation incgradient init_rfpattern init_gradpattern init_vscan obl_gradient oblique_gradient obl_shapedgradient oblique_shapedgradient msloop peloop pe_gradient pe2_gradient pe3_gradient pe_shapedgradient pe2_shapedgradient pe3_shapedgradient phase_encode_gradient phase_encode3_gradient phase_encode_shapedgradient phase_encode3_shapedgradient poffset position_offset poffset_list position_offset_list shapedgradient shaped2Dgradient shapedincgradient shapedvgradient sli vagradient vagradpulse vashapedgradient vashapedgradpulse vdelay vdelay_list vfreq vgradient voffset vscan vsli zero_all_gradients Create table of delays Create table of frequencies Create table of frequency offsets Ends a loop started by the msloop peloop Retrieves all values of arrayed parameter Read image plane orientation Dynamic variable gradient function Create rf pattern file Create gradient pattern file Initialize real time vari
426. l list statements support real time selection of frequencies offsets and delays Global lists are different from AP tables in that the lists are sent down to the acquisition console when the experiment starts up and remain accessible until the experiments completes The lists can be arrayed parameters with a protection bit set to prevent an arrayed acquisition read into the pulse sequence using the get array statement or standard C language arrays calculated within the pulsesequence The lists are initialized with the statements create_freq_list create_offset_list and create_delay_list and then selected and set using the vfreq voffset and vdelay_list statements which use a real time parameter as an index into the list The position statements set the rf frequency from a given position or an array of positions These statements are poffset poffset_list position_offset and position_offset_list The position list statements use global lists which initialize the list and select and set the position in a single statement When creating global list parameters create them as acquisition parameters and set protection bit 8 value 256 or else PSG tries to array them as standard arrayed acquisitions Looping Statements The looping statements ms loop and peloop define multislice and phase encode loops when creating imaging pulse sequences The looping statements also allow selection of a standard arrayed acquisition or a compressed a
427. l types of parameters minvalue is areal number for the minimum value that the parameter can contain or an index to a minimum value in the parameter parmin found in vnmr conpar Applies to real types of parameters only stepsize is areal number for the step size in which parameters can be entered or index to a step size in the parameter parstep found in vnmr conpar If stepsize is 0 it is ignored Applies to real types only Ggroup is an integer value 0 ALL 1 SAMPLE 2 ACQUISITION 3 PROCESSING 4 DISPLAY 5 SPIN Dgroup is an integer value The specific application determines the usage of this integer protection isa 32 bit word made up of the following bit masks which are summed to form the full mask Bit Value Description 0 1 Cannot array the parameter 1 2 Cannot change active not active status 2 4 Cannot change the parameter value 3 8 Causes _parameter macro to be executed e g if parameter is named sw the macro _ sw is executed when sw is changed 4 16 Avoids automatic redisplay 5 32 Cannot delete parameter 6 64 System parameter for spectrometer or data station 7 128 Cannot copy parameter from tree to tree 8 256 Cannot set array parameter 9 512 Cannot set parameter enumeral values 10 1024 Cannot change the parameter s group 11 2048 Cannot change protection bits 12 4096 Cannot change the display group 13 8192 Take max min step from vnmr conpar parameters parmax parmin parstep a
428. lank amplifier associated with third decoupler UNITYTNOVA and UNITYplus systems with third decoupler dec3blank Disables the amplifier for the third decoupler This is generally used after a call to dec3unblank dec3unblank Unblank amplifier associated with third decoupler revroff Turn off receiver revron Turn on receiver Return first decoupler back to normal power declvloff Switches the decoupler power to the power level set by the appropriate parameters defined by the amplifier type dhp for class C amplifiers or dpwr for linear amplifiers If dhp n declvloff has no effect on systems with class C amplifiers but still functions for systems with linear amplifiers On GEMINI 2000 systems dhp n has no meaning and the power level is reversed from declvlon declvlon Turn on first decoupler to full power power Change transmitter or decoupler power lin amp sys pwrf Change transmitter or decoupler fine power rlpower Change transmitter or decoupler power lin amp sys rlpwrf Set transmitter or decoupler fine power Turn on first decoupler to full power declvlon Switches the first decoupler power level between the power level set by the high power parameter s to the full output of the decoupler If dhp n declvloff has no effect on systems with class C amplifiers but still functions for systems with linear amplifiers On GEMINI 2000 systems dhp n has no meaning On GEMINI 2000 broadband systems declvlon switc
429. larly decstepsize base dec2stepsize base and dec3stepsize base set the step size of the small angle phase increment to base for the first decoupler second decoupler and third decoupler respectively assuming that system is equipped with appropriate hardware The base argument is a real number or variable The base phase shift selected is active only for the xmt rphase statement if the transmitter is the requested device only for the dcplrphase statement if the decoupler is the requested device only for the dcp1lr2phase statement if the second decoupler is the requested device or only for the dcp1r3phase if the third decoupler is the required device that is every transmitter has its own base phase shift Phase information into pulse rgpulse decpulse decrgpulse dec2rgpulse dec3rgpulse and simpulse is still expressed in units of 90 The statements xmt rphase multiplier dcplrphase multiplier dcplr2phase multiplier anddcplr3phase multiplier set the phase of transmitter first decoupler second decoupler or third decoupler respectively in units set by stepsize If stepsize has not been used the default step size is 90 The argument multiplier is a small angle phaseshift multiplier The small angle phaseshift is a product of the multiplier and the preset st epsize for the rf device observe transmitter first decoupler second decoupler or third decoupler multiplier must be an real time variable
430. latching shaped_pulse 1 25 pre 5s ee 135405 15 45 decshaped_pulse 0 5 post dec2shaped_pulse dec3shaped_pulse simshaped_pulse bs 1135 30 1 30 50 sim3shaped_pulse L229 45 15 45 35 obsprgon 1 25 5e t3 10 575 10 95 decprgon dec2prgon dec3prgon obsprgoff 0 5 252 3 4 3 4 5 decprgoff dec2prgoff dec3prgoff j spinlock 29 pre Gat 15 05 15 45 decspinlock 0 5 post dec2spinlock dec3spinlock rgradient and 4 0 6 9 1229 Not an vgradient with option gradtype p rgradient and 0 5 3 45 6 9 No vgradient with op gradtype w an ion Gre Ct zgradpulse delay delay delay Not an gradtype p 8 0 13 8 25 8 option zgradpulse delay delay delay Not an gradtype w 12 0 6 9 13 8 option simshaped_pulse 1 75 pre 0 5 post sim3shaped pulse 2 25 pre 0 5 post 144 VNMR 6 1C User Programming 01 999165 00 A0800 2 12 Internal Hardware Delays Finally these delays are added up for each channel and this becomes the delay incurred for status or set status For example if dm nnnss dmm cpfwp and dm2 y then dmm2 cccpc Table 33 summarizes the internal intervals assuming Table 33 Example of AP Bus Overhead Delays for status Statement Delay us Delay us Delay us Statement UNITY INOVA apinterface 3 UNITYplus R480 status B 0 0 0 dmm from c to p WFG not started because dm n in B status C 1 0 4 3 2AN dmm from p to f no WFG to
431. lated decon Syntax Description Related dec2on Applicability Syntax Description 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference Change offset frequency of third decoupler dec3o0ffset frequency double frequency offset frequency in Hz Changes the offset frequency of the third decoupler parameter dof 3 It is functionally the same as offset frequency DO3DEV frequency is the offset frequency desired in hertz dec3o0ffset do3 decoffset Change offset frequency of first decoupler dec2offset Change offset frequency of second decoupler obsoffset Change offset frequency of observe transmitter offset Change offset frequency of transmitter or decoupler Change offset frequency of fourth decoupler UNITYTNOVA systems with a deuterium decoupler channel as the fourth decoupler dec4offset frequency double frequency offset frequency in Hz Changes the offset frequency of the fourth decoupler parameter dof 4 It is functionally the same as of fset frequency DO4DEV frequency is the offset frequency desired in hertz dec4offset do4 decoffset Change offset frequency of first decoupler dec2offset Change offset frequency of second decoupler obsoffset Change offset frequency of observe transmitter offset Change offset frequency of transmitter or decoupler rftype Type of rf generation Turn on first decoupler decon Explicitly gates on the first dec
432. le width is the length in seconds of the gradient statl stat2 stat3 are values in gauss cm of the components for the static portion of the gradient in the logical reference frame step2 is the value in gauss cm of the component for the step size change in the variable portion of the gradient 01 999165 00 A0800 VNMR 6 1C User Programming 229 Chapter 3 Pulse Sequence Statement Reference Related vmult2 is a real time math variable v1 to v14 ct zero one two three or reference to AP tables t 1 to t 60 whose associated values vary dynamically in a manner controlled by the user lim2 is the value representing the dynamic step that will generate the maximum gradient value for the component This provides error checking in pulse sequence generation and is normally nv 2 ang is the Euler angle psi in degrees with the range of 90 to 90 ang2 is the Euler angle phi in degrees with the range of 180 to 180 ang3 is the Euler angle theta in degrees with the range of 90 to 90 vloops is a real time math variable v1 to v14 ct zero one two three or references to AP tables t 1 to t 60 that dynamically sets the number of times to loop the waveform wait is a keyword either WAIT or NOWAIT that selects whether or not a delay is inserted to wait until the gradient has completed before executing the next statement tag is a unique integer that tags the gradient element from any other
433. le dmf2 Decoupler modulation frequency extern double fb Filter bandwidth extern double vttemp VT temperature setting extern double vtwait VT temperature time out setting extern double vtc VT temperature cooling gas setting extern double cpflag Phase cycling 1 no cycling 0 quad detect extern double dhpflag Decoupler high power flag 01 999165 00 A0800 VNMR 6 1C User Programming 111 Chapter 2 Pulse Sequence Programming Table 22 Global PSG Parameters continued Pulse Widths extern double pw Transmitter modulation frequency extern double pl A pulse width extern double pw90 90 pulse width extern double hst Time homospoil is active Delays extern double alfa Time after receiver is turned on that acquisition begins extern double beta Audio filter time constant extern double dl Delay extern double d2 A delay used in 2D experiments extern double d3 A delay used in 3D experiments extern double d4 A delay used in 4D experiments extern double pad Preacquisition delay extern double padactive Preacquisition delay active parameter flag extern double rofl Time receiver is turned off before pulse extern double rof2 Time receiver is turned on before receiver is turned on Total Time of Experiment extern double extern int extern int extern int extern int extern int extern int totaltime phasel phase2 phase3 d2_index d3_index d4_index Total timer events for an experiment duration estimate 2D a
434. le gradient pulse vashapedgradpulse Variable angle shaped gradient pulse zero_all_gradients Zero all gradients 01 999165 00 A0800 VNMR 6 1C User Programming 26 7 Chapter 3 Pulse Sequence Statement Reference vashapedgradpulse Variable angle shaped gradient pulse Applicability Syntax Description Arguments Examples Related vdelay Applicability Syntax Description Not applicable on MERCURY VX MERCURY and GEMINI 2000 vashapedgradpulse pattern gradlvl gradtime theta phi char pattern gradient shape text file double gradlvl gradient amplitude in G cm double gradtime gradient time in seconds double theta angle from z axis in degrees double phi angle of rotation in degrees Applies a gradient shape pattern with an amplitude gradlv1 at an angle theta from the z axis and rotated about the xy plane at an angle phi Information from a gradient table is used to scale and set the values correctly The amplitudes applied to each gradient axis are as follows x gradlvl sin phi sin theta y gradlvl cos phi sin theta z gradivl cos theta The gradient are turned off after gradt ime seconds Note that vashapedgradpulse assumes that the gradient pattern zeroes the gradients at its end and does not explicitly zero the gradients vashapedgradpulse is simpler to use then the vashapedgradient statement if there are no other act
435. le gro gro2 gro3 Readout gradient strength extern double gpe gpe2 gpe3 Phase encode for 2D 3D and 4D extern double gss gss2 gss3 Slice select gradients extern double gror Readout focus extern double gssr Slice select refocus extern double grof Readout refocus fraction extern double gssf Slice select refocus fraction extern double g0 gl g9 Numbered levels extern double gx JY gZ X Y and Z levels extern double gvox1 gvox2 gvox3 Voxel selection extern double gdiff Diffusion encode extern double gflow Flow encode extern double gspoil gspoil2 Spoiler gradient levels extern double gcrush gcrush2 Crusher gradient levels extern double gtrim gtrim2 Trim gradient levels extern double gramp gramp2 Ramp gradient levels 114 VNMR 6 1C User Programming 01 999165 00 A0800 2 6 Accessing Parameters Table 23 Imaging Variables continued extern double gpemult Shaped phase encode multiplier extern double gradstepsz Positive steps in the gradient DAC extern double gradunit Dimensional conversion factor extern double gmax Maximum gradient value G cm extern double gxmax X maximum gradient value G cm extern double gymax Y maximum gradient value G cm extern double gzmax Z maximum gradient value G cm extern double gtotlimit Limit combined gradient values G cm extern double gxlimit Safety limit for X gradient G cm extern double gylimit Safety limit for Y gradient G cm extern double gzlimit Safety limit for
436. le_resoln is the resolution in tip angle degrees to which the decoupling pattern is stored in the waveform generator 257 VNMR 6 1C User Programming Chapter 3 Pulse Sequence Statement Reference Examples Related phase is the phase angle of the spin lock It must be a real time variable v1 to v14 oph etc ncycles is the number of times that the spin lock pattern is to be executed spinlock mlev16 pw90 90 0 v1 50 spinlock locktype pw resol vl cycles decspinlock First decoupler spin lock waveform control dec2spinlock Second decoupler spin lock waveform control dec3spinlock Third decoupler spin lock waveform control starthardloop Start hardware loop Applicability 258 Syntax Description All systems except the GEMINI 2000 and any system equipped with an Output board Part No 00 953520 0 where is from 0 to 4 starthardloop vloop codeint vloop real time variable for loop count Starts a hardware loop The number of repetitions of the hardware loop must be two or more If the number of repetitions is 1 the hardware looping feature is not activated A hardware loop with a count equal to O is not permitted and generates an error Depending on the pulse sequence additional code may be needed to trap for this condition and skip the starthardloop and endhardloop statements if the count is 0 Only instructions that require no further intervention by the acquisition computer pulses
437. led the shape is addressed and started The minimum pulse length is 0 2 us The overhead at the start and end of the shaped pulse varies e UNITYTNOVA 1 us start O end e UNITYplus 5 75 us start 0 end e System with Acquisition Controller board 10 75 us start 4 3 us end e System with Output board 10 95 us start 4 5 us end If the length is less than 0 2 us the pulse is not executed and there is no overhead When using the linear attenuator and the small angle phase shifter to generate a shaped pulse the dec2 shaped_pulse statement creates AP tables on the fly for amplitude and phase It also uses the real time variables v12 and v13 to control the execution of the shape It does not use AP table variables For timing and more information see the description of apshaped_dec2pulse Note that if using AP tables with shapes that have a large number of points the FIFO can become overloaded with words generating the pulse shape and FIFO Under flow errors can result pattern is the name of a text file in the shapelib directory that stores the rf pattern leave off the RF file extension width is the duration in seconds of the pulse phase is the phase of the pulse It must be a real time variable v1 to v 14 etc or a real time constant zero one etc RG1 is the delay in seconds between gating the amplifier on and gating the second decoupler on the phaseshift occurs at the beginning of this delay RG2 is
438. lines Because the SLI has 32 bits and the real time variables have only 16 bits two real time variables are used for each call The one specified in the calling sequence is used for the high order word and the next sequential real time variable is used for the low order word Thus legal values for var are v1 to v13 Examples pulsesequence int SLIaddr Address of SLI board SLIaddr getval address vsli SLIaddr SLI_SET vl Notice that address is not a standard parameter but needs to be created by the user if it is mentioned in a user pulse sequence for details see the description of the create command Related sli Set SLI lines sp off Turn off specified spare line sp on Turn on specified spare line 274 VNMR 6 1C User Programming 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference X xgate Applicability Syntax Description Arguments Examples Related xmtroff Syntax Description Related xmtron Syntax Description Related xmt rphase Applicability Syntax Description 01 999165 00 A0800 Gate pulse sequence from an external event All systems except MERCURY VX MERCURY and GEMINI 2000 xgate events double events number of external events Halts the pulse sequence When the number of external events has occurred the pulse sequence continues events is the number of external events xgate 2 0 x
439. ling interval Examples acquire np 1 0 sw Related endhardloop End hardware loop starthardloop Start hardware loop add Add integer values Syntax add vi vj vk codeint vi real time variable vi for addend codeint vj real time variable vj for addend codeint vk real time variable vk for sum Description Sets vk equal to the sum of integer values of vi and vj Arguments vi vj and vk are real time variables v1 to v14 oph etc Examples add vl1 v2 v3 Related assign Assign integer values dbl Double an integer value decr Decrement an integer value divn Divide integer values hlv Half the value of an integer indr Increment an integer value mod2 Find integer value modulo 2 mod4 Find integer value modulo 4 modn Find integer value modulo n mult Multiply integer values sub Subtract integer values apovrride Override internal software AP bus delay Applicability UNITY and VXR S systems with the 63 step Output board Part No 00 953520 0 where is an integer This board shipped prior to 1988 Syntax apovrride Description Systems with the 63 step Output board can use this statement to prevent a delay of 0 2 us from being inserted prior to the next and only the next occurrence of one of the AP analog port bus statements dcplrphase dcplr2phase dcplr3phase decprgoff dec2prgoff dec3prgoff decprgon 160 VNMR 6 1C User Programming 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Referen
440. ll angle phase shifting i e a preceding xmt rphase and step size setting on the observe transmitter channel After apshaped_pulse observe transmitter channel small angle phase shifting is reset to zero and the step size is set to 0 25 degrees apshaped_pulse capability is now integrated into the shaped_pulse statement The shaped_pulse statement calls aoshaped_pulse without table variables if a waveform generator is not configured on the decoupler channel shaped_pulse creates AP tables on the fly for amplitude and phase and does not use the AP tables allocated for users It still uses real time variables v12 and v13 pattern is a shape file without the RF extension in vnmr shapelib orin vnmrsys shapelib The amplitude and phase fields of the shape file are used The relative duration field field 3 should be left at the default value of 1 0 or at least small numbers and the gate field field 4 is currently not used because the transmitter is switched on throughout the shape On MERCURY VX and MERCURY systems no phase is changed or set pulse_width is the total pulse width in seconds excluding amplifier gating delays around the pulse pulse_phase is the 90 phase shift of the pulse For small angle phase shifting note that apshaped_pulse sets the phase step size to the minimum on the one channel that is used power_table and phase_table are two table variables t 1 to t 60 used as intermediate storage addresses for the
441. lly set to zero for this statement dmm should be set to c during any period of time in which decoupler pulses occur width is the duration of the pulse in seconds phase is the phase of the pulse The value must be a real time variable v1 to v14 etc or a real time constant zero one etc decpulse pp v3 decpulse 2 0 pp zero decrgpulse Pulse decoupler transmitter with amplifier gating idecpulse Pulse the decoupler transmitter with IPA rgpulse Pulse observe transmitter with amplifier gating simpulse Pulse observe decoupler channels simultaneously sim3pulse Simultaneous pulse on 2 or 3 rf channels Set first decoupler high power level class C amplifier All systems except for the GEMINI 2000 with class C amplifiers decpwr level double level new power level for DODEV channel Changes the first decoupler high power level to the value specified To reset the power back to the standard dhp level use decpwr dhp Switching between low power decoupling dhp n and high power decoupling dhp x as well as switching between different levels of low power decoupling uses relays whose switching time is about 10 ms and are not provided for in the standard pulse sequence capability Neither function should prove necessary because extremely low levels of decoupling are provided for in dhp mode by using very small 0 to 30 values of dhp level specifies the decoupler high power level from 0 lowest to 25
442. lso controlled Each of these parameters can have multiple states status A sets each parameter to the state described by the first letter of its value status B uses the second letter etc If a pulse sequence has more status statements than there are status modes for a particular parameter control reverts to the last letter of the parameter value Thus if dm ny status C will look for the third letter find none and then use the second letter y and turn the decoupler on actually leave the decoupler on The states do not have to increase monotonically during a pulse sequence It is perfectly possible to write a pulse sequence that starts with status A goes later to status B then goes back to status A then to status C etc Homospoil is treated slightly differently than the decoupler If a particular homospoil code letter is y delays coded as hsde lay that occur during the time the st atus corresponds to that code letter will begin with a homospoil pulse the duration of which is determined by the parameter hst Thus if hs ny all hsdelay delays that occur during status B will begin with a homospoil pulse The final status always occurs during acquisition at which time a homospoil pulse is not permitted Thus if a particular pulse sequence uses Status A status B and status C dm and other decoupler parameters can have up to three letters but hs has only two because having hs y during status C is mean
443. lso create local variables containing arrayed information by itself No dimensioning statement is required the variable just expands as necessary The only constraint is that the array must be created in order element 1 is first element 2 01 999165 00 A0800 VNMR 6 1C User Programming 33 Chapter 1 MAGICAL II Programming 34 second and so on The following example shows how an array might be created and all values initialized to 0 i 1 repeat newarray i 0 i i 1 until 1 gt 10 Arrays of string variables are identical in every way to arrays of real variables except that the values are strings If for example a user has entered dm nny yyy the following macro plots each spectrum with the proper label i 1 repeat select i pl write plotter 0 wc2max 10 Decoupler mode s dm i page i Sitl until i gt size dm Accessing an array element that does not exist displays the error message variable_name index index out of bounds Using a string as an index rather than an integer displays the error message Index for variable_name index must be numeric or Index must be numeric Finally using an array as an index displays the error message Index for variable_name must be numeric scalar or Index must be numeric scalar Expressions An expression is a combination of variables constants and operators Parentheses can be used to group together a combination of expressions Multiple nesti
444. lso updated Refer to the VNMR Command and Parameter Reference and the User Guide Imaging for additional information about creategtable Pulse Sequence Programming Table 37 lists the pulse sequence statements related to the XYZ PFG module The system can be programmed by using the statements rgradient channel value and zgradpulse value delay Pulse sequences g2pul cand profile cin vnmr psglib are examples of using the gradaxis parameter and the rgradient statement Table 37 Performa XYZ PFG Module Statements magradient gradlvl Simultaneous gradient at the magic angle magradpulse gradlvl gradtime Simultaneous gradient pulse at the magic angle mashapedgradient Simultaneous shaped gradient at the magic angle mashapedgradpulse Simultaneous shaped gradient pulse at the magic angle rgradient axis value Set gradient to specified level vagradpulse Variable angle gradient pulse vashapedgradient Variable angle shaped gradient vashapedgradpulse Variable angle shaped gradient zgradpulse value delay Create a gradient pulse on the z channel mashapedgradient pattern gradlvl gradtime theta phi loops wait mashapedgradpulse pattern gradlvl gradtime theta phi vagradpulse gradlvl gradtime theta phi vashapedgradient pattern gradlvl gradtime theta phi loops wait vashapedgradpulse pattern gradlvl gradtime theta phi 154 To produce a gradient at any angle by the combination of two or more gradi
445. lt src_expno gt src_blk_no src_trace_no dest_expno dest_blk_no dest_trace_no rfblk lt src_expno gt src_blk_no dest_expno dest_blk_no rfdata lt src_expno gt src_blk_no src_start_loc dest_expno dest_blk_no dest_start_loc num_points rftrace lt src_expno gt src_blk_no src_trace_no dest_expno dest_blk_no dest_trace_no 296 Compress or Uncompress Data The most common form of reformatting for imaging has been to use the 1ashc command to convert compressed data sets to standard data sets in order to run ft 2d on the data With the implementation of t2d nf lt index gt flashc is no longer necessary However use of lashc is still necessary for converting compressed compressed data to compressed or standard formats Move and Reverse Data The commands mf mfb1k m data and mft race are available to move data around in a FID file or to move data from one experiment FID file to another experiment FID file These commands give users more control in reformatting their data by allowing them to move entire FID files individual blocks within a FID file individual traces within a block of a FID file or sections of data within a block of a FID file To illustrate the use of the move FID commands Listing 12 is an example with code from a macro that moves a 3D dataset from an arrayed 3D dataset to another experiment that runs ft3d on the data The index variable is the array index
446. luate to the characters x y or z Be sure not to confuse the characters x y or z with the strings x y or z loops is a value from 1 to 255 that allows the user to loop the selected waveform Note that the given value is the number of loops to be executed and that the values 0 and 1 cause the pattern to execute once Due to a digital hardware bug affecting looping patterns must be carefully constructed to achieve the desired results wait is a keyword either WAIT or NOWAIT that selects whether or not a delay is inserted to wait until the gradient is completed before executing the next element The total time it will wait is width loops tag 1s a unique integer that tags the gradient element from any other gradient elements used in the sequence include standard h pulsesequence shaped2Dgradient hsine d3 0 0 gpe x 0 NOWAIT 1 delay d3 shaped2Dgradient hsine d4 gpe y 0 NOWAIT 2 01 999165 00 A0800 VNMR 6 1C User Programming 24 7 Chapter 3 Pulse Sequence Statement Reference Related dps_show Draw delay or pulses in a sequence for graphical display rgradient Set gradient to a specified level shapedgradient Provide shaped gradient pulse to gradient channel vgradient Set gradient to a level determined by real time math shapedincgradient Generate dynamic variable gradient pulse Applicability Syntax Description Arguments Systems with WFG on imaging or
447. lues in gauss cm of the components for the static portion of the gradient in the logical reference frame stepl step2 step3 are values in gauss cm of the components for the step size change in the variable portion of the gradient vmulti1 vmult2 vmult3 are real time math variables v1 to v14 ct zero one two three or references to AP tables t 1 to t 60 whose associated values vary dynamically in a manner controlled by the user pe3_gradient gro sgpe nv 2 0 sgpe2 nv2 2 0 0 0 sgpe sgpe2 zero v6 v8 phase_encode3_gradient Oblique gradient with phase encode in 3 axes pe_shapedgradient Oblique shaped gradient with phase encode in one axis Applicability Syntax Description Arguments Not applicable on MERCURY VX MERCURY and GEMINI 2000 pe_shapedgradient pattern width statl stat2 stat3 step2 vmult2 wait tag char pattern name of gradient shape file double width width of gradient in sec double statl stat2 stat3 static gradient components double step2 variable gradient step size codeint vmult2 real time math variable int wait WAIT or NOWAIT int tag tag to a gradient element Sets a static oblique shaped gradient plus one oblique phase encode shaped gradient This is same as phase_encode_shapedgradient except in pe_shapedgradient the Euler angles are read from the default set for imaging 1im2 is automatically set to nv 2 where nv is usually the
448. maining fields Ggroup is 2 ACQUISITION Dgroup is 1 ACQUISITION active is 1 ON and intptr is 64 not used 2 Parameter tof has 1 value the real number 1160 3 Parameter tof has 0 enumerable values The following file is an example of a multielement array character parameter beatles 1 beatles 228002101 64 2 4 john 3 paul george ringo 4 0 01 999165 00 A0800 VNMR 6 1C User Programming 303 Chapter 5 Parameters and Data The beatles file is made up of the following lines 1 The parameter has the name of beatles subtype is 2 string basictype is 2 string 8 0 0 is max min step not really used for strings Ggroup is 2 acquisition Dgroup is 1 ALL protection is 0 active is 1 ON 64 is a terminating number 2 There are four elements to this variable therefore it is arrayed john is the first element in the array 3 paul george and ringo are the other three elements in the array 4 0 zero is the terminating line 5 5 Modifying Parameter Displays in VNMR The VNMR display commands and macros dg dg1 dg2 dgs and ap are controlled by template parameters specifying the content and form of the information displayed The template parameters have the same name as the respective command or macro for example the display created by the dg command is controlled by the parameter dg in the experiment s current parameter set To modify an existing template parameter such as dg enter param
449. manufacturer or contact the pacemaker manufacturer to determine the effect on a specific pacemaker Pacemaker wearers should also always notify their physician and discuss the health risks of being in proximity to magnetic fields Wearers of metal prosthetics and implants should contact their physician to determine if a danger exists Refer to the manuals supplied with the magnet for the size of a typical 5 gauss stray field This gauss level should be checked after the magnet is installed WARNING Keep metal objects outside the 10 gauss perimeter from the centerline of the magnet The strong magnetic field surrounding the magnet attracts objects containing steel iron or other ferromagnetic materials which includes most ordinary tools electronic equipment compressed gas cylinders steel chairs and steel carts Unless restrained such objects can suddenly fly towards the magnet causing possible personal injury and extensive damage to the probe dewar and superconducting solenoid The greater the mass of the object the more the magnet attracts the object Only nonferromagnetic materials plastics aluminum wood nonmagnetic stainless steel etc should be used in the area around the magnet If an object is stuck to the magnet surface and cannot easily be removed by hand contact Varian service for assistance 01 999165 00 A0800 VNMR 6 1C User Programming 19 SAFETY PRECAUTIONS Warning Notices continued 20 Refer to the man
450. mbered then when the transient number is ct the 01 999165 00 A0800 VNMR 6 1C User Programming 105 Chapter 2 Pulse Sequence Programming 106 number of the statement of the table that will be used is ct mod n remember that ct starts at 0 on the first transient since ct represents the number of completed transients AP Table Notation Special notation is available within the table file to simplify entering the table statements and to impart specific attributes to any table within that file Indicates the table segment within the parentheses is to be replicated in its entirety times where ranges from 1 to 64 before preceding to any succeeding statements or segments Do not include any space after For example t1 0 1 2 3 tl table 012012012 Indicates each statement in the table segment within square brackets is to be replicated times where ranges from 1 to 64 before going to the next statement in that segment Do not include any space after For example t1 0 1 2 3 t1 table 000111222 Imparts the divn return attribute to the table and indicates that the actual index into the table is to be the index divided by the number where ranges from 1 to 64 is called the divn factor and can be explicitly set within a sequence for any table see setdivnfactor This attribute provides a fold level of table compaction to the acquisition processor The notation mu
451. me lt num gt returns the names of the selected files If you have selected more than one file all their names are returned each separated with a space from its neighboring names in the list An optional second argument lets you return an individual file name This argument is a number giving the position in the list of the file names to return e filesinfo redisplay displays again the files in the current directory Use the filesinfo command with this argument whenever a change occurs in the file system for example a file is deleted or created Using the Files Program with the Menu System To better understand how the i1esinfo command interacts with MAGICAL programming consider how the Display button might work We will use the cat command to display the file The first requirement is to limit the number of selected files to 1 because additional steps would be necessary to distinguish between the different files if more than one file is selected later we will show how to work with more than one file A first attempt might be as follows filesinfo number S f Sn if f 1 then filesinfo name Sn cat n else write error You must select one element abort endif 01 999165 00 A0800 VNMR 6 1C User Programming 59 Chapter 1 MAGICAL II Programming This becomes the text of a macro that the menu arranges to have executed when the Display button is pressed But suppose the user selected a directory or a compile
452. me gradient strength horizontal bore imaging system or if the axes have different gradient strengths vertical bore PFG gradients Next the user is prompted for a name for the gradient coil and that name is then used in the gcoil and sysgcoil parameters in order to correctly translate between DAC and gauss cm values Finally the macro prompts the user for the boresize of the magnet 51 mm the gradient rise time 40 us and the maximum gradient strength obtainable for each axis Note that the gradient strengths are not equal and the amplifier does not limit the combined output If the parameter gcoil does not exist in a parameter set and must be created you must set the protection bit that causes the macro __gcoil to be executed when the value for gcoil is changed Setting the protection bit can be done two ways e Use the macro updtgcoil which will create the gcoil parameter if it does not exist e Create gcoil with the following commands create gcoil string setprotect gcoil set 9 In an experiment that uses gradient coils the sysgcoil parameter can be set to the coil name specified with the creategt able macro and then the updt gcoil macro can be run to update the local gcoil parameter from the global sysgcoil parameter When the local gcoil parameter is updated the local gxmax gymax gzmax trise and 01 999165 00 A0800 VNMR 6 1C User Programming 153 Chapter 2 Pulse Sequence Programming boresize parameters are a
453. me of the header values it is possible to make a program that reads FDF data files to perform simple transformations For example to flip data left to right set span j spang origin g origing span y Creating FDF Files To generate files in the FDF format the following macros are available to write out single or multislice images e For the current imaging software including sequences sems mems and flash use the macro svib directory lt f m i o gt where directory is the directory name desired dat is appended to the name f outputs data in floating point format this is the default m or i outputs data as 12 bit integer values in 16 bit words and b outputs data in 8 bit integer bytes e For older style SIS imaging sequences and microimaging sequences use the macro svsis directory lt f m gt where directory f and m are defined the same as svib Raw data from the FID file of the current experiment can be saved as an FDF file with the svfdf directory macro where directory is the name of the directory in which to store the files dat is appended to the name Data is saved in multiple files with one trace per file The files are named id0001 fdf fid0002 fdf etc The procpar file from the current experiment is also saved in the same directory Another way to create the FDF files is to edit or create a header defining a set of data with no headers and attach it to the data file with the
454. ments apply to the GEMINI 2000 and only coarse power can be controlled on MERCURY VX and MERCURY systems Table 13 Power Control Statements apovrride declvloff declvlon decpower value dec2power value dec3power value dec4power value decpwr level decpwrf value dec2pwrf dec3pwrf ipwrf val ipwrm val obspower va va va lue lue lue device string lue device string lue obspwrf value power val lue device pwrf value device pwrm value device rlpwrm rJ lvalue device 01 999165 00 A0800 Override internal software AP bus delay Return first decoupler back to normal power Turn on first decoupler to full power Change first decoupler power linear amplifier Change second decoupler power linear amplifier Change third decoupler power linear amplifier Change deuterium decoupler power linear amplifier Set decoupler high power level class C amplifier Set first decoupler fine power Set second decoupler fine power Set third decoupler fine power Change transmitter or decoupler fine power with IPA Change transmitter or decoupler linear mod with IPA Change observe transmitter power linear amplifier Set observe transmitter fine power Change transmitter or decoupler power linear amplifier Change transmitter or decoupler fine power Change transmitter or decoupler linear mod power Set transmitter or decoupler linear mod
455. menu system and displays the menu menu_name e g menu workspace To select a menu without immediate activation enter newmenu menu_name This is most useful when selecting which menu will be active when an interactive command exits For example entering newmenu manipulate_1D ds causes the menu manipulate_1D to be displayed when the Return button in the ds menu is selected The command newmenu current_menu returns the name of the currently active menu to the string parameter current_menu The lastmenu parameter contains the name of the menu that displays when the Return button is selected Programming Menus An active menu consists of two arrayed string parameters mlabel and mst ring e mlabel i contains the label that is displayed on the ith button The total length of all the displayed labels cannot exceed the width of the screen 80 characters e mstring i contains the text string that is executed when the ith button is selected The mst ring text string is essentially identical to a macro with three exceptions e No new lines that is carriage returns should appear in the text string e As with all strings single quotes in the text string must be replaced by reverse single quotes C or by the escape sequence backslash with single quote e The length for the text string is subject to a maximum Of course a menu string can simply contain the name of a macro which is not subject to any limitat
456. meters with units The 1 4 U unit is applied as a suffix to the numerical value e g 10k 100p suffix identifies the name for the unit e g k label is the name to be displayed when the axis parameter is set to the value of the suffix e g kHz mand b are the slope and intercept respectively of the linear relationship A convenient place to put unit commands for all users is in the boot up macro Put private unit commands in a user s login macro sing Dialog Boxes from a Macro A macro can pop up a dialog box for obtaining user input through the dialog command This command has the following syntax dialog definition_file output_file lt nowait gt The definition_file argument is the name of the definition file specified as an absolute path that specifies the layout of the dialog box The syntax of this file is the same as the def files for GLIDE discussed in the manual Walkup NMR Using GLIDE Normally this file is stored in Svnmruser dialoglib or vnmrsystem dialogl1lib Note however that dialog does not follow the VNMR standard of first looking for a file in vnmruser and then in vnmrsystem The output_file argument is a text output file as specified in the definition file A good place for the output file is in tmp After the user answers the prompts and clicks the OK button the answers are written to this output file The macro can then use the command lookup to read the results Existing macros can be wr
457. milarly interleaved The format of the integers and the organization as complex pairs must be specified in the data file header VNMR Use of Binary Data Files To understand how VNMR uses individual binary data files consider the example of a simple Fourier transform followed by the display of the spectrum The FT is performed with the command ft which acts as follows 1 Copy processing parameters from curpar into procpar 2 If FID is not in the fid file buffer open the fid file if not already open and load it into buffer Initialize the data file with the proper size using parameter fn Convert integer FID into floating point and store result in data file buffer 3 4 5 Apply de drift correction and first point correction 6 Apply weighting function if requested 7 Zero fill data if required 8 Fourier transform data in data file buffer At this point the data file buffer contains the complex spectrum Unless other FTs are done which use up more memory space than assigned to the data file buffer the data is not automatically written to the file expn datdir data at this time Joining a different experiment or the command flush would perform such a write operation The ds command takes the following steps in displaying the spectrum 1 If data is not in phasefile buffer or if the phase parameters have changed ds tries to open the phase file if not already open and load data into the buffer if it is there If d
458. mitter setstatus channel on mode sync mod_freq Gating States Use status state to control decoupler and homospoil gating in a pulse sequence where state is A to Z e g status A or status B Parameters controlled by status are dm first decoupler mode dmm first decoupler modulation mode and hs homospoil For systems with a third or fourth rf channel dm2 and dm3 second and third decoupler modes and dmm2 and dmm3 second and third decoupler modulation mode are also under status control For systems with a deuterium decoupler channel as the fourth decoupler dm4 and dmm4 are under status control Each of these parameters can have multiple states st atus A sets each parameter to the state described by the first letter of its value status B uses the second letter etc If a pulse sequence has more st at us statements than there are status modes for a particular parameter control reverts to the last letter of the parameter value Thus if dm ny status C will look for the third letter find none and then use the second letter y and turn the decoupler on The st atus statement is available on the GEMINI 2000 although homospoil is not possible on GEMINI 2000 systems Use setstatus channel on mode sync mod_freq to control decoupler gating as well as decoupler modulation modes GARP CW WALTZ etc channel is VNMR 6 1C User Programming 01 999165 00 A0800 2 3 Spectrometer Control OBSch DE
459. mples Related rlpower Applicability Syntax Description Arguments CAUTION Examples Related Chapter 3 Pulse Sequence Statement Reference channel specifies the gradient to set It uses one of the characters X x y y Z or z In imaging channel can be gread gphase or gslice value specifies the gradient level by a real number a DAC setting in imaging from 4096 0 to 4095 0 for the Performa I PFG module and from 32768 0 to 32767 0 for the Performa II PFG module rgradient z 1327 0 dps_show Draw delay or pulses in a sequence for graphical display getorientation Read image plane orientation shapedgradient Generate shaped gradient vgradient Set gradient to a level determined by real time math zgradpulse Create a gradient pulse on the z channel Change power level linear amplifier systems Systems with linear amplifiers This statement is due to be eliminated in future versions of VNMR software Although it is still functional you should not write pulse sequences using it and should replace it in existing sequences with obspower decpower dec2power or dec3power as appropriate rlpower power device double power new level for coarse power int device OBSch DECch DEC2ch or DEC3ch Changes transmitter or decoupler power the same as the power statement but avoids consuming a real time variable for the value On systems with the Outp
460. mpressed data sets nf can be set to nv ns or nv nv2 where nv is the number of phase encode increments in the second dimension nv2 is the number of phase encode increments in the third dimension and ns is the number of slices To give another view of data formats which will help when using the move FID commands each ni increment or array element is stored as a data block in a FID file and each nf FID is stored as a trace within a data block in a FID file 01 999165 00 A0800 VNMR 6 1C User Programming 295 Chapter 5 Parameters and Data Table 39 Commands for Reformatting Data Commands flashc Convert compressed 2D data to standard 2D format mf lt from_exp gt to_exp Move FIDs between experiments mfblk Move FID block mfclose Close memory map FID mfdata Move FID data mfopen lt src_expno gt dest_expno Memory map open FID file mftrace Move FID trace rfblk Reverse FID block rfdata Reverse FID data rftrace Reverse FID trace rsapply Reverse data in a spectrum tabc lt dimension gt Convert data in table order to linear order tcapply lt file gt Apply table conversion reformatting to data tcclose Close table conversion file tcopen lt file gt Open table conversion file x flashc lt ms mi rare lt traces gt lt echoes gt mfblk lt src_expno gt src_blk_no dest_expno dest_blk_no mfdata lt src_expno gt src_blk_no src_start_loc dest_expno dest_blk_no dest_start_loc num_points mftrace
461. ms with an Output board only see page 72 for types of boards a 0 2 us delay internally precedes the AP analog port bus statements power obspower decpower and dec2power The apovrride statement prevents this 0 2 us delay from being inserted prior to the next and only the next occurrence of one of the these AP bus statements Decoupler Power Level Switching On UNTYINOVA UNITY plus and UNITY systems with class C or linear amplifiers declvlon and declvloff switch the decoupler power level between the power level set by the high power parameter s to the full output of the decoupler The statement declvlon gives full power on the decoupler channel declvloff switches the decoupler to the power level set by the appropriate parameters defined by the amplifier type dhp for class C amplifiers or dpwr for a linear amplifiers If dhp n these statements do not have any effect on systems with class C amplifiers but still function for systems with linear amplifiers If declvlon is used make sure declv1lof f is used prior to time periods in which normal controllable power levels are desired for example prior to acquisition Full decoupler power should only be used for decoupler pulses or for solids applications On GEMINI 2000 broadband systems declvlon sets the power of the decoupler to the level set by the parameter pp1v1 This is an important distinction decoupler pulse power on the GEMINI 2000 broadband is controlled by the
462. n e x sets XY32 modulation On the YINOVA and UNITYplus c g m p r u w and x are available On the UNITY and VXR S c f n p and w are available sync is TRUE decoupler is synchronous on UN TYINOVA and UNITYplus systems only or FALSE decoupler is asynchronous mod_freq is the modulation frequency setstatus DECch TRUE w FALSE dmf setstatus DEC2ch FALSE c FALSE dmf2 status Change status of decoupler and homospoil Store an array of integers in a real time AP table All systems except the GEMINI 2000 settable tablename numelements intarray codeint tablename real time table variable int numelements number in array int intarray pointer to array of elements Stores an integer array in a real time AP table The autoincrement or divn return attributes can be subsequently associated with a table defined by sett able by using setautoincrement and setdivnfactor table is the name of the table t1 to t 60 number_elements is the size of the table intarray is aC array that contains the table elements which can range from 32768 to 32767 Before calling settable this array must be predefined and predimensioned in the pulse sequence using C statements settable t1 10 int_array getelem Retrieve an element from an AP table loadtable Load AP table elements from table text file 01 999165 00 A0800 VNMR 6 1C User Programmi
463. n gt gt Brings the graphics or text window to the top of the screen It also controls whether parameter changes or commands that write to a window cause a window to appear Format a real number or convert a string for output format real_number length precision string_var format string upper lower isreal return_var Using first syntax takes a real number and formats it into a string with the given length and precision Using second syntax converts a string variable into a string of characters all upper case or all lowercase or tests the first argument to verify that it satisfies the rules for a real number 1 is returned if the first argument is a real number otherwise a zero is returned 01 999165 00 A0800 input Syntax Description lookup Syntax Description nrecords Syntax Description psgset Syntax Description vnmr_confirmer Syntax Description write Syntax Description 01 999165 00 A0800 1 3 Relevant VNMR Commands Receive input from keyboard input lt lt prompt gt lt delimiter gt gt varl var2 Receives characters from the keyboard and stores them into one or more string variables prompt is a string that is displayed on the command line The default delimiter is acomma Look up and return words and lines from text file lookup options returnl return2 number_returned Searches a text file for a word and returns to the user subsequent
464. n in seconds for a 90 tip angle tipangle_resoln is the resolution in tip angle degrees to which the decoupling pattern is stored in the waveform generator phase is the phase of the spin lock It must be a real time variable v1 to v14 etc or a real time constant zero one etc ncycles is the number of times that the spin lock pattern is to be executed 1 dec2spinlock mlev16 p290 dres2 v1 42 2 dec2spinlock lock2 pwx2 dres2 vl1 cycles decspinlock Set spin lock waveform control on first decoupler spinlock Set spin lock waveform control on obs transmitter Set spin lock waveform control on third decoupler UNITYINOVA and UNITYplus systems with a waveform generator on rf channel for the third decoupler dec3spinlock pattern 90_pulselength tipangle_resoln phase ncycles char pattern name of DEC text file double 90_pulselength 90 deg pulse length of channel double tipangle_resoln resolution of tip angle codeint phase phase of spin lock int ncylces number of cycles to execute 01 999165 00 A0800 VNMR 6 1C User Programming 187 Chapter 3 Pulse Sequence Statement Reference Description Arguments Examples Related decstepsize Applicability Syntax Description Arguments Examples Related dec2stepsize Applicability Syntax Description Arguments Examples Related 188 VNMR 6 1C User Programming Executes a w
465. n 3 axes rgradient channel value Set gradient to specified level shapedgradient Shaped gradient pulse shaped2Dgradient Arrayed shaped gradient function shapedincgradient Dynamic variable gradient function shapedvgradient Dynamic variable shaped gradient function vgradient Set gradient to level determined by real time math vagradient Variable angle gradient vagradpulse Pulse controlled variable angle gradient vashapedgradient Variable angle shaped gradient vashapedgradpulse Variable angle pulse controlled shaped gradient zgradpulse value delay Create a gradient pulse on the z channel zero_all_gradients Set all gradients to zero For the argument list refer to the statement reference in Chapter 3 Generating a Gradient Pulse To create a gradient pulse on the z channel with given amplitude and duration use zgradpulse value delay where value is used the same as in rgradient and delay is any delay parameter e g zgradpulse 1234 0 d2 shapedgradient pattern width amp channel loops wait generates a shaped gradient where pattern isa file in shapelib width is the pulse length amp is a value that scales the amplitude of the pulse channel is the same as used with rgradient loops is the number of times 1 to 255 to loop the waveform and wait is WAIT or NOWAIT for whether or not a delay is inserted to wait until the gradient is completed before executing the next statement e g shapedgradient hsin
466. n filenames spell filename awk pattern filename chmod newmode filenam date du k df k filesystem kill process id login username mail man commandname ps units W uname a gt filename gt gt filename lt filename vertical bar Wildcard character for a single character in filename operations Wildcard character for multiple characters in filename operations 01 999165 00 A0800 VNMR 6 1C User Programming 279 Chapter 4 UNIX Level Programming Run program in background amp Abort the current process Control C Logout or end of file Control D 4 3 UNIX Commands Accessible from VNMR Several UNIX commands are accessible directly from VNMR including the vi edit shell shelli and w commands Opening a UNIX Text Editor from VNMR Entering vi file or edit file from VNMR invokes a UNIX text editor for editing the name of the file given in the argument e g vi myfile On the Sun workstation a popup screen contains the editing window On the GraphOn terminal the main screen becomes the editing window Exiting from the editor closes the editing window The most useful UNIX program you can learn is vi the powerful UNIX text editor UNIX provides at least two other text editors ed and text edit that are easier to learn than vi but vi is the most widely used UNIX text editor and worth learning because of its many features A text editor is necessary if you wish to prepare or edit
467. n processor memory Applicability All systems except MERCURY VX MERCURY and GEMINI 2000 Syntax clearapdatatable Description Zeroes the acquired data table at times other than at the start of the execution of create_delay Applicability Syntax Description Arguments a pulse sequence when the data table is automatically zeroed This statement is generally not needed list Create table of delays Not applicable on MERCURY VX MERCURY and GEMINI 2000 create_delay_list list nvals list_number double list pointer to list of delays int nvals number of values in list int list_number number 0 255 for each list Stores global lists of delays that can be accessed with a real time variable or table element for dynamic setting in pulse sequences The lists need to be created in order starting from 0 using the 1ist_number argument or by setting the 1ist_number argument to 1 which makes the software allocate and create the next free list and give the list number as a return value Each list must have a unique and sequential 1ist_number There can be a maximum of 256 lists depending on the size of the lists The lists are stored in data memory and compete for space with the acquisition data for each array element If a list is created the return value is the number of the list 0 to 255 if an error occurs the return value is negative create_delay_list creates what is called a global list Global lis
468. name of the destination table t 1 to t 60 263 VNMR 6 1C User Programming Chapter 3 Pulse Sequence Statement Reference Examples Related ttmult Applicability Syntax Description Arguments Examples Related ttsub Applicability Syntax Description Arguments table_modis the name of the table t 1 to t 60 that modifies table_dest Each element in table_dest is modified by the corresponding element in table_modand the result is stored in t able_dest The number of elements in table_dest must be greater than or equal to the number of elements in table_mod No element in table_mod can equal 0 moduloval is the modulo value taken on the result of the operation if moduloval is greater than 0 ttdiv t28 t42 6 ttadd Add an AP table to a second table ttmult Multiply an AP table by a second table ttsub Subtract an AP table from a second table Multiply an AP table by a second table All systems except the GEMINI 2000 ttmult table_dest table_mod moduloval codeint table_dest real time table variable codeint table_mod real time table variable int moduloval modulo value of result A run time vector operation that multiplies one AP table by a second table table_dest is the name of the destination table t 1 to t 60 table_modis the name of the table t 1 to t 60 that modifies table_dest Each element in table_dest is modified by the corresponding el
469. names Try to use concise natural language to describe the value rather than leaving the user to look it up a manual For example Spectral Width is much better than sw Don t over use capital letters in labels Spectral width is better than SPECTRAL WIDTH e Group parameters in logical blocks For example group decoupling parameters together e Try to always display a parameter in about the same spot on the same pane Don t make the user hunt all over a pane or many panes e Use color but use it wisely We have used blue for titles seagreen for important fields and indianred for alert conditions These colors are easy to read and somewhat 01 999165 00 A0800 VNMR 6 1C User Programming 341 Chapter 6 Customizing Graphics Windows 342 muted but still convey some sense of meaning Remember that some people are color blind and that a particular color such as red may not always carry the same connotations for others e Try not to clutter the pane There is no need to fill every cell in the matrix Use space to highlight regions of interest on the pane e We have chosen a 16 x 10 matrix The first column of entries is 3 columns wide with a fourth for menus of units The other columns of entries are in general 3 matrix columns wide including the units e Keep things neat Watch the size of value boxes Most entry fields in the samples have a width of 7 and are justified center Thi
470. nary experiments then generate an effective transient counter as follows if phasel 0 assign ct vl10 v10 01234 else phasel 1 dbl ct vl10 v10 02468 if phasel 2 incr vl10 v10 13579 01 999165 00 A0800 VNMR 6 1C User Programming 149 Chapter 2 Pulse Sequence Programming Now a single phase cycle can be derived from v10 instead of from ct If phase1 0 each element of this phase cycle is selected If phase1 1 only the odd elements are selected the first third fifth etc transients for which ct 0 2 4 If phase1 2 the even elements only are selected ct odd Real Mode Phased 2D TPPI For TPPI experiments the increment index is typically needed at some point in the phase calculation The simplest way to obtain the index is to use the built in real time constant id2 This can be used in a construction such as if phasel 3 add v11 id2 v11 which adds the increment value which starts at 0 to the phase contained in v11 2 15 Gradient Control for PFG and Imaging 150 UNITYTNOVA MERCURY VX MERCURY UNITYplus UNITY and GEMINI 2000 systems support gradient control for applications using the optional pulsed field gradient PFG and imaging The configuration parameter gradt ype set by the config program specifies the presence of gradient hardware and its capabilities The available gradient control statements are listed in Table 35 MERCURY VX MERCURY and GEMINI 2000
471. nclude lt standard h gt include lt revmode c gt for reverse configuration pulsesequence hsdelay d1 decrgpulse pl zero rofl rofl delay d2 decrgpulse pw oph rofl rof2 In addition to setting the proper modes for each channel of the amplifier the revmode file also configures the local oscillator L O relay properly so that the local oscillator signal is taken from the decoupler board When used in the reverse mode the X nucleus decoupling signal comes from the observe board This board does not contain any of the hardware decoupler modulations such as WALTZ decoupling Furthermore this decoupling signal is not controlled by the parameter dm which controls under status control the H signal For these reasons any pulse sequence in which X nucleus decoupling is desired during acquisition on a single broadband system must use programmed decoupling with explicit acquisition see the hmqcr c sequence for an example Do not code sequences in which the status statement is used to switch on the decoupler If the parameter dm is used it must be used indirectly as in hmqcr c The legrelay parameter provides override capability over the magnet leg high band and low broad band rf signal routing This is useful when a probe has a high and low band nucleus double tuned to a coil and the standard logic would switch to the wrong probe connection A system has this override capability if it us
472. nd 10 75 us on other systems Stopping a waveform generator adds 1 us on the UN TYINOVA 2 3 us on UNITYplus and 4 3 us on other systems The modulation mode is to or from p The waveform generator also has an offset or propagation delay which is discussed below e Modulation frequency If the modulation frequency changes us is added on the UNITYTNOVA 4 6 us on the UNITYplus and 6 45 us on other systems Note that for the UNITYTNOVA and UNITYplus this is different for a shaped pulse The modulation frequency can change if the statement set status is called with a modulation frequency different from the parameter corresponding to the transmitter set or if the modulation mode changes to or from g and r Ifthe change isto g and r the modulation frequency is internally scaled changing the frequency 01 999165 00 A0800 VNMR 6 1C User Programming 143 Chapter 2 Pulse Sequence Programming Table 32 AP Bus Overhead Delays Internal Delay us MERCURY VX GEMINI UNITY UNITYplus 2000 VXR S Output Board Systems Pulse Sequence UNITY Statements WOVA and MERCURY acquire 1 0 pre 0 0 pre 0 0 pre 0 5 post 0 0 post 0 0 post xmtrphase 0 5 Wad 3 45 2S 2539 dcphase dcplrphase dcplr2phase dcplr3phase power obspower 0 5 4 8 2 3 4 3 4 5 decpower dec2power dec3power pwrf obspwrf 0 5 4 6 6 45 decpwrf dec2pwrf dec3pwrf offset 4 0 86 4 10 35 15 25 15 05 S 15 25 S standard 2b 35 E Pee E L
473. nd gating the amplifier off dec3shaped_pulse gauss pl v9 rofl rof2 decshaped_puls Perform shaped pulse on first decoupler shaped_pulse Perform shaped pulse on observe transmitter Set spin lock waveform control on first decoupler Systems with waveform generator on rf channel for the first decoupler decspinlock pattern 90_pulselength tipangle_resoln phase ncycles char pattern name of DEC text file double 90_pulselength 90 deg pulse length in sec double tipangle_resoln resolution of tip angle codeint phase phase of spin lock int ncylces number of cycles to execute Executes a waveform generator controlled spin lock on the first decoupler handling both rf gating and the mixing delay Arguments can be variables which require the appropriate get val and get st r statements to permit changes via parameters see the second example below pattern is the name of the text file in the shape1lib directory that stores the decoupling pattern leave off the DEC file extension 90_pulselength is the pulse duration in seconds for a 90 tip angle 186 VNMR 6 1C User Programming 01 999165 00 A0800 Examples Related dec2spinlock Applicability Syntax Description Arguments Examples Related dec3spinlock Applicability Syntax Chapter 3 Pulse Sequence Statement Reference tipangle_resoln is the resolution in tip angle degrees to which the decoupl
474. nd their order The label on each button is controlled by the label attribute of each button definition When an entry in the scrolling window is clicked on with the left mouse button a full summary of that entry is displayed below the buttons The results parameter controls the details of the scrolling window and the summary display Figure 12 shows the default status window The num attribute sets the number of experiments to be displayed in the scrolling window This value along with the number of items in the showfields parameter determines the overall height of the status window The col attribute defines how much space to make available for character display This attribute controls the overall width of the status window The logt ite attribute specifies the title to be displayed above the summary window Color is used by the st at us program to indicate the experiment status Possible statuses are queued active complete shimming and error Color selection for each status are made with the appropriate color attribute Two other color attributes are defined e selectcolor sets the color of the currently selected entry from the scrolling window That is the entry where the left mouse was clicked e totalcolor is the color of the number of total experiments shown at the top of the status command The sort attribute defines the default sorting criterion to be used to display the experiments in the scrolling window The choices
475. nd turned on during acquisition The default state of the receiver is off 01 999165 00 A0800 VNMR 6 1C User Programming 23 7 Chapter 3 Pulse Sequence Statement Reference Related rgpulse Syntax Description Arguments Examples Related rgradient Applicability Syntax Description for UNTYINOVA systems except for whole body systems and for imaging pulses sequences that have the initparms_sis_ statement at the beginning initparms_sis Initialize parameters for spectroscopy imaging sequences LOvrolt Turn off receiver gate and amplifier blanking gate revron Turn on receiver gate and amplifier blanking gate recoff Turn off receiver gate only Pulse observe transmitter with amplifier gating rgpulse width phase RG1 RG2 double width length of pulse in sec codeint phase real time variable for phase double RG1 gate delay before pulse in sec double RG2 gate delay after pulse in sec Pulses the observe transmitter with amplifier gating The amplifier is gated on prior to the start of the pulse by RG1 sec and gated off RG2 sec after the end of the pulse The total length of this event is therefore not simply width but width RG1 RG2 The amplifier gating times RG1 and RG2 may be specified explicitly The parameters rofl and rof2 are often used for these times These parameters are normally hidden parameters not displayed on the screen and entered by the user Their v
476. ne S par lookup readline steps lookup readline S start lookup readline delta gain y Scount 0 repeat Spar S count 1 start Scount delta count count 1 until count gt steps if lt gt 5 then da endif 50 Lines 13 16 checks if the output file tmp array exists and if so deletes it Next the dialog command is called Line 17 which pops up the dialog box as shown in Figure 1 The dialog command waits for the user to click the OK or Cancel button OK executes the SAVE command that is dialog saves the output to the output file and then CLOSE closes the dialog box VNMR 6 1C User Programming 01 999165 00 A0800 Figure 1 Dialog Box for array Macro 1 4 Using Dialog Boxes from a Macro Cancel closes the dialog box without creating the output file e Lines 18 21 check if the output file exists If Cancel was clicked the output file does not exist and return is executed this is why it was deleted in lines 12 16 If OK was clicked the output file can be read by the lookup macro as is done in lines 22 26 e The remainder of the macro stores the values into the array Listing 2 is the definition file in this case Svnmruser dialoglib array Listing 2 Definition File for dialog Version of array Macro label Parameter input output Sinput cols 30 remark Enter the name of the pa
477. ne list 33 38 linear amplifier systems decoupler power 175 power control 91 power level 233 239 stabilization 83 transmitter power level 221 linear attenuator used for pulse shaping 135 linear modulator power 240 linear modulators 93 lines in a file 41 linewidth measurement 38 link loading 70 lint command UNIX 70 list files in a directory UNIX 278 listenoff command 47 listenon command 47 listing names of macros 44 lists frequency 166 global 167 offset 167 lk_hold statement 128 151 211 Ik_sample statement 128 151 211 llamp parameter 33 llfrq parameter 33 In command 43 278 loading AP table elements from file 107 211 loading AP table statements 105 loading macros into memory 28 45 loadtable statement 105 107 211 loc parameter 318 local oscillator frequency 89 local variables 32 33 34 lock correction circuitry 151 set to hold 211 set to sample 211 lock feedback loop 152 lock level 48 locList file 321 log directory 284 log files 281 284 logarithm of a number 43 logical frame 155 login command 47 login command UNIX 279 login macro 27 28 46 login procedure 277 logout UNIX 280 long type variables 74 lookup command 41 loop end 194 195 multislice end 195 multislice start 216 phase encode end 195 phase encode start 227 start 212 statements 157 types 36 loop statement 100 101 125 141 212 low band nuclei 83 01 999165 00 A0800 Index l
478. nent for the step size change in the variable portion of the gradient vmult 2 is areal time math variable v1 v14 ct zero one two three or reference to AP tables t 1 to t 60 whose associated values vary dynamically in a manner controlled by the user lim2 is a value representing the dynamic step that will generate the maximum gradient value for each component This provides error checking in pulse sequence generation and is normally nv 2 ang is Euler angle psi in degrees with the range 90 to 90 ang2 is Euler angle phi in degrees with the range 180 to 180 ang3 is Euler angle theta in degrees with the range 90 to 90 oblique_gradient Execute an oblique gradient oblique_shapedgradient Execute a shaped oblique gradient pe_gradient Oblique gradient with PE on 1 axis phase_encode_shapedgradient Oblique sh gradient with PE on 1 axis phase_encode3_gradient Oblique gradient with PE on 3 axes phase_encode3_shapedgradient Oblique sh gradient with PE on 3 axes phase_encode3_gradient Oblique gradient with phase encode in three axes Applicability Syntax Description Not applicable on MERCURY MERCURY VX and GEMINI 2000 phase_encode3_gradient statl stat2 stat3 stepl step2 step3 vmultl vmult2 vmult3 liml lim2 1im3 angl ang2 ang3 double statl stat2 stat3 static gradient components double stepl step2 step3 var gradient stepsize codeint vmultl vmult2 vmult3 real
479. never be called from a macro because it will remove all macros from memory including the macro containing purge Furthermore purge where the argument is the name of the macro containing the purge command should never be called e Ifa macro is loaded in memory and you try to modify the macro from a separate UNIX window the copy in memory is not changed so if you execute the macro again VNMR executes the old copy To avoid this use macrovi or macroedit to edit the macro or if you have already edited the macro from another window use macrold to replace the macro loaded in memory with the new version e If you wish to create a personal macro with the same name as a system macro already in memory you must use purge to clear the system macro from memory so the version in your personal maclib directory will subsequently be executed If one macro calls another macro inside a loop you might improve performance by having the calling macro load the called macro before entering the loop execute the loop and then remove the called macro from memory with the purge command 1 2 Programming with MAGICAL MAGICAL has many features including tokens variables expressions conditional statements and loops To program in MAGICAL you need to know about the main features described in this section Tokens In a computer language a token is defined as a character or characters that is taken by the language as a single thing or unit T
480. ng 243 Chapter 3 Pulse Sequence Statement Reference setuserap Applicability Syntax Description Arguments Examples Related shapedpulse Applicability shaped_pulse Applicability Syntax Description setautoincrement Set autoincrement attribute for an AP table setdivnfactor Set divn return attribute and divn factor for AP table setreceiver Associate the receiver phase cycle with an AP table Set user AP register UNITYTINOVA systems setuserap value register real value value sent to user AP register int register AP bus register number 0 1 2 or 3 Sets a value in one of the four 8 bit AP bus registers that provide an output interface to user devices The outputs of these registers go to the USER AP connectors J8212 and J8213 located on the back of the left console cabinet These outputs have a 100 ohm series resistor for circuit protection value isa signed or unsigned number real or integer to output to the specified user AP register The number is truncated to an 8 bit byte register is the AP register number mapped to output lines as follows e Register 0 is J8213 lines 9 to 16 e Register 1 is J8213 lines 1 to 8 e Register 2 is J8212 lines 9 to 16 e Register 3 is J8212 lines 1 to 8 setuserap 127 0 0 readuserap Read input from user AP register vsetuserap Set user AP register using real time variable Perform shaped pulse on observe transmitter This statement is
481. ng of parentheses is allowed In making expressions combine only variables and constants of the same type e Real variables and constants only with other real variables and constants e String variables and constants only with other string variables and constants The type of a local variable a variable whose name begins with a is determined by the context in which it is first used The only ambiguity is when a local variable is first used as a return argument of a command such as input as discussed in the previous section on local variables If an illegal combination is attempted an error message is displayed Can t assign STRING value value to REAL variable variable_name or Can t assign REAL value value to STRING variable variable name VNMR 6 1C User Programming 01 999165 00 A0800 1 2 Programming with MAGICAL Mathematical Expressions Expressions can be classified as mathematical or Boolean Mathematical expressions can be used in place of simple numbers or parameters Expressions can be used in parameter assignments such as in pw 0 6 pw90 or as input arguments to commands or macros such as in pa 5 sc 50 vp When parameters are changed as a result of expressions the normal checks and limits on the entry of that particular parameter are followed For example if nt 7 the statement nt 0 5 nt will end with nt 3 just as directly entering nt 3 5 would have resulted in nt 3 Other examples of t
482. ngth is 0 2 us The overhead at the start and end of the shaped pulse varies e UNITYINOVA 1 us start 0 end e UNITYplus 5 75 us start 0 end e System with Acquisition Controller board 10 75 us start 4 3 us end e System with Output board 10 95 us start 4 5 us end If the length is less than 0 2 us the pulse is not executed and there is no overhead When using the linear attenuator and the small angle phase shifter to generate a shaped pulse the dec3shaped_pulse statement creates AP tables on the fly for amplitude and phase It also uses the real time variables v12 and v13 to control the execution of the shape It does not use AP table variables For timing and more information see the description of apshaped_dec3pulse Note that if using AP tables with shapes that have a large number of points the FIFO can become overloaded with words generating the pulse shape and FIFO Under flow errors can result pattern is the name of a text file in the shapelib directory that stores the rf pattern leave off the RF file extension width is the duration in seconds of the pulse phase is the phase of the pulse It must be a real time variable v1 to v14 etc or a real time constant zero one etc RG1 is the delay in seconds between gating the amplifier on and gating the third decoupler on the phaseshift occurs at the beginning of this delay RG2 is the delay in seconds between gating the third decoupler off a
483. ning of this delay RG2 is the delay in seconds between gating the final rf transmitter off and gating the amplifier off sim3pulse pw pl p2 oph v10 vl1l rofl rof2 sim3pulse pw 0 0 p2 oph v10 vl rofl rof2 decpulse Pulse the decoupler transmitter decrgpulse Pulse decoupler transmitter with amplifier gating dps_show Draw delay or pulses in a sequence for graphical display rgpulse Pulse observe transmitter with amplifier gating simpulse Pulse observe decoupler channels simultaneously sim4pulse Simultaneous pulse on four channels Simultaneous pulse on four channels UNITYTNOVA UNIT Yplus and UNITY systems with two or more independent rf channels sim4pulse pwl pw2 pw3 pw4 phasel phase2 phase3 phase4 RG1 RG2 double pwl pw2 pw3 pw4 pulse length in sec codeint phasel phase2 variables for phase codeint phase3 phase4 variables for phase double RG1 gating delay before pulse double RG2 gating delay after pulse Allows for simultaneous pulses on up to four different channels If any of the pulses are set to 0 0 no pulse is executed on that channel Timing limitations connected with the difference in pulse widths is covered in the description of simpulse pwl pw2 pw3 and pw4 are the pulse length in seconds of channels OBSch DECch DEC2ch and DEC3ch respectively phasel phase2 phase3 and phase4 are the phases of the corresponding pulses Each must be real time variable v
484. nnel RF power amp maximum duty cycle exceeded on decouple channel RF power amp overheated on decouple channel RF power amp power supply failed on decouple channel RF power monitoring disabled on decouple channel Reflected power monitoring disabled on decouple channel RF power amp monitoring disabled on decouple channel Quad reflected power too high RF Power Monitor board not responding STOP button pressed on operator s station Cable to Operator s Station disconnected Main gradient coil over temperature limit Main gradient coil water is off Head gradient coil over temperature limit RF limit read back error RF Power Monitor Board watchdog error RF Power Monitor Board self test failed RF Power Monitor Board power supply failed RF Power Monitor Board CPU failed ILI Board power failed SDAC duty cycle too high ILI Spare 1 trip ILI Spare 2 trip Quad hybrid reflected power monitor BYPASSED SDAC duty cycle limit BYPASSED Head Gradient Coil errors BYPASSED Main Gradient Coil errors BYPASSED Channel 1 RF power exceeds 10s SAR limit Channel 1 RF power exceeds 5min SAR limit Channel 1 peak RF power exceeds limit Channel 1 RF Amp control cable error Channel 1 RF Amp reflected power too high 78 VNMR 6 1C User Programming 01 999165 00 A0800 2 3 Spectrometer Control Table 5 Acquisition Status Codes continued 1536 Chann
485. notation called shell scripts can be created allowing users to build their own commands This section provides a very short overview of such programming refer to the UNIX literature for more information Shell Variables and Control Formats As a programming language the shell provides string valued variables 1 2 The number of variables is available as and the file being executed is available as 0 Control flow is provided by special notation including if case while and for The following format is used if command list not Boolean while command list then command list do command list else command list done fi case word in for name in wl w2 pattern command list do command list Dss done esac Shell Scripts The shell scripts below show two ways a shell script might be written for the same command In both scripts the command name lower is selected by the user and the intent of the command is to convert a file to lower case but the scripts differ in features The first script lower command to convert a file to lower case usag lower filenam output filename lower tr A 2 a z lt 1 gt 1 lower The second script lower a command to convert a file to lower case usag lower filename or lower inputfile outputfile output filename lower or output file case S in 1 tr A Z a z lt 1 gt Sl lower 2 tr A Z a z lt Sl gt 27 echo Usa
486. ns For example for rotorperiod v4 if v4 contains the value 1700 the rotor period is 170 us and the rotor speed is 1E 7 1700 5882 Hz rotorperiod v4 rotorsync Gated pulse sequence delay from MAS rotor position xgate Gate pulse sequence from an external event Gated pulse sequence delay from MAS rotor position Systems with MAS magic angle spinning rotor synchronization hardware rotorsync rotations codeint rotations variable for turns to wait Inserts a variable length delay that allows synchronizing the execution of the pulse sequence with a particular orientation of the sample rotor When the rotorsync Statement is encountered the pulse sequence is stopped until the number of rotor rotations has occurred rotations isa real time variable that specifies the number of rotor rotations to occur before restarting the pulse sequence rotorsync v6 rotorperiod Obtain rotor period of MAS rotor xgate Gate pulse sequence from an external event S setautoincrement Set autoincrement attribute for an AP table Applicability Syntax Description Arguments Examples Related 01 999165 00 A0800 All systems except the GEMINI 2000 setautoincrement table codeint table real time table variable Sets the autoincrement attribute in an AP table The index into the table is set to 0 at the start of an FID acquisition and is incremented after each access into the table Tables using th
487. nt and can range from 0 to 4095 60 dB on YNTYZNOVA or UNITYplus about 6 dB on other systems device is OBSch for the observe transmitter or DECch first decoupler On N YINOVA and UNITYplus only device can also be DEC2ch second decoupler or DEC3ch third decoupler MERCURY VX MERCURY and GEMINI 2000 systems do no have fine power control You can use the fixed channel statement obspwrf value decpwrf value dec2pwrf value and dec3pwrf or rlpwrm value device to avoid arguments using real time variables These statements change transmitter or decoupler VNMR 6 1C User Programming 01 999165 00 A0800 2 3 Spectrometer Control power on systems with linear amplifiers but value is either a real number or a variable and is stored in a C variable of type double The ipwrf value device string and ipwrm value device string statement changes interactively the transmitter or decoupler fine power or linear modulators by adjusting the optional fine attenuators The value and device arguments are the same as pwrf string canbe any string the first six letters are used in acqi This statement will generate interactive parameter adjustment IPA information only when the command gf or go acqi is typed When the command go is typed this statement is ignored by the pulse sequence Use the pwr f pulse statement for this purpose Do not execute pwrf and ipwrf in the same pulse sequence as they cancel each other s effect On syste
488. nt as set by the parameter lockacqtc The correction remains in effect until the statement 1k_hold is called Related 1k_hold Set lock correction circuitry to hold correction loadtable Load AP table elements from table text file Applicability All systems except the GEMINI 2000 Syntax loadtable file char file name of table file Description Loads AP table elements from a table file a UNIX text file It can be called multiple times within a pulse sequence but make sure that the same table name is not used more than once within all the table files accessed by the sequence Table values can be greater than equal to or less than zero Arguments file is the name of a table file in a user s private tablib or in the system tablib Examples loadtable tabletest Related getelem Retrieve an element from an AP table 01 999165 00 A0800 setautoincrement Set autoincrement attribute for an AP table setdivnfactor Set divn return attribute and divn factor for AP table setreceiver Associate the receiver phase cycle with an AP table settable Store an array of integers in a real time AP table 211 VNMR 6 1C User Programming Chapter 3 Pulse Sequence Statement Reference loop Start loop Syntax 1 loop count index codeint count number of times to loop codeint index real time variable to use during loop Syntax 2 loop n count index int n 1 2 3 same as corresponding endloop double co
489. nt based parameters 32 expfit command UNIX 42 expl command 42 explicit acquisition 74 129 159 expn directory file 284 exponential curves 42 exponential value of a number 43 expressions 34 external device interface 157 external event gating 275 external timebase 131 external user devices 97 external variables 32 extr directory 284 extracted 2D planes 284 F f3 file 284 FALSE Boolean value 35 FDF files attach header to data file 294 creating 294 directory naming convention 290 format 291 header format 291 magic number 291 splitting data and header parts 295 transformations of data 294 why developed 290 fdf files 290 fdfgluer command 294 fdfsplit command 295 FID complete 75 FID data 287 fid file 284 288 fid file extension 283 FID files 283 290 310 350 VNMR 6 1C User Programming FIFO underflow error 77 file binary format 283 existence test 46 header of binary file 283 information 47 protection mode UNIX 279 text format 283 file attribute 317 File button 59 files command 59 Files Main Menu 59 Files program 58 files_main menu 59 filesinfo command 59 61 fine attenuators 92 142 fine power 209 234 240 control 91 decoupler 179 transmitter 222 fine power routine 125 199 fine grained pulse shaping 141 Finish button 70 first point correction 288 fixed phases entry 67 fixpar macro 27 flag of a parameter test 48 flag type parameter 299
490. nt in the ms loop loop that it is ending apv2 is a real time variable that holds the current counter value This variable should be the same variable that was in the apv2 counter variable in the ms loop loop that it is ending endmsloop seqcon 1 vl12 msloop Multislice loop endloop End loop endpeloop End phase encode loop End phase encode loop Not applicable on MERCURY VX MERCURY and GEMINI 2000 endpeloop state apv2 char state compressed or standard codeint apv2 current counter value Ends a loop that was started by a pe loop statement state is either c to designate the compressed mode or s to designate the standard arrayed mode It should be the same value that was in the state argument in the peloop loop that it is ending apv2 is areal time variable that holds the current counter value This variable should be the same variable that was in the apv2 counter variable in the peloop loop that it is ending endpeloop seqcon 1 v12 peloop Phase encode loop 01 999165 00 A0800 VNMR 6 1C User Programming 195 Chapter 3 Pulse Sequence Statement Reference endloop End loop endmsloop End multi slice loop G gate Description getarray Applicability 196 Syntax Description Arguments Examples Related Device gating obsolete Not supported Replace gate statements as follows gate DECUPLR TRUE by a decon statement gate DECUPLR FALSE bya decof
491. nt pulse zero_all_gradients Zero all gradients Variable angle gradient pulse Not applicable on MERCURY VX MERCURY and GEMINI 2000 vagradpulse gradlvl gradtime theta phi double gradlvl gradient amplitude in G cm double gradtime gradient time in sec double theta angle from z axis in degrees double phi angle of rotation in degrees Applies a gradient pulse of amplitude gradlv1 at an angle theta from the z axis and rotated about the xy plane at an angle phi Information from a gradient table is used to scale and set the values correctly The values applied to each gradient axis are as follows x gradlvl sin phi sin theta y gradlvl cos phi sin theta gradivl cos theta Zz The gradients are turned off after gradtime seconds vagradpulse is simpler to use if there are no other actions while the gradients are on vagradient is used if there are actions to be performed while the gradients are on gradlvl1 is the gradient amplitude in gauss cm gradt ime is the time in seconds to apply the gradient theta is the angle in degrees from the z axis phi is the angle of rotation in degrees about the xy plane vagradpulse 3 0 0 001 54 7 0 0 magradient Simultaneous gradient at the magic angle magradpulse Simultaneous gradient pulse at the magic angle mashapedgradient Simultaneous shaped gradient at the magic angle mashapedgradpulse Simultaneous shaped grad
492. nteger to AP table elements tsdiv Divide an integer into AP table elements tsmult Multiply an integer with AP table elements Add an AP table to a second table All systems except the GEMINI 2000 ttadd table_dest table_mod moduloval codeint table_dest real time table codeint table_mod real time table int moduloval modulo value of variable variable result A run time vector operation that adds one AP table to a second table tablenamedest is the name of the destination table t 1 to t 60 table_modis the name of the table t 1 to t 60 that modifies table_dest Each element in table_dest is modified by the corresponding element in table_modand the result is stored in t able_dest The number of elements in table_dest must be greater than or equal to the number of elements in table_mod moduloval is the modulo value taken on the result of the operation if is greater than 0 ttadd t28 t42 6 moduloval ttaiv Divide an AP table into a second table ttmult Multiply an AP table by a second table Etsub Subtract an AP table from a second table Divide an AP table into a second table All systems except the GEMINI 2000 ttdiv table_dest table_mod moduloval codeint table_dest real time table variable codeint table_mod real time table variable int moduloval modulo value of result A run time vector operation that divides one AP table into a second table table_dest is the
493. nter 71 99 idecpulse statement 84 201 idecrgpulse statement 84 202 idelay statement 80 202 identifier 29 35 IEFE standard floating point format 283 if then else endif conditional form 36 ifzero statement 101 105 202 image file names 290 image plane orientation 197 imaginary component of FID data 287 imaging module 150 imaging related statements 155 implicit acquisition 74 implicit expressions 35 implicitly arrayed delay 148 inactive parameter 48 incdelay statement 80 203 incgradient statement 155 203 incr statement 99 204 increment an integer value 204 increment counts 71 increment index 150 incremental delay 80 203 207 incrementing a loop 37 index out of bounds 34 indices of an array 33 indirect detection 205 indirect detection experiments 146 147 indirect statement 205 infields parameter 314 info directory 284 init_gradpattern statement 157 206 init_rfpattern statement 157 205 init_vscan statement 157 207 initdelay statement 80 207 initialize incremental delay 207 initialize parameters for imaging sequences 207 initialize real time variable 207 208 initialize string variable 33 initparms_sis statement 96 initval statement 101 208 input arguments 35 input command 41 input tools 40 inset command 58 integ command 39 integer array stored in AP table 243 integer mathematical statements 99 integer values add 160 assign 164 decrement 180 352 VNMR 6 1C
494. nterpreting files Applications should not assume certain names for certain file however specific applications may assume default names when outputting files Directories The directory naming convention is lt name gt dat The directory can contain a parameter file and any number of FDF files The name of the parameter file is procpar a standard VNMR name File Names Each type of file has a different name in order to make the file more recognizable to the user For image files the name is image nnnn fdf where nnnn is a numeric string from 0000 to 9999 For volumes the name is volume nnnn fdf where nnnn is also a numeric string from 0000 to 9999 Programs that read FDF files should not depend on these names because they are conventions and not definitions VNMR 6 1C User Programming 01 999165 00 A0800 5 2 FDF Flexible Data Format Files Compressed Files Although not implemented at this time compression will be supported for the data portion of the file The headers will not be compressed A field will be put in the header to define the compression method or to identify the command to uncompress the data File Format The format of an FDF file consists of a header and data e Listing 11 is an example of an FDF header The header is in ASCII text and its fields are defined by a data definition language Using ASCII text makes it easy to decipher the image content and add new fields and is compatible with the ASCII fo
495. nulib can be changed by the system administrator only however changes to it are available to all users Menus are themselves a special form of macros Specifically menus are macros containing other macros Invoking a menu macro sets up the menu bar in which each button is itself a macro This combination of macros allows the entire system to be run using menus without limiting operation to just a simplified mode Help Files Custom help files can be created to go with custom menus The help file for a particular menu has the same name as the menu file When a user clicks on the Help button or enters the help command VNMR looks for the help file in the following order 1 Inthe user s help directory This directory is a subdirectory of the user s VNMR directory A typical path is home vnmrl vnmrsys help 2 Inthe directory pointed to by the he lppath parameter if the parameter helppath is defined in the user s global parameter file This parameter must contain an absolute path not a relative path 3 Inthe system help directory This directory is a subdirectory of the system VNMR directory A typical path might be vnmr help The same as with menu files each user can have their own private help files A file in the user s help directory takes precedence over the system he 1p directory The system help directory can only be changed by the system administrator however changes to the help directory are available to all use
496. number of purposes but the two most important are control of the pulse sequence execution for looping and conditional execution for example and calculation of phases For each pulse in the sequence the phase is calculated dynamically at the start of each transient rather than entirely at the start of this experiment This allows phase cycles to attain essentially unlimited length because only one number must be calculated for each phase during each transient By contrast attempting to calculate in advance a phase cycle with a cycle of 256 transients and different phases for each of 5 different pulses would require storing 256 x 5 or 1280 different phases Real Time Variables and Constants The following variables and constants can be used for real time calculations vi tov14 Real time variables used for calculations of loops phases etc They are at the complete disposal of the user The variables point to 16 bit integers which can hold values of 32768 to 32767 ct Completed transient counter points to a 32 bit integer that is incremented after each transient starting with a value of 0 prior to the first experiment This pattern 0 1 2 3 4 is the basis for most calculations Steady state transients invoked by the ss parameter do not change ct VNMR 6 1C User Programming 01 999165 00 A0800 2 4 Pulse Sequence Statements Phase and Sequence Control bsctr Block size counter points to a 76 bit integer that is decremented
497. number of rotations to delay for example rotorsync v6 The delay allows synchronizing the execution of the pulse sequence with a particular orientation of the sample rotor When the rotorsync statement is encountered the pulse sequence is stopped until the number of rotor rotations has occurred as referenced by the real time variable given e To halt the pulse sequence from an external event use xgate events where events is a double variable e g xgate 2 0 When the number of external events has occurred the pulse sequence continues Both rotorsync and xgate can be used but there is a very important distinction between the two rotorsync synchronizes to the exact position of the rotor whereas xgate synchronizes to the zero degree position of rotation For example if the rotor is at 90 then for xgate 1 0 the pulse sequence will begin when the rotor is at zero degrees a rotation of 270 however for the equivalent rotorsync the pulse sequence will begin when the rotor is at 90 or 360 rotation 2 10 Pulse Shaping Waveform generators are an optional piece of equipment available on UN TYINOVA UNITYplus and UNITY for controlling rf pulse shapes on one or more rf channels programmed decoupling patterns and gradient shapes for imaging applications For pulse shaping programming using Pbox see the manual User Guide Liquids Pulse control of the waveform generators consists of two separate parts 01 999165 00 A08
498. nz endif codeint vi real time variable to check for zero Executes succeeding statements if vi is zero If vi is non zero and an elsenz statement exits before the next endif statement execution moves to the 202 VNMR 6 1C User Programming 01 999165 00 A0800 Arguments Examples Related incdelay Applicability Syntax Description Arguments Examples Related incgradient Applicability Syntax Chapter 3 Pulse Sequence Statement Reference elsenz statement Conditional execution ends when the endif statement is reached It is not necessary for any statements to appear between the if zero and the elsenz or between the el senz and the endif statements Syntax 1 is used with UTYINOVA MERCURY VX MERCURY UNITY plus UNITY and VXR S systems Syntax 2 is used with GEMINI 2000 systems vi is a real time variable v1 to v14 oph etc that is tested for being either zero or non zero n is the same value 1 2 or 3 as used in the corresponding el senz or endif statements mod2 ct vl w1 010101 ifzero v1 test if vl is zero pulse pw v2 execute if vl is zero delay d3 execute if vl is zero elsenz vl test if vl is non zero pulse 2 0 pw v2 execute if vl is non zero delay d3 2 0 execute if vl is non zero endif v1 end conditional execution elsenz Execute succeeding statements if argument is nonzero endif End ifzero
499. o a bidirectional TTL compatible 8 bit buffer which has a 100 ohm series resistor for circuit protection readuserap Stops parsing acodes acquisition codes until the lines in the buffer have been read and the value placed in to the specified real time variable In order for the parser to parse and stuff more words into the FIFO before underflowing the readuserap statement puts in a 500 us delay after reading the input However depending on what is to be done after reading the lines a longer delay may be needed to avoid FIFO underflow If an error occurs in reading a warning message is sent to the host and a value of 1 is returned to the real time variable 236 VNMR 6 1C User Programming 01 999165 00 A0800 Arguments Examples Related recoff Applicability Syntax Description Related recon Applicability Syntax Description Chapter 3 Pulse Sequence Statement Reference vi is a real time variable v1 to v14 etc that indexes a signed or unsigned number read from user AP register 3 Check a value read in from input register and execute a pulse if it is the expected value double testval testval getval testval set value to check initval testval v2 loop two vl reset below makes loop go readuserap vl until expected value reads in delay d2 sub vl1 v2 v3 ifzero v3 pulse pw oph assign one v1 elsenz v3 assign zero vl reset counter endif
500. o be turned off without affecting other protection bits settype parameter type lt tree gt changes the type of an existing parameter A string parameter can be changed into a string or flag type or a real parameter can be changed into a real delay frequency pulse or integer type setvalue parameter value lt index gt lt tree gt sets the value of any parameter in a tree set value bypasses normal range checking for parameter entry It also bypasses any action that would be invoked by the parameter s protection bits 300 VNMR 6 1C User Programming 01 999165 00 A0800 5 4 Creating and Modifying Parameters e setenumeral parameter N enuml enum2 enumN lt tree gt sets possible values of a string type or flag type parameter in a parameter tree e setgroup parameter group lt tree gt sets the group also called the Ggroup of a parameter in a tree The group argument can be all sample acquisition processing display or spin e setdgroup parameter dgroup lt tree gt sets the Dgroup of a parameter in a tree The dgroup argument is an integer The usage of set dgroup is set by the application Only the experimental user interface uses this command currently To Display a Parameter Use display parameter lt txree gt to display one or more parameters and their attributes from a parameter tree The first argument can be one of the following three options a parameter name to display the at
501. o is entered ipwrf is ignored by the pulse sequence use rlpwrf for this purpose Do not execute rlpwrf and ipwrf together because they cancel each other s effect power Is the new fine power level It can range from 0 0 to 4095 0 60 dB on UNITYTNOVA and UNITYplus about 6 dB on other systems 01 999165 00 A0800 VNMR 6 1C User Programming 209 Chapter 3 Pulse Sequence Statement Reference Examples Related ipwrm Applicability Syntax Description Arguments Examples Related irgpulse Applicability Syntax Description Arguments device is OBSch observe transmitter or DECch first decoupler For the UNITYINOVA and UNITYplus only device can also be DEC2ch second decoupler or DEC3ch third decoupler label1 is the short character string to be given to the slider when displayed in the Acquisition window acqi program ipwrf powr OBSch fpower ipwrf 2000 0 DECch dpwrf rlpwrf Set transmitter or decoupler fine power Change transmitter or decoupler lin mod power with IPA All systems except MERCURY VX MERCURY and GEMINI 2000 ipwrm value device label double value new linear modulator power level int device OBSch DECch DEC2ch or DEC3ch char label slider label in acqi Functions the same as r1pwrm statement except that ipwrm generates interactive parameter adjustment IPA information when gf or go acqi is ent
502. o other actions while the gradients are on magradient is used if there are actions to be performed while the gradients are on gradlv1 is the gradient pulse amplitude in gauss cm gradt ime is the time in seconds to apply the gradient magradpulse 3 0 0 001 magradient Simultaneous gradient at the magic angle mashapedgradient Simultaneous shaped gradient at the magic angle mashapedgradpulse Simultaneous shaped gradient pulse at the magic angle vagradient Variable angle gradient vagradpulse Variable angle gradient pulse vashapedgradient Variable angle shaped gradient vashapedgradpulse Variable angle shaped gradient pulse zero_all_gradients Zero all gradients mashapedgradient Simultaneous shaped gradient at the magic angle Applicability Syntax Description Not applicable on MERCURY VX MERCURY and GEMINI 2000 mashapedgradient pattern gradlvl gradtime theta phi loops wait char pattern name of gradient shape text file double gradlvl gradient amplitude in G cm double gradtime gradient time in seconds double theta angle from z axis in degrees double phi angle of rotation in degrees int loops number of waveform loops int wait WAIT or NOWAIT Applies a simultaneous gradient with shape pat tern and amplitude gradlv1 on the x y and z axes at the magic angle to Bo Information is used 01 999165 00 A0800 VNMR 6 1C User Programming 213 Chapter 3 Pulse Sequenc
503. oacsugescbatoundeceashiesansoonibvsysueoasterionsens 81 Figure 4 Pulse Observe and Decoupler Channels Simultaneously 0 0 0 0 eee eeeeseceteeseeeeeeees 85 Figure 5 Waveform Generator Offset Delay on UN YINOVA Systems ccceecccceeeceeeeeeeseeceeeeeneens 145 Figure 6 Magnet Coordinates as Related to User Coordinates 0 cee eeeeseceecsseeeeeeseeeeeeeees 292 Figure 7 Single String Display Template with Output 200 0 eee eeeece cnet cee caeeseceaeeeeeneeees 304 Figure 8 Multiple String Display Template o oo eee eeeeeeceseeeeeeaeecaecaeecaessaeaeseaeeeeneeees 305 Figure 9 Default Interface enter Program eeeeeessesecseeseeseeseceeeeceseneeeeseeseeseeseeaecaeeeeeaeeaees 315 Figure 10 Alternate Interface enter Program 0 c cc teeeeecseeseesesseceeeeceseneeeesecseeseeseeaecaeeeeeneeaees 317 Figure 11 Second Alternate Interface enter Program 000 0 eee eeesecseeseeceeeeeceeeeseeeeeseeeeeeetees 318 Figure 12 Default Interface status Program ee ssesessecseeeeesecsecaeeseesecaecesesesaeceseeesaesaeeteees 325 Figure 13de Window wssessessvessevseacsvsncvsahestascesacsavasves SEa EEEE EEE E E TESERO E EEEE EEE EEEN ES 325 Figure 14 Matrix Window dg Program messesssrsssrescireisiisestiiesresrrveoiiresrreescrvsiseusireveeredoisosstes 330 Figure 15 Interaction Elements Window dg Program 0 cceceeesseesceeseceeeeseceeeeeeeeeeseeeeeeeeees 330 01 999165 00 A0800 VNMR 6 1C User Programming 17 List of Tables T
504. observe and decouple channels simultaneously sim3pulse Pulse simultaneously on 2 or 3 rf channels simshaped_pulse Perform simultaneous two pulse shaped pulse sim3shaped_pulse Perform a simultaneous three pulse shaped pulse vgradient Set gradient to a level determined by real time math zgradpulse Create a gradient pulse on the z channel dps_skip Skip graphical display of next statement Syntax dps_skip Description Skips dps display of the next statement The statement following dps_skip is not shown in the graphical display Related dps_off Turn off graphical display of statements dps_on Turn on graphical display of statements dps_show Draw delay or pulses for graphical display of a sequence E elsenz Execute succeeding statements if argument is nonzero Syntax 1 elsenz vi codeint vi 01 999165 00 A0800 real time variable tested as 0 or not 193 VNMR 6 1C User Programming Chapter 3 Pulse Sequence Statement Reference Syntax Description Arguments Examples Related endhardloop Applicability Syntax Description Related endif Syntax Description Arguments Examples Related endloop Syntax 194 VNMR 6 1C User Programming 2 elsenz n int n 1 2 or 3 same as corresponding ifzero Placed between the if zero and endif statements to execute succeeding statements if vi is nonzero The elsenz statement can be omitted if it is not desired It is also not neces
505. obsphase decphase RG1 RG2 performs a simultaneous two pulse shaped pulse on the observe transmitter and the first decoupler under waveform generator control obsshape is the name of the text file that contains the rf pattern to be executed on the observe transmitter decshape is the name of the text file that contains the rf pattern to be executed on the first decoupler obswidth is the duration of the pulse on the observe transmitter decwidth is the duration of the pulse on the first decoupler obsphase is the phase of the pulse on the observe transmitter it must be a real time variable decphase is the phase of the pulse on the first decoupler it must be a real time variable RG1 is the delay between unblanking the amplifier and gating on the first rf transmitter all phase shifts occur at the beginning of this delay and RG2 is the delay between gating off the final rf transmitter and blanking the amplifier for example simshaped_pulse gauss hrm180 pw pl v2 v5 rofl rof2 The overhead at the beginning and end of the simultaneous two pulse shaped pulse varies with the system and acquisition controller board e On UNTYINOVA 1 45 us at start 0 at end e On UNITYplus 11 5 us at start O at end 01 999165 00 A0800 VNMR 6 1C User Programming 135 Chapter 2 Pulse Sequence Programming 136 e On systems with an Acquisition Controller board 21 5 us at start 8 6 us at end e On systems with an Output board 21 7 Us at start 8 8 us
506. of NUR spectrometers The worst that could happen is that the previous user logged out requiring the next user to log back in with their name and password After completing this login procedure the VNMR software starts automatically and again you do not need to have contact with UNIX if you don t wish to do so UNIX provides more than a hundred tools that can perform almost anything short of complex mathematical manipulations like a Fourier transform For example UNIX has commands to search through your files to sort line lists to tell you who is on the system to run a program unattended at night and much more The more performance you want to get out of your computer and the more you want to be able to do the more it will benefit you to learn about UNIX Dozens of manuals are available for your Sun computer system and surely you will not want to or be able to read them all For those with no exposure to UNIX however we strongly recommend that you read any user s guides that accompanied your Sun workstation After that a book we have found to be particularly useful is The UNIX System by S R Bourne Addison Wesley For coverage of the Solaris environment a good book is Guide to Solaris by John Pew ZD Press 01 999165 00 A0800 VNMR 6 1C User Programming 2 7 Chapter 4 UNIX Level Programming 4 2 UNIX A Reference Guide A brief overview of the UNIX computer operating system and its associated commands appears below For
507. off Stop blanking observe or decoupler amplifier obsolete 4 164 blankon Start blanking observe or decoupler amplifier obsolete 165 clearapdatatable Zero all data in acquisition processor MEMOTY ou cece ee eeeeeeeeeeeee 165 create_delay_list Create table of delays ei eecsseseeseesececeesessecaeeecsseeaeseseeceaeatseeees 165 create_freq_list Create table of frequencies cecesceesecseceseceeceeeeeceeeeeeeeeenseeseeeeeees 166 ereate_offset_list Create table of frequency offsets cceceseceeceseeeeceeeeeeeeeeeeeeeseeeeeees 167 dbl Double an integer value oo eee eee cee ceecseeeeceseeeceeeeeeeeeeeeeeeeeeeeeees 168 dcphase Set decoupler phase Obsolete eee eesecesecesseceececeteeeneeeeeeeeneeeeeeens 168 dcplrphase Set small angle phase of 1st decoupler rf type C or D ue 169 dcplr2phase Set small angle phase of 2nd decoupler rf type Cor D ee 169 dcplr3phase Set small angle phase of 3rd decoupler rf type C or D ow 170 decblank Blank amplifier associated with first decoupler cee eeeeeeseeeeeeeee 170 dec2blank Blank amplifier associated with second decoupler cesses 170 dec3blank Blank amplifier associated with third decoupler cs ceeeeseeeeeeeee 171 declvloff Return first decoupler back to normal power eseeeeeeeseeeeeeeee 171 01 999165 00 A0800 VNMR 6 1C User Programming 9 Table of Contents declvlon decoff dec2off dec30ff decof fiset
508. oints sampling_interval Explicitly acquire data clearapdatatable Zero data in acquisition processor memory endhardloop End hardware loop starthardloop num_repetitions Start hardware loop Controlling Hardware Looping Hardware looping capability is determined by the type of acquisition controller board used on the system see Types of Acquisition Controller Boards page 72 e Data Acquisition Controller boards Pulse Sequence Controller boards and Acquisition Controller boards offer expanded capability with respect to hardware looping and timing precision e Output boards with Part No 00 953520 05 or 00 953520 06 have hardware looping capability but are limited in the implementation of hardware loops within a pulse sequence e Output boards with Part No 00 953520 0 where is from 0 to 4 have no hardware looping capability and will not be discussed further e STM Output board on MERCURY VX and MERCURY systems offers expanded capability with respect to hardware looping Use the starthardloop numrepetitions and endhardloop statements start and end a hardware loop The numrepetitions argument to starthardloop must be a real time integer variable such as v2 and not a regular integer a real number or a variable The number of repetitions of the hardware loop must be two or more If the number of repetitions is 1 the hardware looping feature itself is not activated A hardware loop with a count equal to 0 is no
509. omizing the enter interface Almost everything about the enter interface can be modified by the user This includes whether certain choices are presented and whether choices are presented as check boxes or require typed input Requests for alternative information also can be added Window Configuration Files The interface to the enter program is controlled by one of following configuration files supplied in the directory vnmr asm e auto conf when defining an experiment for a current automation run e enter conf when setting up an automation run with a Carousel SMS or NMS sample changer e entervast conf when setting up an automation run with the VAST accessory e enterlcnmr conf when setting up an automation run with the LC NMR accessory The enter conf file is duplicated in Listing 14 with the lines numbered for reference Any line in the file that starts with a is a comment line The interface presented by this configuration file is shown in Figure 9 01 999165 00 A0800 VNMR 6 1C User Programming 311 Chapter 6 Customizing Graphics Windows Listing 14 Text of enter conf File I Enter configuration information 2 3 5 infields identifies the items that will be displayed by the 4 enter program The order of the listed items is the order De in which they will be displayed 6 set infields
510. ommand 308 wtlib directory 308 309 wtp file extension 308 X X channel 287 X nucleus decoupling 147 xcheck style 316 xcheckcustom style 317 xgate statement 131 275 xmtroff statement 95 275 VNMR 6 1C User Programming 361 Index xmtron statement 95 275 xmtrphase statement 87 88 128 144 275 xradio style 316 xradiocustom style 317 XY32 modulation 243 Y Y channel 287 Z z channel gradient pulse 276 zero acquired data table 129 zero all gradients 276 zero data in acquisition processor memory 165 zero fill data 288 zero pointer 99 zero_all_gradients statement 276 zgradpulse statement 144 151 154 276 362 VNMR 6 1C User Programming 01 999165 00 A0800
511. ommand line any time you wish to use your new pulse sequence Most of the pulse sequences in vnmr psglib are set up ina similar fashion and so are easily accessible The newpul c pulse sequence also contains examples of phase cycling There are two basic ways to perform arbitrary user defined phase cycling e Use the real time variables v1 v14 oph zero one two and three and perform math integer operations on them using functions in Table 17 e Use the real time AP tables t1 t 60 which may be assigned either by static variable declarations and using settable or by loading in a table from tablib using loadtable see Table 20 An example of using the real time variable v1 is given in newpul c used by assign and pulse An example of using real time AP tables is given using ph2 and t2 We could also replace v2 with t 2 in the shaped_pulse statement in this particular pulse sequence In some cases however it is necessary to perform further integer math operations on the phase cycle which is easier to perform on real time variables than on AP tables so we give the example using getelem to assign the table t 2 to variable v2 For other examples of phase cycling calculations see the pulse sequences in vnmr psglib To add 2D parameters to the newpul c pulse sequence make the following changes e In step 2 change d2new to d2 e In step 4 enter par2d set2d newpul plnew 40 e Instep7 addpar2d set2d newpul
512. ommands were implemented to support EPI Echo Planar Imaging processing Listing 13 is an example of using these commands to reverse every other FID echo for EPI data Note that the mfopen and mfclose commands can significantly speed up the data reformatting by opening and closing the data files once instead of every time the data is moved The rfb1lk rftrace and rfdata commands can also be used with the move FID commands CAUTION For speed reasons the move FID and reverse FID commands work directly on the FID and follow data links These commands can modify data returned to an experiment with the rt command To avoid modification enter the following sequence of VNMR commands before 01 999165 00 A0800 VNMR 6 1C User Programming 297 Chapter 5 Parameters and Data manipulating the FID data cp curexp acqfil fid curexp acqfil fidtmp rm curexp acqfil fid mv curexp acqfil fidtmp curexp acqfil fid Table Convert Data VNMKR supports reconstructing a properly ordered raw data set from any arbitrarily ordered data set acquired under control of an external AP table The data must have been acquired according to a table in the tab1lib directory The command for table conversion is tabc Reformatting Spectra The commands rsapply to reverse a spectrum and tcapp1y to reformat a 2D set of spectra using an AP table support reformatting of spectra within a 2D dataset The types of reformatting are the re
513. on 2 or 3 rf channels sim4pulse Simultaneous pulse on four channels Pulse simultaneously on 2 or 3 rf channels UNITYINOVA UNITYplus UNITY and VXR S systems with two or more independent rf channels sim3pulse pwl pw2 pw3 phasel phase2 phase3 RG1 RG2 double pwl pw2 pw3 pulse lengths in sec codeint phasel phase2 phase3 variables for phases double RG1 gating delay before pulse double RG2 gating delay after pulse 01 999165 00 A0800 VNMR 6 1C User Programming 251 Chapter 3 Pulse Sequence Statement Reference Description Arguments Examples Related sim4pulse Applicability Syntax Description Arguments Performs a simultaneous three pulse pulse on three independent rf channels A simultaneous two pulse pulse on the observe transmitter and second decoupler can also be performed by setting the pulse length for the first decoupler to 0 0 see the second example below for how this is done Timing limitations connected with the difference in pulse widths are covered in the description of simpulse pw1 pw2 and pw3 are the pulse length in seconds of channels OBSch DECch and DEC2ch respectively phasel phase2 and phase3 are the phases of the corresponding pulses These must be real time variables v1 to v14 oph etc RG1 is the delay in seconds between gating the amplifier on and gating the first rf transmitter on all phase shifts occur at the begin
514. on can be specified by supplying low_fieldand high_field frequencies in Hz Calculate maximum signal to noise dsnmax lt noise_region gt Finds best signal to noise in a region noise_region in Hz can be specified or the cursor difference delta can be used by default Get line frequency and intensity from line list getll line_number lt height frequency gt Returns the height and frequency of the specified line number Get frequency limits of a specified region getreg region_number lt minimum maximum gt Returns the minimum and maximum frequencies in Hz of the specified region number 01 999165 00 A0800 integ Syntax Description mark Syntax Description nll Syntax Description numreg Syntax Description peak Syntax Description select Syntax Description 1 3 Relevant VNMR Commands Find largest integral in specified region integ lt highfield lowfield gt lt size value gt Finds the largest absolute value integral in the specified region or the total integral if no reset points are present between the specified limits The default values for highfield and lowfield are parameters sp and sp wp respectively Determine intensity of the spectrum at a point mark lt mark lt fl_position gt left_edge region_width gt mark lt fl_position f2_position gt mark lt fl_start fl_end f2_ start f 2_end gt mark lt trace lt
515. on of the create command sp on Turn on specified spare line sp off Turn off specified spare line yesli Set SLI lines from real time variable Turn off specified spare line Not available on MERCURY VX and MERCURY systems NITYINOVA sploff to sp5off UNITYplus UNITY or VXR S sploff sp2off GEMINI 2000 splof Turns off the specified user dedicated spare line connector sploff for SPARE 1 sp2off for SPARE 2 etc for high speed device control e UNITYTNOVA has five spare lines available from the Breakout panel on the back of the left console cabinet 256 VNMR 6 1C User Programming 01 999165 00 A0800 Examples Related sp on Applicability Syntax Description Examples Related spinlock Applicability Syntax Description Arguments 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference e UNITYplus has two spare lines located on the front panel of the Pulse Sequence Controller board in the digital cardcage e UNITY and VXR S have two spare lines on the Interface board e GEMINI 2000 has one spare line sploff sp4off sp on Turn on specified spare line Turn on specified spare line Not available on MERCURY VX and MERCURY systems YNTYINOVA splon to sp5o0n UNITYplus UNITY or VXR S splon sp2on GEMINI 2000 splon Turns on the specified user dedicated spare line connector sp1on for SPARE 1 sp2on for SPARE 2 etc for high spee
516. on systems with a Digital Acquisition Controller board an Acquisition Controller board or a Pulse Sequence Controller board or must be a multiple of 32 on systems with a Output board each board is described below Inside a hardware loop systems with a Digital Acquisition Controller board or a Pulse Sequence Controller board can accept a maximum of 2048 complex points systems with an Acquisition Controller board can accept a maximum of 01 999165 00 A0800 VNMR 6 1C User Programming 159 Chapter 3 Pulse Sequence Statement Reference 1024 complex points and systems with an Output board can accept a maximum of 63 complex points The following list identifies the acquisition controller boards used on Varian NMR spectrometer systems e Data Acquisition Controller boards Part No 01 902010 00 Started shipping in mid 1995 with the introduction of the UNYINOVA system e Pulse Sequence Controller boards Part No 00 992560 00 Started shipping in early 1993 with the introduction of the UNITYplus system e Acquisition Controller boards Part No 00 969204 00 or 00 990640 00 Started shipping 00 969204 00 in late 1988 as a replacement for the Output boards Part No 00 990640 00 replaced 00 969204 00 in mid 1990 e Output boards Part No 00 953520 0 where is an integer Shipped with systems prior to 1988 Arguments number points is the number of data point to be acquired sampling_interval is the length in seconds of the samp
517. onditional and Arrayed Displays Use of parentheses allows the conditional display of an entire column and or individual parameters If the real parameter within parentheses is not present or is equal to 0 or to n then the associated parameter or section is not displayed In the case of string parameters if the real number is not present or is equal to the NULL string or the character n then the associated parameter or section is not displayed The following examples from the dg template above demonstrate this format e pl pl1 1 means display parameter p1 only when p1 is non zero e sbs sb 3 means display sbs only when sb is active not equal to n e 4 ni 2D PROCESSING means display entire 2D PROCESSING section only when parameter ni is active and non zero Note that if a parameter is arrayed the display status is derived from the first value of the array Thus if p1 is arrayed and the first value is 0 p1 will not appear if the first value is non zero p1 will appear with arrayed as its parameter value Similarly a multiple variable expression can also be placed within the parentheses for conditional display of parameters Each expression must be a valid MAGICAL II expression see Programming with MAGICAL page 29 and must be written so there is no space between the last character of the expression and the closing parenthesis In summary if a single variable expression is placed in the
518. only what to call the coordinates of a given datum There are no standard header entries to specify the orientation of the data display Currently data is always displayed or plotted in the same order that it is stored The fastest data dimension is plotted horizontally from left to right the next dimension is plotted vertically from top to bottom e origin isa set of rank floating point values giving the user coordinates of the first point in the data set e g float origin 5 0 6 91 e span isa set of rank floating point values for the signed length of each axis in user units A positive value means the value of the particular coordinate increases going away from the first point e g float span 10 000 15 000 e abscissa isa set of rank strings hz s cm cm s cm s2 deg ppm1 ppm2 ppm3 that identifies the units that apply to each dimension e g char abscissa cm cm e ordinate isa string intensity s deg that gives the units that apply to the numbers in the binary part of the file e g char ordinate intensity Nuclear Data Fields Data fields may contain data generated by interactions between more than one nucleus e g a 2D chemical shift correlation map between protons and carbon Such data requires interpreting the term ppm for the specific nucleus if ppm to frequency conversions are necessary and properly labeling axes arising from different nuclei To prop
519. options gt gt mark reset aN a Functions similarly to the MARK button of ds and dconi 1D or 2D operations can be performed in the cursor or box mode for a total of four separate functions In the cursor mode the intensity at a particular point is found In the box mode the integral over a region is calculated For 2D operations this is a volume integral In addition the mark command in the box mode finds the maximum intensity and the coordinate s of the maximum intensity Find line frequencies and intensities nll lt pos lt noise_mult gt lt number_lines gt Returns the number of lines using the current threshold but does not display or print the line list Return the number of regions in a spectrum numreg number_regions Finds the number of regions in a previously divided spectrum Find tallest peak in specified region peak lt min_frequency max_frequency gt lt height freq gt Finds the height and frequency of the tallest peak in the selected region min_frequency and max_frequency are the frequency limits in Hz of the region to be searched default values are the parameters sp and sp wp Select a spectrum or 2D plane without displaying it select lt lt f1f3 f2f3 f 1f 2 gt lt proj gt lt next prev plane gt gt lt index gt Sets future actions to apply to a particular spectrum in an array or to a particular 2D plane of a 3D data set index is the index number of spectrum or
520. or it sets sw to 100 The corrected value is then returned to the Tcl Cmd so that the value displayed will change to the corrected one Common Constructs In this section we look at some strategies for the Vnmr Cmd and Tcl Cmd entries The simplest case is that of a numeric value for a parameter such as tof Vnmr Cmd tof SVALUE Tcl Cmd Stof Where we expect a string the VALUE should be in single quotes for example Vnmr Cmd tn SVALUE Tcl Cmd Stn This avoids the need for the user to quote the entry When entering numeric fields the question of precision and of decimal places may arise If you want to display an integer a trick is required if any math is involved Here is one example that introduces two concepts Vnmr Cmd np SVALUE 2 Tcl Cmd expr Snp 2 In this case we wish to display the number of complex points This is of course np 2 0 The Vnmr Cmd entry is straightforward Tcl Cmd requires some explanation Tcl needs to be told when math is involved This is done with the expr command We need the square brackets to tell Tcl to evaluate the expression in first Each term in the expression is best separated by blanks Finally by dividing by 2 rather than 2 0 we do integer math rather than real math so that the result is an integer displayed as 8000 rather than 8000 00 In some cases we want to display some decimal places but not necessarily all available For example if sb 2 3 the v
521. or NOWAIT that selects whether or not a delay is inserted to wait until the gradient has completed before executing the next statement pe3_shapedgradient Oblique sh gradient with PE in 3 axes phase_encode_shapedgradient Oblique sh gradient with PE on 1 axis phase_encode3_gradient Oblique gradient with PE in 3 axes Set phase pulse technique rf type A or B Systems with rf type A or B MERCURY VX MERCURY and GEMINI 2000 systems are rf type E or F phaseshift base multiplier device double base base small angle phase shift codeint multiplier real time variable int device channel TODEV or DODEV Implements the phase pulse technique base is areal number expression or variable representing the base phase shift in degrees Any value is acceptable multiplier isa real time variable v1 to v14 ct etc The value must be positive The actual phase shift is base multiplier mod360 device is TODEV observe transmitter or DODEV first decoupler phaseshift 60 0 ct TODEV phaseshift 30 0 v1 DODEV Set frequency based on position Not applicable on MERCURY VX MERCURY and GEMINI 2000 poffset position level double position slice position in cm double level gradient level in G cm Sets the rf frequency from position and conjugate gradient values poffset is functionally the same as position_offset except that poffset takes the value of re
522. or pw3 tpwr3 extern char pw4pat MAXSTR Pattern for pw4 tpwr4 01 999165 00 A0800 VNMR 6 1C User Programming 113 Chapter 2 Pulse Sequence Programming Table 23 Imaging Variables continued extern char pwSpat MAXSTR Pattern for pw5 tpwr5 extern char pipat MAXSTR Pattern for pi tpwri extern char satpat MAXSTR Pattern for pw tpwr extern char mtpat MAXSTR Pattern for psat satpat extern char pslpat MAXSTR Pattern for spin lock extern double tpwrl Transmitter pulse power extern double tpwr2 Transmitter pulse power extern double tpwr3 Transmitter pulse power extern double tpwr4 Transmitter pulse power extern double tpwr5 Transmitter pulse power extern double tpwri Inversion pulse power extern double satpwr Saturation pulse power extern double mtpwr Magnetization transfer pulse power extern double pwxlvl pwx pulse level extern double pwxlvl2 pwx2 power level extern double tpwrsl Spin lock power level RF Decoupler Pulses extern char decpat MAXSTR Pattern for decoupler pulse extern char decpat1 MAXSTR Pattern for decoupler pulse extern char decpat2 MAXSTR Pattern for decoupler pulse extern char decpat3 MAXSTR Pattern for decoupler pulse extern char decpat 4 MAXSTR Pattern for decoupler pulse extern char decpat5 MAXSTR Pattern for decoupler pulse extern char dpwrl Decoupler pulse power extern char dpwr4 Decoupler pulse power extern char dpwr5 Decoupler pulse power Gradients extern doub
523. os can read or write information into these parameters and hence information can be passed from one macro to another in this way They thus provide a useful place to store information that must be retained for some time or must be accessed by more than one macro be sure that some other macro does not change the value of this variable in the meantime Local Variables Any number of local variables can be created within a macro These temporary variables are distinguished by beginning with the dollar sign character such as number and Speakht The type of variable real or string is decided by the first usage there is no variable declaration as in many languages Therefore setting Snumber 5 and select all1 establishes number as a real variable and select as a string variable A special initialization is required in one situation When the first use of a string variable is as the return argument from a procedure it must be initialized first by setting it to a null string For example a line such as input Input Your Name Sname produces an error Use instead Sname input Input Your Name Sname By definition local variables are lost upon completion of the macro Furthermore they are completely local which means that each macro even a macro that is being run by another macro has its own set of variables If one macro sets number 5 and then runs another macro that sets S number 10 when the second macro completes
524. otebook window pane You could instead edit the infields and outfields definitions on lines 6 and 11 directly These changes add the notebook field to each entry in the enter queue for the automation run The auto_au macro probably needs to be updated to take advantage of the new notebook field You might set a VNMR parameter to the value of the notebook number Or in conjunction with the aut oname parameter you could imbed the notebook entry in the file name used to save the data New fields are the primary addition to the gilson conf configuration file Added were entries to specify the rack location on the sample changer up to 5 rack locations are possible and the zone location each rack location can have up to 3 different zones A specific configuration files for the status command statgil conf is present to handle the extra out fields members 6 2 Customizing the status Window 322 The status window displays the contents of the enterQ and done files used to control automation e enterd contains the list of experiments remaining to be submitted This file is constructed by the ent er program which uses the out fields parameter to specify which items are written into the enterd file e doneQ contains the list of experiments that either are currently active or are finished This file is derived from the enter file VNMR 6 1C User Programming 01 999165 00 A0800 6 2 Customizing the status Window Window Configuration File
525. oupler in the pulse sequence First decoupler gating is handled automatically by the statements declvloff declvlon decpulse decrgpulse decshaped_pulse decspinlock simpulse sim3pulse simshaped_pulse sim3shaped_pulse decprgon generally needs to be enabled with an explicit decon statement and followed by a decoff call decoff Turn off first decoupler dec2on Turn on second decoupler dec3on Turn on third decoupler Turn on second decoupler Systems with a second decoupler dec2on Explicitly gates on the second decoupler in the pulse sequence Second decoupler gating is handled automatically by the statements dec2rgpulse dec2shaped_pulse dec2spinlock sim3pulse and sim3shaped_pulse 173 VNMR 6 1C User Programming Chapter 3 Pulse Sequence Statement Reference Related dec3on Applicability Syntax Description Related decphase Syntax Description Arguments Examples Related dec2phase Applicability Syntax Description Arguments Examples Related dec3phase Applicability Syntax Description 174 VNMR 6 1C User Programming dec2prgon generally needs to be enabled with an explicit dec2on statement and followed by a dec2off call dec2off Turn off second decoupler Turn on third decoupler UNITYTNOVA and UNITYplus systems with a third decoupler dec3on Explicitly gates on the third decoupler in the pulse sequence Third decoupler gating
526. ow in characters logtitle sets the title above the Log window rows sets the number of rows in the Log window the selectcolor set the color of an entry which is selected with a mouse click The other color parameters set colors of entries based on the STATUS field for that entry sort defines the way that the entries will be sorts The choices are std loc user or stat set results num 8 set results col 60 set results logtitle Log information set results rows 15 set results selectcolor pink set results errorcolor red set results queuecolor blue set results completecolor black set results activecolor magenta set results totalcolor black set results sort std set results sort user 01 999165 00 A0800 VNMR 6 1C User Programming 323 Chapter 6 Customizing Graphics Windows order of the items in the out fields parameter must also match that used by the enter program The status command displays a scrollable window with the separate experiments listed Not all fields that define an ent erQ entry need to be displayed in this window The showfields parameter is a subset of the items in out fields These are displayed in the order they are defined by the showfields parameter Defining Buttons and Window Attributes Three buttons can be defined to be displayed below the scrolling list of experiments The choices are rt locate and quit The parameter cnt rls is used to define to buttons a
527. ow core acquisition variables 102 lower shell script 282 low noise signal 75 low power decoupling 96 lp command UNIX 279 ls command UNIX 278 M maclib directory 27 maclibpath parameter 27 macro automatic execution 28 302 calling a macro in a loop 29 clear system macro 29 concept 25 defined 25 directory 27 editing 28 execution 27 existence test 46 faster execution 28 files 27 loading into memory 28 output to variables 28 parsing 28 passing information 33 remove from memory 29 VNMR activation 47 macro name list 44 45 macro parameter 28 macro tracing 37 macrocat command 44 45 macrocp command 44 macrodir command 44 macroedit macro 28 44 macrold command 28 29 45 macrorm command 45 macros h file 120 macrosyscat command 45 macrosyscp command 45 macrosysdir command 45 macrosysrm command 45 macrovi command 28 45 magic number 291 MAGICAL language defined 25 MAGICAL language features 29 magnet leg override capability 147 magnet quench warning 20 magnetic media caution 21 magradient statement 212 magradpulse statement 154 155 213 mail command UNIX 279 makefid command 310 man command 55 man command UNIX 279 manual directory 55 74 manual entry UNIX 279 manualpath parameter 55 MARK button 39 mark command 39 MAS rotor 240 241 mashapedgradient statement 155 213 VNMR 6 1C User Programming 353 Index mashapedgradpulse statement 214 mathema
528. ower seeeeeeeees 190 Divide integer ValUeS iisisti cosescsnevessanvencsenssstvasnsasstbasessieesbasreves 190 Turn off graphical display of statements 0 0 0 ccc eeseeseeeeeeeteneeeeeees 190 Turn on graphical display of statements 0 0 esse eeeeeeeseeeeeeeeeeeeeeeeeee 191 Draw delay or pulses in a sequence for graphical display 191 Skip graphical display of next statement 00 0 eee eeeeseeeeeeeeeneeeees 193 01 999165 00 A0800 elsenz endhardloop endif endloop endmsloop endpeloop gate getarray getelem getorientation gelstr getval G_Delay G_Offset G_Power G_ Pulse hdwshiminit hly hsdelay idecpulse idecrgpulse idelay ifzero incdelay ncgradient ner ndirect nit_rfpattern nit_gradpattern nit_vscan nitdelay nitparms_sis nitval iobspulse ioffset ipulse ipwrf H H H H H H H H H ipwrm irgpulse ik held 1k_sample loadtable loop magradient magradpulse mashapedgradient mashapedgradpulse mod2 mod4 modn ms loop mult obl_gradient oblique_gradient 01 999165 00 A0800 Table of Contents Execute succeeding statements if argument is NONZETO eee 193 End hardware lOOp scscs sscssaacvonscsestessaesshastesbecasestessbelacsvenevbaseseapesyebiress 194 End execution started by ifzero or elsenZz ee eeeeeeeeeeeeeeeeeeeeeeeeees 194 End LOOP cesisnss vase cescces cacescepedcvaasaseuscesvsoansececcesinseis deckacousacvenbeesvadesmsavae 194 End
529. ower DECch pulse sequence statements control the two attenuators The simplest approach is to use one of the two attenuators to control the shape while using the second to set the overall level of the pulse Assuming that there are also hard pulses in the pulse sequence you ll also need to remember to write your pulse sequence to return both attenuators to values suitable for the hard pulse System with a Third Attenuator On systems specially configured with a third attenuator not available on UN TYINOVA MERCURY VX MERCURY UNITYplus or GEMINI 2000 systems connect the hardware so that control of the additional attenuator is through one of the two fine attenuator controls Note that if this system also has two real fine attenuators a 0 to 6 dB attenuator used for solid state NMR applications one of the fine attenuators will have to be disconnected while the third 0 dB to 63 dB attenuator uses its control circuitry In a system configured this way the pulse sequence statement pwrf or pwrm is used to control the power of the pulse either pwrf 0BSch or pwrf DECch depending on how the additional attenuator was connected If a 0 dB to 63 dB attenuator is connected to the fine attenuator control the controlling hardware and software runs backwards In other words 0 gives no attenuation maximum power while 63 gives full attenuation minimum power This is the opposite of the standard power control
530. ower greater than 49 about 2 watts Performing continuous decoupling or long pulses at power levels greater than this can result in damage to the probe Use config to set a safety maximum for the tpwr dpwr dpwr2 and dpwr3 parameters decpower Change first decoupler power linear amplifier systems dec2power Change second decoupler power linear amplifier systems dec3power Change third decoupler power linear amplifier systems rlpower Change power level linear amplifier systems End programmable control of observe transmitter Systems with a waveform generator on the observe transmitter channel obsprgoff Terminates any programmable phase and amplitude control on the observe transmitter started by the obsprgon statement under waveform generator control obsprgon Start programmable control of observe transmitter Start programmable control of observe transmitter Systems with a waveform generator on the observe transmitter channel obsprgon pattern 90_pulselength tipangle_resoln name of DEC text file 90 deg pulse length in sec tip angle resolution char pattern double 90_pulselength double tipangle_resoln Executes programmable phase and amplitude control on the observe transmitter under waveform generator control It returns the number of 50 ns ticks as an integer value in one cycle of the decoupling pattern Explicit gating of the observe transmitter with xmt ron and xmt roff is generally required
531. parentheses it is FALSE under the following conditions e Variable does not exist e Variable is real and equals 0 or is marked inactive e Variable is a string variable equal to the NULL string or equal to the character n Multiple variable expressions are evaluated the same as in MAGICAL II If a variable does not exist it is considered an error Examples of multiple parameter expressions include the following e 2 numrfch gt 2 2nd DECOUPLING means display entire 2nd DECOUPLING section only when numrfch number of rf channels is greater than 2 VNMR 6 1C User Programming 01 999165 00 A0800 5 6 User Written Weighting Functions e 3 myflag lt gt n or myni gt ni and mysw lt sw My Section means display entire My Section section only when myflag is not equal to n or when myni is greater than ni and mysw is less than sw The asterisk is a special parameter designator that allows the value of a series of string parameters to be displayed in a single row without names This is more commonly used with the parameters aig dcg and dmg for example aig dcg dmg For tabular output of arrayed parameters square brackets are used For example 1 Sample Table Output pw pl dl1 d2 Notice that all parameters in the column must be in the brackets thus the following is illegal 1 Sample Table Output pw p1 d1 d2 Since arrayed variables are normally displayed with da th
532. pecify if the configuration file is Experiment Specific where Experiment will be substituted with the current value of seqfil e If Experiment Specific is selected the file is saved in an Experiment directory where Experiment is substituted with the current value of the seqfil parameter e If Experiment Specific is not selected the file is saved in the default directory These are subdirectories of the vnmr user_templates dg directory or the user s vnmrsys templates dg directory If you have write permission in the vnmr system directories you are presented a choice of System and User Selecting one or the other saves the configuration files in the directories vnmr user_templates dg or the user s vnamrsys templates dg directory If you do not have write permission in the vnmr system directories you do not see this choice In all cases the name of the file is shown in the Panel File entry at the top of the window Note that the file name is editable and can be used to create new configuration files In order for them to become active you need to add an appropriate entry into the dg conf file As already mentioned the geometry of the dg pane is defined in the dg conf file Entering a new value in the geometry field of the configuration window and then pressing Refresh Display causes the dg window to resize and reposition to the new geometry Alternatively the mouse can be used to resize and reposition the dg window Whenever the
533. ped_puls Shaped pulse on second decouple r simshaped_pulse Simultaneous two pulse shaped pulse sim3shaped_pulse Simultaneous three pulse shaped pulse shapedgradient Generate shaped gradient pulse Applicability Syntax Description Arguments Systems with waveform generation on imaging or PFG module shapedgradient pattern width amp channel loops wait char pattern name of shape text file double width length of pulse double amp amplitude of pulse char channel gradient channel x y or z int loops number of loops int wait WAIT or NOWAIT Operates the selected gradient channel to provide a gradient pulse to the selected set of gradient coils The pulse is created using a gradient waveform generator and has a pulse shape determined by the arguments name width amp and loops Unlike the shaped rf pulses the shaped gradient leaves the gradients at the last value in the gradient pattern when the pulse completes pattern is the name of a text file without a GRD extension to describe the shape of the pulse The text file with a GRD extension should be located in Svnmrsystem shapelib or in the users directory Svnmruser shapelib 01 999165 00 A0800 VNMR 6 1C User Programming 245 Chapter 3 Pulse Sequence Statement Reference width is the requested length of the pulse in seconds The pulse length is affected by two factors 1 the minimum time of every element in the s
534. phase RG1 RG2 double width width of pulse in sec codeint phase real time variable for phase double RG1 gating delay before pulse in sec double RG2 gating delay after pulse in sec Syntactically equivalent to rgpulse statement and functionally equivalent to rgpulse with two exceptions First the first decoupler instead of the transmitter is pulsed at its current power level Second if homo n the slow gate about 100 ns switching time on UNITYplus systems to 3 us switching time on other systems homo not available on MERCURY VX MERCURY and GEMINI 2000 systems on the first decoupler board is always open and therefore need not be switched open during RG In contrast if homo y the slow gate on the first decoupler board is normally closed and must therefore be allowed sufficient time during RG to switch open For systems with linear amplifiers RG for a decoupler pulse is important from the standpoint of amplifier stabilization under the following conditions tn dn equal 3H 1H 19F high band nuclei 3H does not apply to MERCURY VX MERCURY and GEMINI 2000 systems or tn dn less than or equal to 31p low band nuclei For these conditions the decoupler amplifier module is placed in pulse mode in which it remains blanked as long as the receiver is on In this mode RG must be sufficiently long to allow the amplifier to stabilize after blanking is removed 5 to 10 us 2 us typical for ME
535. phase control 87 power adjustment 92 power level 176 programmable decoupling 177 178 pulse with receiver gating 182 quadrature phase 174 shaped pulse 185 simultaneous pulses 85 small angle phase 170 spin lock waveform control 187 step size 189 turn off 172 turn on 174 unblank amplifier 189 three attenuators system 142 three pointer 99 three pulse pulse 84 three pulse shaped pulse 136 254 tilde character notation display templates 307 tilde character notation UNIX 278 time increments 73 time sharing pulse shaping 139 timing in a pulse sequence 103 tip angle 133 title fields 326 TODEYV constant 82 tof parameter 90 token defined 29 total weighting vector 308 TPPI experiments 150 TPPI phase increments 71 tpwr parameter 92 142 transformations of FDF data files 294 transformed complex spectrum storage file 284 transformed phased spectrum storage file 284 transformed spectra storage files 283 transient blocks 99 transmitter blanking 220 fine power 222 234 240 fine power adjustment 92 fine power with IPA 209 gating 95 133 275 hardware control of phase 87 linear modulator power 235 240 linear modulator power with IPA 210 offset frequency 90 220 223 phase control 85 87 power adjustment 92 power level 221 233 239 programmable control 136 221 360 VNMR 6 1C User Programming pulse shaping via AP bus 163 pulse with IPA 208 209 210 pulse with receiver gating 222
536. phase of third decoupler UNITYTNOVA and UNITYplus systems with a third decoupler dec3phase phase codeint phase real time variable for quad phase Sets quadrature phase multiple of 90 for the third decoupler rf 01 999165 00 A0800 Arguments Examples Related dec4phase Applicability Syntax Description Arguments Examples Related decpower Applicability Syntax Description Arguments CAUTION Related dec2power Applicability Syntax Description 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference phase is the quadrature phase for the third decoupler rf The value must be a real time variable v1 to v14 oph ct etc dec3phase v9 dcplr3phase Set small angle phase of third decoupler rf type C or D decphase Set quadrature phase of first decoupler Set quadrature phase of fourth decoupler UNITYTNOVA systems with a deuterium decoupler channel as the fourth decoupler dec4phase phase codeint phase real time variable for quad phase Sets quadrature phase multiple of 90 for the fourth decoupler rf phase is the quadrature phase for the third decoupler rf The value must be a real time variable v1 to v14 oph ct etc dec4phase v9 rftype Type of rf generation decphase Set quadrature phase of first decoupler Change first decoupler power level linear amp systems Systems with linear amplifiers decpower pow
537. pi secdesi raveesiirsote escea rui r a E E E EE 324 6 3 Customizing the Interactive dg Window oo cece eeseeseceseeeeceeceeeceeeteeeeeeeeeecaeescecaeesaecaessaecsecaeeeeeeeareees 324 STDS fs es eS he ces ches aces tact ge socige Moots E E E E T 326 selecting the New Interface janis ei i AAAI A ea SI A AS 328 Deselecting the WOW Mierfane ciinei sce dguscaecordaseesecbepsaces cb stozoustesn o a EN ES SERES 328 Window Contienranom Piles ise sieviis assis aiaee uaea ase abe cia Riad eae 328 Editing thie Contguration FUES ssic5 okccsciscedibaceecases ipevs ep ssacess tevenssssucsocnse dudes teorenssaseanaurbansetencustasnteten 328 Interaction Elements lt iccccs0s ci kes aen e asd Aieetie Bi nadelan aati dia E 332 Tips forde Despi snsc enee E E TEER E cneis Miodaaaavbavebealebvanse 339 Utilities tor Accessing VNMR Parameters css ccccsssssvsistspsdcssiessenscsatessascasseoanesdap EEEE EEC EEE RRi 342 Sende a Tel SCG ariii irinenn e E EE Gill E EE EEE EOE EE S AET EE EE 343 NG ea E E E mae Ee 345 01 999165 00 A0800 VNMR 6 1C User Programming 15 Table of Contents 16 VNMR 6 1C User Programming 01 999165 00 A0800 List of Figures Figure 1 Dialog Box forarray Macro s ca icssss spesdes ested ssstasebedeseracestbsoecpeeds oiin rae aaa aiaei ai 50 Figure 2 Homonuclear 2D J Pulse Sequence ssssscrsierriessiresriseiveriisisireeseieieriiereiverrnsksrssksis 64 Figure 3 Amplifier Gating sc saccssesesscaeescesepeccasedesois tensespesecicnensvt
538. pinner did not regulate in the allowed time period RSPINFAIL 303 Spinner went out of regulation during experiment SPINOUT 395 Unknown spinner device specified SPINUNKNOWN 396 Spinner device is not powered up SPINNOPOWER 397 RS 232 cable not connected from console to spinner SPINRS232 398 Spinner does not acknowledge commands SPINTIMEOUT 400 VT variable temperature errors 400 VT did not regulate in the given time vt t ime after being set 401 VT went out of regulation during the experiment VTOUT 402 VT in manual mode after auto command see Oxford manual 403 VT safety sensor has reached limit see Oxford manual 404 VT cannot turn on cooling gas see Oxford manual 405 VT main sensor on bottom limit see Oxford manual 406 VT main sensor on top limit see Oxford manual 407 VT sc ss error see Oxford manual 408 VT oc ss error see Oxford manual 495 Unknown VT device specified VTUNKNOWN 496 VT device not powered up VTNOPOWER 497 RS 232 cable not connected between console and VT VTRS232 498 VT does not acknowledge commands VTTIMEOUT 500 Sample changer errors 501 Sample changer has no sample to retrieve 502 Sample changer arm unable to move up during retrieve 503 Sample changer arm unable to move down during retrieve 504 Sample changer arm unable to move sideways during retrieve 01 999165 00 A0800 VNMR 6 1C User Programming 75 Chapter 2 Pulse Sequence Programming 505 506 50
539. poffset_list pss gss ns vl12 pe_gradient gror 0 5 sgpe nv gssr sgpe v6 acquire np 1 0 sw endmsloop seqcon 1 v12 endpeloop seqcon 2 v6 endpeloop End phase encode loop loop Start loop msloop Multislice loop 01 999165 00 A0800 VNMR 6 1C User Programming 227 Chapter 3 Pulse Sequence Statement Reference phase_encode_gradient Oblique gradient with phase encode in one axis Applicability Syntax Description Arguments Related Not applicable on MERCURY VX MERCURY and GEMINI 2000 phase_encode_gradient statl stat2 stat3 step2 vmult2 lim2 angl ang2 ang3 double statl stat2 stat3 static gradient components double step2 variable gradient stepsize codeint vmult2 real time math variable double lim2 max gradient value step double angl ang2 ang3 Euler angles in degrees Sets static oblique gradient levels plus one oblique phase encode gradient The phase encode gradient is associated with the second axis of the logical frame This corresponds to the convention read phase slice for the functions of the logical frame axes It has no return value Pulse sequence generation aborts if the DACs on a particular gradient are overrun after the angles and amplitude have been resolved statl stat2 stat3 are values in gauss cm of the components for the Static portion of the gradient in the logical reference frame step2 is the value in gauss cm of the compo
540. pressure from weather fronts If the readings for either gas should change abruptly contact qualified maintenance personnel Failure to correct the cause of abnormal readings could result in extensive equipment damage Never operate solids high power amplifiers with liquids probes On systems with solids high power amplifiers never operate the amplifiers with a liquids probe The high power available from these amplifiers will destroy liquids probes Use the appropriate high power probe with the high power amplifier Take electrostatic discharge ESD precautions to avoid damage to sensitive electronic components Wear a grounded antistatic wristband or equivalent before touching any parts inside the doors and covers of the spectrometer system Also take ESD precautions when working near the exposed cable connectors on the back of the console Radio Frequency Emission Regulations The covers on the instrument form a barrier to radio frequency rf energy Removing any of the covers or modifying the instrument may lead to increased susceptibility to rf interference within the instrument and may increase the rf energy transmitted by the instrument in violation of regulations covering rf emissions It is the operator s responsibility to maintain the instrument in a condition that does not violate rf emission requirements 22 VNMR 6 1C User Programming 01 999165 00 A0800 Introduction Varian s VNMR software provides NMR users wit
541. quadrature phase 87 quadrature phase of decoupler 174 175 quadrature phase of transmitter 265 quadrature phase shift 85 question mark character 279 quit button 319 quotation mark notation 26 R rl r2 r7 parameters 32 33 radio button field 327 radio style 316 radio frequency emission regulations 22 revroff statement 96 235 rcvron statement 96 236 read parameters from a file 301 readlk command 48 readuserap statement 97 98 real command 32 real component of FID data 287 real number formatting for output 40 real parameters 32 real number arguments 73 real time gradient statements 155 real time incremental delay 80 203 real time statements 102 real time variables 73 98 100 208 real type parameter 298 300 real type variables 32 receiver default state 207 gating 68 80 96 97 222 234 238 mode 87 phase 87 phase control 99 phase cycle 242 turn off 237 turn on 236 receiver gate 235 237 receiver overflow warning 75 recoff statement 237 recon statement 237 record macro 46 records in file 41 rectangular pulse 139 recursive calls 27 redefinition warning 72 reference to statements 159 reformatting data for processing 295 reformatting spectra 298 regions in spectrum 39 regression analysis 42 regression inp file 42 relief valves warning 21 removable quench tubes warning 21 removing an empty directory UNIX 278 removing macros 45 removing macros
542. quence for i 32000 i lt 32000 i 16000 shapedgradient hsine pwtd3 rxlt rx2 i x 1 NOWAIT shapedpulse sinc pw oph rxl1 rx2 delay d3 This step sets a square gradient froma low value to a high value while executing a shaped pulse and a delay during each gradient value Related dps_show Draw delay or pulses in a sequence for graphical display rgradient Set gradient to a specified level shapedgradient Provide shaped gradient pulse to gradient channel shaped2Dgradient Arrayed shaped gradient function vgradient Set gradient to a level determined by real time math shaped2Dgradient Generate arrayed shaped gradient pulse Applicability Systems with WFG on imaging or PFG module Syntax shaped2Dgradient pattern width amp channel loops wait tag char pattern name of pulse shape text file double width length of pulse 246 VNMR 6 1C User Programming 01 999165 00 A0800 Description Arguments Examples Chapter 3 Pulse Sequence Statement Reference double amp amplitude of pulse char channel gradient channel x y or z int loops number of loops int wait WAIT or NOWAIT int tag unique number for gradient element Operates the selected gradient channel to provide a gradient pulse to the selected set of gradient coils This statement is basically the same as the shapedgradient statement except that shaped2Dgradient is tailored
543. quence S2PULR you just run S2PUL with rfchannel 21 The rfchannel mechanism only works for pulse sequences that eliminate all references to the constants TODEV DODEV DO2DEV and DO3DEV To take advantage of rfchannel you must remove statements such as power and offset that use these constants and replace them with the corresponding statements such as obSpower and decoffset that do not contain the constants On UNTYINOVA all standard pulse sequences have been edited to take advantage of the rf channel independence afforded by the rfchanne1l parameter This parameter makes it a simple matter to redirect for example the dn nucleus to use the third or fourth rf channel On MERCURY VX MERCURY and GEMINI 2000 there are only two channels The software automatically determines which channel is observe or decouple based on tn and dn Pulsing the Decoupler Transmitter Statements related to decoupler pulsing are decpulse decrgpulse idecpulse idecrgpulse dec2rgpulse and dec3rgpulse Table 8 summarizes these statements VNMR 6 1C User Programming 01 999165 00 A0800 2 3 Spectrometer Control Table 8 Decoupler Transmitter Pulse Related Statements decpulse width phase decrgpulse width phase RG1 RG2 dec2rgpulse width phase RG1 RG2 dec3rgpulse width phase RG1 RG2 dec4rgpulse width phase RG1 RG2 idecpulse width phase string idecrgpulse idecrgpulse width phase RG1 RG2 string
544. quence features not accessible from the menus The chapter starts therefore by describing this simplified mode of pulse sequence programming 2 1 Programming Pulse Sequences from Menus One way to begin is by making a diagram of the pulse sequence you want to program then adding to the diagram the names of the parameters that describe the pulses and delays shown Also write down the phase cycling to be used Finally decide the points in the pulse sequence at which the status needs to change see the manual Getting Started for a discussion of the status concept With this information you can quickly program the pulse sequence using the menu system 01 999165 00 A0800 VNMR 6 1C User Programming 63 Chapter 2 Pulse Sequence Programming For example Figure 2 displays the diagram for a homonuclear 2D J pulse sequence A B and C represent the status pw p1 revr x at y d1 d2 2 x d2 2 w y A B C Figure 2 Homonuclear 2D J Pulse Sequence Here are the steps to program this sequence l 2 In the Permanent menu the top row of buttons click on Main Menu Click on More gt Write Pulse Sequence gt Start You are now in the Pulse Sequence Entry Main Menu with the prompt Enter a Name for the Pulse Sequence Enter hom2dj A new prompt appears Enter Basic Phase Cycle Length without additional phase cycling Because HOM2DJ has a basic phase cycle that is four transients long en
545. r char internal_name parameter value buffer name Looks up the value of the string parameter parameter_name in the current experiment parameter list and introduces it into the pulse sequence in the variable internal_name If parameter_name is not found in the current experiment parameter list internal_name is set to the null string and PSG produces a warning message parameter_name is a string parameter internal_name is any legitimate C variable name defined at the beginning of the pulse sequence as an array of type char with dimension MAXSTR getstr xpol xpol getval Look up value of numeric parameter Look up value of numeric parameter internal_name getval parameter_name char parameter_name name of parameter Looks up the value of the numeric parameter parameter_name in the current experiment parameter list and introduces it into the pulse sequence in the variable internal_name If parameter_name is not found in the current experiment parameter list internal_name is set to zero and PSG produces a warning message 198 VNMR 6 1C User Programming 01 999165 00 A0800 Arguments Examples Related G Delay Applicability Syntax Description G_Offset Applicability Syntax Description G_Power Applicability Syntax Description G_ Pulse Applicability 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference parameter_name is a numeric parameter in
546. r 6 Customizing Graphics WindOWS cccsseeeeesseeeeeeeeeeeeeeeees 311 ION ss cietsnnzausassiaxakanseasnssdedssanindcntesensecicndasninsusaseuedsanducnaishaeeassntacanindasteaserersnainans 345 01 999165 00 A0800 VNMR 6 1C User Programming 3 4 VNMR 6 1C User Programming 01 999165 00 A0800 Table of Contents 01 999165 00 A0800 SAFETY PRECAUT TIONS cisesisiiecnensctiiesniiieraianesiiainniinisinienaaraienniwenanenaaeneanmiaieiiaukiaieniens 19 NPREROQ UC ike n Pr T E T T 23 Chapter 1 MAGICAL Il Programming sssssnsesunenrnnnnrnnnnnnennnnnnnnnnnnnnennnnennnnnnnnnnnnnennnnn nnmnnn 25 11 Working With Macros sscriceisecieccenrtesiren rores eiiean aee EE nE EE EEE E E REE EE eare ERE E eE KEE i 25 WES Te e a E EE E E EE E E E E EE E AE EE E E 26 Execute a Macio oescsseceni chaste a T O E E E E OE T 26 Transfering Macro Output 2sciciecictiiitici asides Mia ad eo EAE EREA aei 28 Loading Macros mto Memony ceine eremie aose o RoE EE AREER EE EE ROE ETRE 28 1 2 Programming with MAGICAL serinin nne aeae A REE E iSS 29 ge en e a5 E e E E E E E socenentaesteciaegs 29 Variable Types siiin ceciren yare eree ani a E E E E ER E E EREET eara EEE o dated ss V ERE ER E PTE EES 32 ODE D E E EE S EEEE EE E E E E E E EEE E E E EEE 33 EX prESSIONS 2 5 sccisexsecpcassveeanscssbuhavs E E REEE EEE E EEEE EEE EE ERT EEE ER AE EE E EE E TE EE AERE 34 p Arumes eesin a eE sauces EE TEETE E REEE E EE EAE ETE EEE 35 Name Replacement sssetpoirrr d
547. r apshaped_dec2pul1se second decoupler channel small angle phase shifting is reset to zero and the step size is set to 0 25 degrees apshaped_dec2pulse capability is now integrated into the statement dec2shaped_pulse The dec2shaped_pulse statement calls apshaped_dec2pul1se without table variables if a waveform generator is not configured on the decoupler channel dec2shaped_pulse creates AP tables on the fly for amplitude and phase and does not use the AP tables allocated for users It still uses real time variables v12 and v13 shape isa shape file without the RF extension in vnmr shapelib or in vnmrsys shapelib The amplitude and phase fields of the shape file are used The relative duration field field 3 should be left at the default value of 1 0 or at least small numbers and the gate field field 4 is currently not used because the transmitter is switched on throughout the shape pulse_width is the total pulse width in seconds excluding the amplifier gating delays around the pulse pulse_phase is the 90 phase shift of the pulse For small angle phase shifting note that apshaped_dec2pul1se sets the phase step size to the minimum on the one channel that is used power_tableand phase_table are two table variables t 1 to t 60 used as intermediate storage addresses for the amplitude and phase tables respectively If apshaped_dec2pul1se is called more than once different table names should be used in each call RG1 i
548. r by only using 33 dB of the first attenuator for the shape On UNITYplus systems both phase and linear amplitude can be controlled over the AP bus in addition to the 79 dB attenuator It is possible to use this control to create shaped pulses without a waveform generator e Use a time sharing or DANTE approach applying the shaped pulse in such a way that it is switched on and off with a particular duty cycle during the course of the shape A 10 duty cycle for example reduces the power by a factor of ten On YINOVA and UNITYplus systems both the phase and linear attenuator on each transmitter can be controlled through pulse sequence statements see pwrf obspwrf decpwrf dec2pwrf dec3pwrf pwrm rlpwrm and dcplrphase so it is possible to create shaped pulses without a waveform generator AP Bus Delay Constants Table 30 lists the most important AP bus delay constants C macros for the UNITY family of spectrometers Y YINOVA UNITYplus UNITY and VXR S The list is 01 999165 00 A0800 VNMR 6 1C User Programming 139 Chapter 2 Pulse Sequence Programming 140 incomplete but a complete list can be found at the bottom of the text file vnmr psg apdelay h The constants OFF SET_DELAY and OF FSET_LTCH_DELAY are applicable only to UNITYTNOVA and UNITY plus systems that use PTS synthesizers with latching on the input Although the constants are identical use only OFFSET_DELAY on these systems Most UNITY and VXR
549. r maximum minimum step_size lt tree gt or setlimit parameter index lt tree gt setprotect parameter set on off value lt tree gt setvalue parameter value lt index gt lt tree gt To Edit or Set Parameter Attributes Use paramvi parameter lt tree gt to open the file for a parameter in the UNIX vi text editor so that you can edit the attributes To open a parameter file with an editor other than vi use paramedit parameter lt tree gt Refer to entry for paramedit in the VNMR Command and Parameter Reference for information on how to select a text editor other than vi The format of a stored parameter is described in the next section Several parameter attributes can be set by the following commands setlimit parameter maximum minimum step_size lt tree gt sets the maximum and minimum limits and stepsize of a parameter setlimit parameter index lt tree gt sets the maximum and minimum limits and the stepsize but obtains the values from the index th entry of a table in conpar setprotect parameter set on off bit_vals lt tree gt sets the protection bits associated with a parameter The keyword set causes the current protection bits to be replaced with the set specified by bit_vals listed in the VNMR Command and Parameter Reference on causes the bits specified in bit_vals to be turned on without affecting other protection bits off causes the bits specified in bit_vals t
550. r to submit an experiment Changing the value of the required attribute to 1 enforces entry of descriptive text The output attribute specifies the title of a line in the ent erQ file Every parameter listed in out fields must have an output attribute Parameters listed in infields that havea style of radio check xradio xcheck textentry xradiocustom or xcheckcustom have the selected choice printed after the value of the out put attribute Other parameters can define an attribute named va lue the value of which is printed after the value of the output attribute in the enter file The loc parameter has several special attributes e The duplicates attribute specifies whether a user can duplicate a location that is present in a preexisting file By default this is not allowed The locations defined in the preexisting files are shaded out in the location window pane and are not selectable For example notice locations 2 and 6 in Figure 9 Figure 10 and Figure 11 e The errormess attribute specifies an error message to be displayed when a sample tray is filled If this message is set no more samples are accepted If errormess is set to a null string sample locations that are finished can be reused The null setting is useful for continuous walkup operation VNMR 6 1C User Programming 01 999165 00 A0800 6 1 Customizing the Sample Entry Form Window e The errormess2 attribute specifies an error message to be displayed in the con
551. r two fields They are often associated with entries in which case they make the entry value active or inactive The first field of a check box if present is a text string The second field is the actual check box which is a small square When checked the small square is red and is sunken When unchecked it is gray and raised The check box toggles between these two states with alternate mouse clicks on it Generally each check box is independent of all others Radio Buttons Radio buttons are small diamonds arranged in vertical columns Each row in a column has two fields a text string and the actual radio button When a radio button is selected it is colored red and is sunken When it is not selected it is gray and raised Just like their namesake adjacent radio buttons in a column are mutually exclusive If you click on an unselected one it becomes selected and the currently selected one becomes unselected You will find radio buttons controlling mutually exclusive choices such as ph av and pwr Scales Scales are slider bars They have two or three fields The first field is a text string The second field is optional but when present shows the current value of the slider The third field is the slider itself There are two ways of altering the slider The first is to grab the slider itself and drag it to the desired position in the trough The other is to click in the trough itself If you click in the trough with the middl
552. r variable UNIX 28 vnmrMax procedure 343 vnmrmenu file 53 vnmrmenu parameter 52 vnmrmenu variable UNIX 52 vnmrMin procedure 343 vnmrSize procedure 342 vnmrsys directory 27 70 01 999165 00 A0800 Index vnmrtext variable UNIX 328 vnmrUnits procedure 342 voffset statement 157 272 vsadj macro 26 vscan statement 157 272 initialize variable 207 vsetuserap statement 97 vsli statement 157 273 vsmult macro 35 VT errors 75 VT experiment warning 20 vttime parameter 75 W w command 280 w command UNIX 279 WALTZ decoupling 86 WALTZ 16 modulation 243 warning error codes 75 warning messages 71 warnings defined 19 waveform generation 243 waveform generator control 134 135 136 137 waveform generator delays 143 waveform generator gate 133 waveform generators 131 waveform initialization statements 157 wbs command 74 weighting function 288 307 308 werr command 74 wexp command 74 WFG_OFFSET_DELAY macro 146 WFG2_OFFSET_DELAY macro 146 WFG3_OFFSET_DELAY macro 146 which macro 27 while do endwhile loop 36 who is on the system UNIX 279 widget type 316 wildcard character UNIX 279 wnt command 74 working directory UNIX 278 write command 41 writing parameter buffers into disk files 284 wtcalc function 308 wtf file extension 308 wtfile parameter 307 309 wtfilel parameter 307 wtfile2 parameter 307 wtgen shell script 308 309 wti c
553. radient The delay element should be sufficiently long so as to allow the gradient to reach the assigned value new_level old_level delay gt __ _ X risetime 2047 channel specifies the gradient to be set and is one of the characters X x y y Z or z In imaging channel can also be gread gphase or gslice intercept and slope are integers In imaging intercept is the initial gradient DAC setting and slope is the gradient DAC increment mult is a real time variable v1 to v14 etc In imaging mult is set so that intercept slope mulLt is the output 1 mod2 ct v10 vi is 0 1 0 1 0 1 vgradient z 0 2000 v10 z gradient is 0 2000 0 2000 delay d2 delay for duration d2 rgradient z 0 0 gradient turned off 2 mod4 ct vl10 v10 is 0 1 7 2 374 0 1 27 3747 peu FF vgradient z 5000 0 2500 0 v10 z is 5000 2500 0 2500 3 pulsesequence char gphase gread gslice int amplitude igpe stat double gpe gpe getval gpe amplitude int 0 5 ni gpe igpe int gpe stat getorientation amp gread amp gphase amp gslice orient initval nf v9 loop v9 v5 vgradient gphase amplitude igpe v5 endloop v5 01 999165 00 A0800 VNMR 6 1C User Programming 2 1 Chapter 3 Pulse Sequence Statement Reference Related voffset Applicability Syntax Description
554. rahend codeint vk real time variable for difference Description Sets the value of vk equal to vi vj Arguments vi is the integer value of the minuend v j is the integer value of the subtrahend and vk is the difference of vi and vj Each argument must be a real time variable v1 to v14 oph etc Examples sub v2 v5 v6 Related add Add integer values assign Assign integer values dbl Double an integer value decr Decrement an integer value divn Divide integer values hlv Half the value of an integer iner Increment an integer value mod2 Find integer value modulo 2 mod4 Find integer value modulo 4 modn Find integer value modulo n mult Multiply integer values tsadd Add an integer to AP table elements Applicability All systems except the GEMINI 2000 Syntax tsadd table scalarval moduloval codeint table real time table variable int scalarval integer added int moduloval modulo value of result 01 999165 00 A0800 VNMR 6 1C User Programming 261 Chapter 3 Pulse Sequence Statement Reference Description Arguments Examples Related tsdiv Applicability Syntax Description Arguments Examples Related tsmult Applicability Syntax Description Arguments Examples Related 262 VNMR 6 1C User Programming A run time scalar operation that adds an integer to elements of an AP table table specifies the name of the table t 1 to t 60 sc
555. rameter label Size input output Sinput cols 30 remark Enter the number of steps in the array label Start input output Sinput cols 30 remark Enter the first value in the array label Step input cols 30 output Sinput remark Enter the increment for the array button 1 OK exec 1 SAVE CLOSE remark 1 Done with this window button 2 Cancel exec 2 CLOSE remark 2 Cancel this command button 3 Help rtoutput 3 man array remark Show help for array 01 999165 00 A0800 51 VNMR 6 1C User Programming Chapter 1 MAGICAL II Programming Note that the dialog command runs until the OK button or Cancel button is clicked VNMR is therefore busy because the macro still executes However the man command used with the rtoutput 3 on button 3 is executed before dialog returns rtoutput provides a back door into VNMR 1 5 Customizing the Menu System 52 Fully integrated into the VNMR software package are a series of user programmable menus Accessible to the user at all times are two rows of menu buttons selected by clicking the left mouse button on the relevant choice or by pressing the corresponding function key on the keyboard The upper row of buttons called the Permanent menu contains functions that must be accessible to the user at all time The next section describes how to customize the Permanent menu The lower row of buttons contains choices for a large number of different m
556. rameter wt file can be set to the name of the file containing a user written weighting function If the parameter wt file or wt filel or wt file2 does not exist it can be created with the commands create wtfile flag setgroup wtfile processing setlimit wtfile 15 0 0 If wt file exists but wt file two single quotes VNMR does not look for the file wt file is inactive To enable user written weighting functions set wt file filename where filename is the name of the executable weighting 01 999165 00 A0800 VNMR 6 1C User Programming 307 Chapter 5 Parameters and Data function enclosed in single quotes that was created by compiling the weighting function source code with the UNIX shell script wt gen a process described in the next section VNMR first checks if filename exists in wt 1ib subdirectory of the user s private directory If the file exists there VNMR then checks if the file filename wtp which may contain the values for up to ten internal weighting parameters exists in the current experiment directory If filename wtp does not exist in the current experiment directory the ten internal weighting parameters are set to 1 VNMR executes the filename program using the optional file filename wtp as the source for parameter input The output of the program is the binary file filename wtf in the current experiment directory This binary file contains the weighting vector that will be read in by VNMR The
557. real time variables v1 to v14 etc modn v3 v5 v4 mod2 Find integer value modulo 2 mod4 Find integer value modulo 4 Multislice loop Not applicable on MERCURY VX MERCURY and GEMINI 2000 msloop state max_count apvl apv2 char state compressed or standard double max_count initializes apvl codeint apvl maximum count codeint apv2 current counter value Provides a sequence switchable loop that can use real time variables in what is known as a compressed loop or it can use the standard arrayed features of PSG In imaging sequences ms loop uses the second character of the seqcon string parameter seqcon 1 for the state argument ms loop is used in conjunction with endms loop state is either c to designate the compressed mode or s to designate the standard arrayed mode max_count initializes apv1 If state is c this value should equal the number of slices If state is s this value should be 1 0 apv 1 is real time variable that holds the maximum count apv2 is a real time variable that holds the current counter value If st ate is c apv2 counts from 0 to max_count 1 If stateis s apv2 is set to zero msloop seqcon 1 ns vll1 v12 poffset_list pss gss ns v12 acquire np 1 0 sw VNMR 6 1C User Programming 01 999165 00 A0800 Related mult Syntax Description Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference endmsloop
558. rection circuitry to sample lock signal eee 211 Load AP table elements from table text file oe eee eeeeeeseeeeeeees 211 SALE LOOP advice sn sassbheseteid vosci vubnpebeseasied N EEE EE ERE aR STEEK EATE ETETE ETOR 212 Simultaneous gradient at the magic angle sesseseseseeeeserereereseerrereee 212 Gradient pulse at the magic angle 0 0 eee cee eee ceseeeeeeeeeeeeeeeeeeeeee 213 Simultaneous shaped gradient at the magic angle 00 eee 213 Simultaneous shaped gradient pulse at the magic angle 214 Find integer value modulo 2 oo elec ceteeseceseeeeceeeeeeeeeeeeeeeeeeeeeeas 215 Find integer value modulo 4 oo lec ceteeseceseeeeceeeeeeeeeeeeeteaeeeeeees 215 Find integer value modulo n oo elec ceeeeeceeeeeceeceeeseeeeeeeeaeeeeeees 216 IMultislicelOOp areca i oreinen eese TEE E E EEEE 216 Multiply integer values eee eeeeeeeessecececeeeeeeeeeeeeceeesaeceeeeaeeenees 217 Execute an oblique gradient 20 0 0 ceeeeescceseceseeeseeeenceceeeeeeceeeesaeeeees 217 Execute an oblique gradient 2 0 0 ee ee eceeeeeeeseecseceeecaecnaeeeeenseeeeneees 218 VNMR 6 1C User Programming 11 Table of Contents obl_shapedgradient oblique_shapedgradient obsblank obsof fiset obspower obsprgoff obsprgon obspulse obspwrf obsstepsize obsunblank ofiser pe_gradient pe2_gradient pe3_gradient pe_shapedgradient pe2_shapedgradient pe3_shapedgradient peloop phase_encode_gradient phase_encode3_gradient phase_encode_shapedgrad
559. ressed and started The minimum pulse length is 0 2 us The overhead at the start and end of the shaped pulse varies e UNITYTNOVA 1 us start O end e UNITYplus 5 75 us start 0 end e System with Acquisition Controller board 10 75 us start 4 3 us end e System with Output board 10 95 us start 4 5 us end If the length is less than 0 2 us the pulse is not executed and there is no overhead When using the linear attenuator and the small angle phase shifter to generate a shaped pulse the decshaped_pulse statement creates AP tables on the fly for amplitude and phase It also uses the real time variables v12 and v13 to control the execution of the shape It does not use AP table variables For timing and more information see the description of apshaped_decpulse Note that if using AP tables with shapes that have a large number of points the FIFO can become overloaded with words generating the pulse shape and FIFO Under flow errors can result pattern is the name of a text file in the shapelib directory that stores the rf pattern leave off the RF file extension width is the duration in seconds of the pulse phase is the phase of the pulse It must be a real time variable v1 to v 14 etc or a real time constant zero one etc RG1 is the delay in seconds between gating the amplifier on and gating the first decoupler on the phaseshift occurs at the beginning of this delay RG2 is the delay in seconds b
560. rf 4 0 decpwrf Set first decoupler fine power dec3pwrf Set third decoupler fine power obspwrf Set observe transmitter fine power rlpwrf Set transmitter or decoupler fine power Set third decoupler fine power UNITYTNOVA and UNITYplus systems with fine power control on the third decoupler dec3pwrf power double power for DO3DEV new fine power valu Changes third decoupler fine power It is functionally the same as rlpwrf value DO3DEV power is the fine power desired dec3pwrf 4 0 decpwrf Set first decoupler fine power dec2pwrf Set second decoupler fine power obspwrf Set observe transmitter fine power rlpwrf Set transmitter or decoupler fine power Decrement an integer value decr vi codeint vi real time variable for starting value Decrements integer value vi by 1 i e vi vi 1 vi is a real time variable v1 to v14 oph etc decr v5 add Add integer values assign Assign integer values dbl Double an integer value divn Divide integer values hlv Half the value of an integer incr Increment an integer value mod2 Find integer value modulo 2 01 999165 00 A0800 decrgpulse Syntax Description Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference mod4 Find integer value modulo 4 modn Find integer value modulo n mult Multiply integer values sub Subtract integer values Pulse first decoupler with amplifier gating decrgpulse width
561. rieves all values of an arrayed parameter position_offset_list Set frequency from position list position_offset Set frequency based on position Applicability Syntax Description Arguments Examples Related Not applicable on MERCURY VX MERCURY and GEMINI 2000 position_offset pos grad resfrq device double pos slice position in cm double grad gradient level in G cm double resfrq resonance offset in Hz int device OBSch DECch DEC2ch or DEC3ch Sets the rf frequency from position and conjugate gradient values It has no return value pos is the slice position in cm grad is the gradient level in gauss cm used in the slice selection process resfrq is the resonance offset value in Hz for the nucleus of interest device is OBSch observe transmitter or DECch first decoupler For the UNITYTNOVA and UNITYplus only device can also be DEC2ch second decoupler or DEC3ch third decoupler position_offset posl gvoxl resto OBSch poffset Set frequency based on position position_offset_list Set frequency from position list position_offset_listSet frequency from position list Applicability Not applicable on MERCURY VX MERCURY and GEMINI 2000 232 VNMR 6 1C User Programming 01 999165 00 A0800 Syntax Description Arguments Related power Applicability Syntax Description Arguments Chapter 3 Pulse Sequence St
562. rking with Parameter Trees 0 0 0 eee ceeeseceeceseceeeeseeeeeeseeeeeeetees 300 18 VNMR 6 1C User Programming 01 999165 00 A0800 SAFETY PRECAUTIONS The following warning and caution notices illustrate the style used in Varian manuals for safety precaution notices and explain when each type is used WARNING Warningsare used when failure to observe instructions or precautions could result in injury or death to humans or animals or significant property damage CAUTION Cautions are used when failure to observe instructions could result in serious damage to equipment or loss of data Warning Notices Observe the following precautions during installation operation maintenance and repair of the instrument Failure to comply with these warnings or with specific warnings elsewhere in Varian manuals violates safety standards of design manufacturing and intended use of the instrument Varian assumes no liability for customer failure to comply with these precautions WARNING Persons with implanted or attached medical devices such as pacemakers and prosthetic parts must remain outside the 5 gauss perimeter from the centerline of the magnet The superconducting magnet system generates strong magnetic fields that can affect operation of some cardiac pacemakers or harm implanted or attached devices such as prosthetic parts and metal blood vessel clips and clamps Pacemaker wearers should consult the user manual provided by the pacemaker
563. rmal WARNING Avoid liquid helium or nitrogen contact with any part of the body In contact with the body liquid helium and nitrogen can cause an injury similar to a burn Never place your head over the helium and nitrogen exit tubes on top of the magnet If liquid helium or nitrogen contacts the body seek immediate medical attention especially if the skin is blistered or the eyes are affected WARNING Do not look down the upper barrel Unless the probe is removed from the magnet never look down the upper barrel You could be injured by the sample tube as it ejects pneumatically from the probe WARNING Do not exceed the boiling or freezing point of a sample during variable temperature experiments A sample tube subjected to a change in temperature can build up excessive pressure which can break the sample tube glass and cause injury by flying glass and toxic materials To avoid this hazard establish the freezing and boiling point of a sample before doing a variable temperature experiment VNMR 6 1C User Programming 01 999165 00 A0800 SAFETY PRECAUTIONS Warning Notices continued WARNING Support the magnet and prevent it from tipping over The magnet dewar has a high center of gravity and could tip over in an earthquake or after being struck by a large object injuring personnel and causing sudden dangerous release of nitrogen and helium gasses from the dewar Therefore the magnet must be supported by at least one of
564. rmat of the procpar file The fields in the data header can be in any order except for the magic number string which are the first characters in the header and the end of header character lt null gt which must immediately precede the data The fields have a C style syntax A correct header can be compiled by the C compiler and should not result in any errors e The data portion is binary data described by fields in the header It is separated from the header by a null character Listing 11 Example of an FDF Header usr local fdf startup int rank 2 char spatial_rank 2dfov char storage float int bits 32 char type absval int matrix 256 256 char abscissa cm cm char ordinate intensity float span 10 000000 15 000000 float origin 5 000000 6 911132 char nucleus H1 H1 float nucfreq 200 067000 200 067000 float location 0 000000 0 588868 0 000000 float roi 10 000000 15 000000 0 208557 float orientation 0 000000 0 000000 1 000000 1 000000 0 000000 0 000000 0 000000 1 000000 0 000000 checksum 0787271376 lt Zero gt Header Parameters The fields in the data header are defined in this section Magic Number The magic number is an ASCII string that identifies the file as a FDF file The first two characters in the file must be followed by the identification string Currently the string is
565. rom the text file vnmr conpar The config program is used to define most of these parameters All users have the same systemglobal tree Tools for Working with Parameter Trees Table 40 lists commands for creating modifying and deleting parameters To Create a New Parameter Use create parameter lt type lt tree gt gt to create a new parameter in a parameter tree with the name specified by parameter For example entering create a real global creates a new real type parameter a in the global tree type canbe real string delay frequency flag pulse or integer If the type argument is not entered the default is real tree canbe current global processed or systemglobal Ifthe tree argument is not entered the default is current See the section above for a description of parameter types and trees Note that these same arguments are used with all the commands appearing in this section To Get the Value of a Parameter The value of most parameters can be accessed simply by using their name in an expression for example sw or r1 np accesses the value of sw and np respectively However parameters in the processed tree cannot be accessed this way Use getvalue parameter lt index gt lt tree gt to get the value of any parameter including the value of a parameter in a processed tree To make this easier the default value of tree is processed The index argument is the number of a s
566. rresponds to a standard PSG variable by removing the variable definition and initialization from the pulse sequence and just using the standard PSG variable A list of the standard PSG variable names is given in Accessing Parameters page 110 Finally if the pulse sequence program is syntactically correct the following message is displayed Done Pulse sequence now ready to use Types of Acquisition Controller Boards Hardware looping timing and other system capabilities are often determined by the type of acquisition controller board used on the system The following list describes the types of acquisition controller boards used on Varian UN YINOVA UNITYplus UNITY and VXR S systems MERCURY VX MERCURY and GEMINI 2000 controller boards are directly described e Data Acquisition Controller boards Part No 01 902010 00 Varian started shipping this board in mid 1995 with the introduction of the UN YZNOVA system e Pulse Sequence Controller boards Part No 00 992560 00 Varian started shipping this board in early 1993 with the introduction of the UNITYplus system e Acquisition Controller boards Part No 00 969204 00 or 00 990640 00 Varian started shipping 00 969204 00 in late 1988 as a replacement for the Output boards and then 00 990640 00 replaced 00 969204 00 in mid 1990 Output boards Part No 00 953520 0 where is an integer These boards were used on systems prior to 1988 Creating a Parameter Table for
567. rs VNMR 6 1C User Programming 01 999165 00 A0800 1 5 Customizing the Menu System Manual Files A VNMR manual directory contains text files with information about VNMR commands macros and parameters When a user enters the man command to look at a manual file e g man go VNMR looks for the manual directory in the following order 1 Inthe user s manual directory This directory is a subdirectory of the user s VNMR directory A typical path is home vnmrl vnmrsys manual 2 Inthe directory pointed to by the nanualpath parameter if the parameter is defined in the user s global parameter file manualpath contains the absolute path to a user s directory of VNMR manual entries This parameter must contain an absolute path not a relative path To create manualpath enter the following command create manualpath string global 3 Inthe system manual directory This directory is a subdirectory of the system VNMR directory A typical path is vnmr manual Each user can have private manual files A file in the user s manual directory takes precedence over the system manual directory The system manual directory can only be changed by the system administrator however changes to the manual directory are available to all users Controlling Menus To turn on the menu system and display the current menu enter the menu command with no arguments menu off turns off the menu system menu menu_name turns on the
568. rt 0 end e UNITYplus 11 5 us 0 e Systems with an Acquisition Controller board 21 5 us 8 6 us e Systems with an Output board 21 7 us 8 8 us These values hold regardless of the values for the arguments obswidth and decwidth If either obswidth or decwidthis 0 0 no pulse occurs on the corresponding channel If both obswidth and decwidth are non zero and either obsshape or decshape is set to the null string then a hard pulse occurs on the channel with the null shape name If either the pulse width is zero or the shape name is the null string then a waveform generator is not required on that channel obsshape is the name of the text file in the shape1lib directory that contains the rf pattern to be executed on the observe transmitter decshape is the name of the text file in the shapelib directory that contains the rf pattern to be executed on the first decoupler obswidth is the length of the pulse in seconds on the observe transmitter decwidth is the length of the pulse in seconds on the first decoupler obsphase is the phase of the pulse on the observe transmitter The value must be a real time variable v1 to v14 oph etc decphase is the phase of the pulse on the first decoupler The value must be a real time variable v1 to v14 oph etc RG1 is the delay in seconds between gating the amplifier on and gating the first rf transmitter on all phase shifts occur at the beginning of this delay RG
569. run after the angles and amplitude have been resolved pattern is the name of the gradient shape file width is the length in seconds of the gradient statl stat2 stat3 are values in gauss cm of the components for the static portion of the gradient in the logical reference frame VNMR 6 1C User Programming 01 999165 00 A0800 Related phaseshift Applicability Syntax Description Arguments Examples poffset Applicability Syntax Description Arguments Chapter 3 Pulse Sequence Statement Reference stepl step2 step3 are values in gauss cm of the components for the step size change in the variable portion of the gradient vmulti1 vmult2 vmult3 are real time math variables v1 to v14 ct zero one two three or references to AP tables t 1 to t 60 whose associated values vary dynamically in a manner controlled by the user lim1 1im2 1im3 are values representing the dynamic step that will generate the maximum gradient value for each component This provides error checking in pulse sequence generation and is normally nv 2 ang1 is the Euler angle psi in degrees with the range of 90 to 90 angZ2 is the Euler angle phi in degrees with the range of 180 to 180 ang3 is the Euler angle theta in degrees with the range of 90 to 90 Loops is non real time integer value from 1 to 255 that sets the number of times to loop the waveform wait is a keyword either WAIT
570. s On NTYINOVA and UNITYplus systems the ampmode parameter gives override capability over the default selection of amplifier modes Unless overridden the observe channel is set to the pulse mode other used channels are set to the CW continuous wave mode and any unused channels are set to the idle mode By using values of d p c and i for the default pulse CW and idle modes respectively ampmode can override the default modes For example anpmode ddp selects default behavior for the first two amplifiers and forces the third channel amplifier into the pulse mode The selection of rf channels on UN TYINOVA and UNITYplus systems also can be independently controlled with the rfchanne1l parameter You do not need rfchannel if you have a single channel broadband system and you set up anormal HMQC experiment tn H1 dn C13 The software recognizes that you cannot do this experiment and swaps the two channels automatically to make the experiment possible The rfchannel parameter becomes important if for example you have a three channel spectrometer and you want to do an HMQC experiment with the decoupler running through channel 3 Instead of rewriting the pulse sequence you can create rfchannel by entering create rfchannel flag and then set for example rfchannel 132 Now channels 2 and 3 are effectively swapped without any changes in the sequence Similarly if you want simply to observe on channel 2 as in the pulse se
571. s and homodecoupler 8 6 us can be set e For systems with the Output board and only those systems all offset statements by default are preceded internally by a 0 2 us delay see the apovrride statement for more details Arguments frequency is the offset frequency desired for the observe channel 220 VNMR 6 1C User Programming 01 999165 00 A0800 Examples Related obspower Applicability Syntax Description Arguments CAUTION Related obsprgoff Applicability Syntax Description Related obsprgon Applicability Syntax Description Arguments 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference obsoffset to decoffset Change offset frequency of first decoupler dec2offset Change offset frequency of second decoupler dec3o0ffset Change offset frequency of third decoupler offset Change offset frequency of transmitter or decoupler Change observe transmitter power level lin amp systems Systems with linear amplifiers obspower power double power new coarse power level Changes observe transmitter power This statement is functionally the same as rlpower value OBSch power Sets the power level by assuming values from 0 minimum power to 63 maximum power on channels with a 63 dB attenuator or from 16 minimum power to 63 maximum power on channels with a 79 dB attenuator On systems with linear amplifiers be careful when using values of obsp
572. s allows everything to line up neatly The definition file dg conf is not mutable This means that the tabs must serve all pulse sequences that a user may wish to use Plan the number of panes and their function to satisfy the most complex experiment Then the panes can be depopulated for simpler pulse sequences Again remember keep each parameter in the same place in the same pane throughout If it is not relevant do not display it e Use the visual cues provided to indicate function Titles are not interactive buttons are Labels are not interactive entries are Radio buttons require the user to choose one of the available options Check boxes do not require a choice none some or all of the options can be selected e Let VNMR and MAGICAL do as much of the work as possible The manipulations done by Tcl should only be those associated with the display and entry functions Excessive use of Tcl adds another layer of complexity that someone will have to untangle later Utilities for Accessing VNMR Parameters Tcl procedures are available to provide access to VNMR parameter attributes Each procedure available takes the VNMR parameter name as an argument The procedures include vnmrOn vnmrSize vnmrUnits vnmrDgroup vnmrMax and vnmrMin vnmrOn The vnmrOn procedure returns 1 if the VNMR parameter is Active 0 if Not Active vnmrSize The vnmrSize procedure returns the number of array values for the parameter If the parameter i
573. s e E EEr SE e SEES 91 Table 14 Gating Control Statements 20 0 eee ceeeeseeeeeeseeseceeeeseceeeesceeaeeseecneesaeraeesaecnesaeeeeeaees 94 Table 15 Interfacing to External User Devices oo ce eeeeeeecseeesseeseeeeeeceseseeseeseeneeseeseeaecateeceaeaeeess 97 Table 16 Mapping of User AP Lines cisssc sccscscevesnssesescveiecuiesuvesssesscenseuss dossocedssssbenscosoesesesecssasniess 97 Table 17 Integer Mathematics Statements 00 eee cee eseeeeceseeeeceseeeeeeseeeeecaeecaecaeesaecsaeeaeeneeeaees 99 Table 18 Pulse Sequence Control Statements 200 000 cece eeeecseeeeeeeeseeeeecoeecaecneesaessacsaeseeeseeseeees 100 Table 19 Statements for Controlling Graphical Display of a Sequence 0 0 eee eeeeeeeteeeeeeeees 104 Table 20 Statements for Handling AP Tables oo ee eeecescseeseeeeceeceeeeeesecaecaeeecsaecaseeeeeenaeeeteees 107 Table 21 Parameter Value Lookup Statements 00 ee eee ceesseeceseeceeceeecaeeeaeeaeseseeeseeeeeeeeetees 110 Table 22 Global PSG Parameters a c2 cisciessessciaeieciecs caeskt ioesaesetiguensetan EE rE E E RENEE iE 111 Table 23 Imaging Variable Sireenin ornina i i a E iE EAS 113 Table 24 Hardware Looping Related Statements esesessesesesseeeserereeresrersstrrrsrerrsrrerrrrererrererrnse 126 Table 25 Number of Events for Statements in a Hardware Loop ssssssseeseeeeeseererererersrrererererens 128 Table 26 Rotor Synchronization Control Statements sssesseeeseeeseereseerestrrrsrerrsrrerrrrererrerenrrsene 1
574. s is unsuccessful the data must be phased a If the data is not in the data file buffer ds opens the data file if not already open and loads it into the buffer b ds initializes the phasefile buffer with the proper size using the same parameter fn as used for last FT c ds calculates the phased or absolute value spectrum and stores it in the phasefile buffer 2 ds calculates the display and displays the spectrum The phasefile buffer now contains the phased spectrum Unless other displays are done which use up more memory space than assigned to the phasefile buffer the data is not automatically written to the file expn datdir phasefile at this time Joining a different experiment or entering the command flush would perform such a write operation Depending on the nature of the data processing the two files data and phasefile will contain different information as follows e Aftera 1D FT data contains a complex spectrum which can be used for phased or absolute value displays e After a ID display phasefile contains either phased or absolute value data depending on which type of display had been selected 288 VNMR 6 1C User Programming 01 999165 00 A0800 5 1 VNMR Data Files e After a2D FID display data contains the complex FIDs floated and normalized for different scaling during the 2D acquisition phasefile contains the absolute value or phased equivalent of this FID data e After the first FT in a 2D e
575. s not arrayed it returns 1 If the parameter does not exist it returns 0 vnmrUnits The vnmrUnits procedure returns a scaling factor based Dgroup Factor on the current Dgroup attribute of a parameter The table on 1 1 the right lists the Dgroup value and scaling factor g i3 e vnmrDgroup 3 le6 4 reffrq The vnmrDgroup procedure returns the value of the fral Dgroup attribute of the parameter 5 reM 6 reffrq2 VNMR 6 1C User Programming 01 999165 00 A0800 6 3 Customizing the Interactive dg Window vnmrMax The vnmrMax procedure returns the value of the maxvalue attribute of the parameter vamrMin The vnmrMin procedure returns the value of the minvalue attribute of the parameter Sending a Tcl Script The command tcl script sends a Tcl Tool Command Language script to the Tcl version of the dg window Any legal Tcl script can be sent Sending the value of curexp to this dg window causes the window to update itself The value of seqfil is also used to determine which configuration files to use to update the window The bootup macro and the jexp macros use the following command for this purpose tcl set seqfil tseqfil set curexp curexp If the Tcl version of the dg window is not active the tcl command does nothing 01 999165 00 A0800 VNMR 6 1C User Programming 343 Chapter 6 Customizing Graphics Windows 344 VNMR 6 1C User Programming 01 999165 00 A0800 Symbols double quotes notation 26
576. s seetessctcesseecteoceusa cn Qedstasesensubiaectiesebasaslantetes crcom Create a user macro without using a text editor eee 44 delcom Delete a user MACTO ou ee eee eee eseeeeeeecaecnnecaeenaeeaees wee 44 hidecommand Execute macro instead of command with same name e ee 44 macrocat Display a user macro on the text window oo eee eteeeeceeeeeeeeeeee 44 macrocp Copy a user macro file oo eee eeesseeeeeeceeceeecesecneceeesesaecaseecsaeaseeeees 44 macrodir List user MACKOS xiseeciscests Reskesvish ack eE ats dead dei EEEE ES EE 44 macroedit Edit a user macro with user selectable editor eee eeeeeeeeees 44 macrold Load a macro into MEMOTY oe eee eee eee ceeeeecaeceseceeeeaeeeeeeeeeeeneees macrorm Remove a user macro macrosyscat Display a system macro on the text window macrosyscp Copy a system macro to become a user MACLO eee eeteeeeeeeeee 45 macrosysdir List system MACTOS cceseessesssenseceesneesesone cone sonessescesssessersneeseessens 45 macrosysrm Remove a system MACTO occ eeeeceeeeeeceseeeeecaeecaecaeesaecsaeeaeeneeeeeeeees 45 macrovi Edit a user macro with vi text editor oo ee eee cee ceseeeeeeseeseeeeees 45 mstat Display memory usage statistics eee eee eee ee ceee ce ceeeeeeeeseeeeeteees 45 purge Remove a macro from Memory ee eeeceseeeeeeeseceeececeeceeneceeeeeaecaees 45 record Record keyboard entries as a MAaCTO oo eee eeese ese ceee ee cneeeseceseeeeeneees 46 Miscellaneous TOO sieneen eei aa AE Poles
577. s the amplifier gating time in seconds before the pulse RG2 is the amplifier gating time in seconds after the pulse apshaped_dec2pulse gauss pw vl t10 t11 rofl rof2 apshaped_decpulse First decoupler pulse shaping via the AP bus apshaped_pulse Observe transmitter pulse shaping via the AP bus dcplr2phase Set small angle phase of 2nd decoupler rf type C or D dec2shaped_puls Perform shaped pulse on second decoupler VNMR 6 1C User Programming 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference apshaped_pulse Observe transmitter pulse shaping via AP bus Applicability Syntax Description Arguments Examples Related UNITYTNOVA and UNITYplus systems On MERCURY VX and MERCURY only shapes with no phase shifts are supported apshaped_pulse shape pulse_width pulse_phase power_table phase_table RG1 RG2 char shape name of RF shape file double pulse_width pulse width in sec codeint pulse_phase real time phase of pulse codeint power_table table variable to store power codeint phase_table table variable to store phase double RG1 gating time before pulse in sec double RG2 gating time after pulse in sec Provides observe transmitter fine grained waveform generator type pulse shaping through the AP bus A pulse shape file for the waveform generator vnmr shapelib RF is used This statement overrides any existing sma
578. s the number of steps in the shape a warning message is generated The shaped gradient software will round each element to a multiple of 50 ns If the requested width differs from the actual width by more than 2 a warning message is displayed amp_const amp_incr and amp_vmul1t scale the amplitude of the pulse according to the formula above amp_const and amp_incr can be values of type double or integer amp_vmul1t must be a real time AP math variable v1 to v14 or a table pointer t 1 to t 60 The amplitude ranges are also given above channel selects the gradient coil channel desired and should evaluate to the characters x y or z Be careful not to confuse the characters x y or z with the strings x y or z vloops allows the user to loop the selected waveform Values range from 1 to 255 This also must be a real time AP math variable v1 to v14 or a table pointer t 1 to t 60 Do not use 0 for vloops because this may cause inconsistencies when WAIT is selected for the wait_4_me argument Due to a digital hardware bug affecting looping patterns must be carefully constructed to achieve the desired results wait is a keyword either WAIT or NOWAIT that selects whether or not a delay is inserted to wait until the gradient is completed before executing the next element The total time it will wait is width vloops It uses the incdelay statement when waiting for the gradient pulse to complete tag is a unique integ
579. s to be meaningful is 2 For example if the phase cycle length has been set to be 4 the additional phase cycle is 00001 11122223333 and selecting this button will give a phase 0202131320203131 More Display Pulse Sequence Entry Phases Secondary Menu below for more phase choices Pulse Sequence Entry Phases Secondary Menu The Pulse Sequence Entry Phases Menu is typically entered by selecting More in the Pulse Sequence Entry Phases Menu or by entering menu psg_phase2 For buttons 1 to 6 the Pulse Sequence Entry Pulses Menu see below the Pulse Sequence Entry Decoupler Pulses Menu page 68 or the Pulse Sequences Entry Main Menu is displayed page 66 as appropriate Button Description 3210 Use a cycling phase 3 2 1 0 270 180 90 0 0321 Use a cycling phase 0 3 2 1 0 270 180 90 0022 Use a cycling phase 0 0 2 2 0 0 180 180 2200 Use a cycling phase 2 2 0 0 180 180 0 0 Fixed 90 Use a fixed phase of 90 that is not phase cycled Fixed 180 Use a fixed phase of 180 that is not phase cycled Return Display Pulse Sequence Entry Phases Menu page 67 Pulse Sequence Entry Pulses Menu The Pulse Sequence Entry Pulses Menu is typically entered by selecting a phase value in the Pulse Sequence Entry Phases Menu or in the Pulse Sequence Entry Phases Secondary 01 999165 00 A0800 VNMR 6 1C User Programming 67 Chapter 2 Pulse Sequence Programming Menu or by entering menu psg_pulse
580. same as for implicit acquisitions by changing oph or by using the set receiver statement setreceiver is not available on GEMINI 2000 The value of oph at the time of the acquisition of the first data point is the value that determines the receiver phase setting for the duration of that particular scan the receiver cannot be changed after acquiring some data points and before acquiring the rest Multiple FID Acquisition Explicit acquisition of data can also be used to acquire more than one FID per pulse sequence simultaneous COS Y NOESY for example This can be done for 1D or 2D experiments The parameter nf for number of FIDs controls this if it is created and set To perform such an experiment enter create nf integer to create nf and then set nf equal to an integer such as 2 Once the data have been acquired a second new parameter cf current FID which must also be created is used to identify the FID to manipulate Setting c 2 for example would recognize the second FID in the COSY NOESY experiment and hence would produce a NOESY spectrum after Fourier transformation Note that this is distinct from the standard array capability and is in fact compatible with the standard arrays Thus you can acquire an array of ten experiments with each consisting of three FIDs that are generated during each pulse sequence To display the second FID of the seventh experiment for example you would type cf 2 dfid 7 VNMR 6
581. sary for any statements to appear between the ifzero andthe elsenz or between the elsenz and the endif statements Syntax 1 is used with UTYINOVA MERCURY VX MERCURY UNITY plus UNITY and VXR S systems Syntax 2 is used with GEMINI 2000 systems vi is areal time variable v1 to v14 oph etc tested for either being zero or non zero n is the same value 1 2 or 3 as used in the corresponding i f zero statement elsenz v2 elsenz 1 endif End ifzero statement ifzero Execute succeeding statements if argument is zero End hardware loop All systems except the GEMINI 2000 and any system equipped with the Output board Part No 00 953520 0 where is from 0 to 4 endhardloop Ends a hardware loop that was started by the st art hardloop statement acquire Explicitly acquire data starthardloop Start hardware loop End execution started by ifzero or elsenz 1 endif vi codeint vi 2 endif n int n real time variable to test if 0 or not 1 2 or 3 same as corresponding ifzero Ends conditional execution started by the i f zero and elsenz statements Syntax 1 is used with UNTYINOVA MERCURY VX MERCURY UNITYplus UNITY and VXR S systems Syntax 2 is used with GEMINI 2000 systems vi is a real time variable v1 to v14 oph etc that is tested for either being zero or non zero n is the same value 1 2 or 3 as used in the corresponding i f zero statement endif v4 endif
582. scalar operation that multiplies an integer with the elements of an AP table table specifies the name of the table t 1 to t 60 scalarval is an integer to be multiplied with each element of the table moduloval is the modulo value taken on the result of the operation if is greater than 0 moduloval tsmult t31 4 4 tsadd Add an integer to AP table elements tsdiv Divide an integer into AP table elements tssub Subtract an integer from AP table elements 01 999165 00 A0800 tssub Applicability Syntax Description Arguments Examples Related ttadd Applicability Syntax Description Arguments Examples Related ttdiv Applicability Syntax Description Arguments 01 999165 00 A0800 Chapter 3 Pulse Sequence Statement Reference Subtract an integer from AP table elements All systems except the GEMINI 2000 tssub table scalarval moduloval codeint table real time table variable int scalarval integer subtracted int moduloval modulo value of result A run time scalar operation that subtracts an integer from the elements of an AP table table specifies the name of the table t 1 to t 60 scalarval is an integer to be subtracted from each element of the table moduloval is the modulo value taken on the result of the operation if is greater than 0 tssub t31 4 4 moduloval tsadd Add an i
583. scription Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference obsstepsize 30 0 decstepsize Set step size of first decoupler dec2stepsize Set step size of second decoupler dec3stepsize Set step size of third decoupler stepsize Set small angle phase step size rf type C or D Unblank amplifier associated with observe transmitter obsunblank Explicitly enables the amplifier for the observe transmitter obSunblank is generally followed by a call to obsblank decblank Blank amplifier associated with first decoupler decunblank Unblank amplifier associated with first decoupler obsblank Blank amplifier associated with observe transmitter LOVEOLE Turn off receiver revron Turn on receiver Change offset frequency of transmitter or decoupler This statement will be eliminated in future versions of VNMR software Although it is still functional you should not write any new pulse sequences using it and should replace it in existing sequences with obsoffset decoffset dec2offset or dec30ffset as appropriate offset frequency device double frequency int device hes frequency offset OBSch DECch DEC2ch or DEC3ch Changes the offset frequency of the observe transmitter parameter t of first decoupler dof second decoupler dof 2 or third decoupler dof 3 frequency is the offset frequency desired device is OBSch observe transmitter or DECch fir
584. se shaped_pulse WFG_STOP_DELAY Overhead at end of decshaped_pulse shaped_puls WFG2_START_DELAY Overhead at start of simshaped_pulse etc WFG2_STOP_DELAY Overhead at end of simshaped_pulse etc WFG3_START_DELAY Overhead at start of sim3shaped_pulse ete WFG3_STOP_DELAY Overhead at end of sim3shaped_pulse ete On UNTYTNOVA systems on other systems this constant is zero no support for FSQ Use OF FSET_DELAY only on UN TYINOVA and UNITYplus systems Only on systems that use PTS synthesizers with latching On UNITYplus systems only this constant is zero Controlling Shaped Pulses Using Attenuators The statements power obspower decpower dec2power dec3power and optionally pwrf obspwrf decpwrf dec2pwrf dec3pwrf pwrm and rlpwrm are used to change the attenuation and hence the power level of either the transmitter or VNMR 6 1C User Programming 01 999165 00 A0800 2 11 Shaped Pulses Using Attenuators decouplers A pulse sequence in which one of these statements is placed in a loop and repeatedly executed with different values for the amount of attenuation therefore results in a shaped pulse This can be a C loop or a soft loop using the Loop statement but not a hard loop The successive values for the power may be calculated in real time read from a table assuming that only positive numbers are involved or set up from a static C variable Although no standard puls
585. set textfield style textentry set textfield file set textfield col 40 set textfield required 0 set textfield output TEXT set userdir id userdir set userdir output USERDIR set userdir value Senv vnmruser set data id data set data output DATA set stat id stat set stat output STATUS set stat value Queued set separator id separator set separator output Button Definitions Possible cntrls are addExp saveExp saveAndExit addSaveAndl set cntrls addExp saveAndExit quit Automation controls are autoSample autoSampleNoExit priortySample quit Exit quit set cntrls addSaveAndExit quit if you prefer a one button exit mechanism uncomment the lin if you prefer a two button exit mechanism uncomment the next lin below In this case the label for quit should be reset to Exit set cntrls saveExp quit 01 999165 00 A0800 VNMR 6 1C User Programming 313 Chapter 6 Customizing Graphics Windows Listing 14 Text of enter conf File continued 115 set addExp id addExp 116 set addExp label Add Entry 117 118 set saveExp id saveExp 119 set saveExp label Save Entry 120 121 set saveAndExit id saveAndExit 122 set saveAndExit label Exit and Save 123 124 set addSaveAndExit id addSaveAndExit 125 set addSaveAndExit label Exit and Save
586. set the pulse width This occurs because the phase of the pulse must be known to the sequence before the pulse can occur In all menus to make a selection move the mouse arrow to the desired button on the screen and press the left mouse button The center and right mouse buttons are inactive For information on the VNMR menu system in general refer to the manual Getting Started The following sections describe the choices on the pulse sequence entry menus 01 999165 00 A0800 VNMR 6 1C User Programming 65 Chapter 2 Pulse Sequence Programming Pulse Sequence Entry Main Menu The Pulse Sequence Entry Main Menu is typically entered by selecting Write Pulse Sequence in the Secondary Main Menu or by entering menu psg_main Button Description Start Show prompts Enter a Name for the Pulse Sequence and Enter Basic Phase Cycle Length without additional phase cycling and uses the information you enter to initialize a pulse sequence file in your pulse sequence directory use Start button first and only once Delay Display Pulse Sequence Entry Delay Menu see below to add a delay at this point of the sequence Pulse Display Pulse Sequence Entry Phases Menu page 67 to select the phase and add a pulse at this point of the sequence DecPulse Display Pulse Sequence Entry Decoupler Pulses Menu page 68 to select decoupler phase and add a decoupler pulse at this point of the sequence Status Display the Sequence Entry S
587. sfrq from the resto parameter and always assumes the device is the observe transmitter device TODEV position is the slice position in cm 01 999165 00 A0800 VNMR 6 1C User Programming 231 Chapter 3 Pulse Sequence Statement Reference Examples Related poffset_list Applicability Syntax Description Arguments Examples Related level is the gradient level in gauss cm used in the slice selection process poffset pss 0 gss position_offset Set frequency based on position Set frequency from position list Not applicable on MERCURY VX MERCURY and GEMINI 2000 poffset_list posarray grad nslices apv1 double position_array position values in cm double level gradient level in G cm double nslices number of slices codeint vi variable or AP table Sets the rf frequency from a position list conjugate gradient value and dynamic math selector poffset_list is functionally the same as position_offset_list except that poffset_list takes the value of resfrq from the resto parameter assumes the device is the observe transmitter device OBSch and assumes that the list number is zero position_array isa list of position values in cm level is the gradient level in gauss cm used in the slice selection process nslices is the number of slices or position values vi is a dynamic real time variable v1 to v14 or AP table t1 to t 60 poffset_list pss gss ns v8 getarray Ret
588. spulse generates interactive parameter adjustment IPA information when gf or go acqi is entered If go is entered iobspulse is the same as obspulse label1 is the short character string to be given to the slider when displayed in the Acquisition window acqi program iobspulse pulse iobspulse pw obspulse Pulse observe transmitter with amplifier gating Change offset frequency with IPA All systems except MERCURY VX MERCURY and GEMINI 2000 ioffset frequency device label 208 VNMR 6 1C User Programming 01 999165 00 A0800 Description Arguments Examples Related ipulse Applicability Syntax Description Arguments Examples Related ipwrf Applicability Syntax Description Arguments Chapter 3 Pulse Sequence Statement Reference double frequency offset frequency int device OBSch DECch DEC2ch or DEC3ch char label slider label in acqi Functions the same as of fset except that iof fset generates interactive parameter adjustment IPA information when gf or go acqi is entered If go is entered ioffset is the same as offset frequency is the new offset frequency of the device specified device is OBSch observe transmitter or DECch first decoupler For the UNITYINOVA and UNITYplus only device can also be DEC2ch second decoupler or DEC3ch third decoupler label1 is the short character string to be given to
589. st enclose all of the table statements for a given table This notation should not be used if this table will be subject to table operations such as tt add see below in this case use which is equivalent except for table compression In entering the notation do not include any space after Indicates that the index into the table starts at O for each new FID in an array or 2D experiment is incremented after each access of the table and is therefore independent of ct This is the autoincrement attribute which can delimit the table name from the table statements It can be explicitly set within a pulse sequence for any table see set autoincrement Tables using the autoincrement feature cannot be accessed within a hardware loop The and notations are expanded by PSG at run time and therefore offer no degree of table compaction to the acquisition processor Nesting of and expressions is not allowed The autoincrement attribute can be used in conjunction with the divn return attribute and with the and notations Multiple expressions within one table are not allowed but and expressions can be placed within a expression The following examples illustrate combining the notation t2 0 1 2 3 4 0 0 2 2 4 t2 table 00001111222233330022002200220022 t3 0 1 0 2 2 0 2 3 1 4 4 t3 table 01020202333311
590. st decoupler For the UNITYTNOVA and UNITYplus only device can also be DEC2ch second decoupler or DEC3ch third decoupler offset do2 DECch offset to2 OBSch delay d2 offset tof OBSch decoffset Change offset frequency of first decoupler dec2offset Change offset frequency of second decoupler dec3o0ffset Change offset frequency of third decoupler obsoffset Change offset frequency of observe transmitter ioffset Change offset frequency with IPA P pe_gradient Applicability 01 999165 00 A0800 Oblique gradient with phase encode in one axis Not applicable on MERCURY VX MERCURY and GEMINI 2000 223 VNMR 6 1C User Programming Chapter 3 Pulse Sequence Statement Reference Syntax Description Arguments Examples Related pe2_gradient Applicability Syntax Description Arguments Examples Related pe3_gradient Applicability pe_gradient statl stat2 stat3 step2 vmult2 double stat1l stat2 stat3 static gradient components double step2 variable gradient stepsize codeint vmult2 real time math variable Sets static oblique gradient levels plus one oblique phase encode gradient The phase encode gradient is associated with the second axis of the logical frame This corresponds to the convention read phase slice for the functions of the logical frame axes This statement is the same as phase_encode_gradient except the Euler angles are rea
591. st significant byte at the lowest address of the full 32 bit word On VAX systems integers are stored with the least significant byte at the lowest address The Sun system also uses the IEEE standard floating point format whereas the VAX uses a slightly different format in which the floating point exponent is different VNMR software contains routines to manipulate data FIDs that has been transferred between Sun and VAX systems Text format Stores all other forms of data such as line lists parameters and all forms of reduced data obtained by analyzing NMR spectra The advantage of storing data in text format is that it can be easily inspected and modified with a text editor and can be copied from one computer to another with no major problems The text on both Sun and VAX systems use the ASCII format in which each letter is stored in one byte Binary Data Files Binary data files are used in the VNMR file system to store FIDs and the transformed spectra FIDs and their associated parameters are stored as filename fid files A filename fid file is always a directory file containing the following individual files e filename fid fidisa binary file containing the FIDs e filename fid procpar is a text file with parameters used to obtain the FIDs e filename fid text isa text file 01 999165 00 A0800 VNMR 6 1C User Programming 283 Chapter 5 Parameters and Data 284 In experiments binary files store FIDs and spectra In non
592. statement applies only to certain hardware or system options an applicability entry is included A change bar indicates new or changed information since the last version of VNMR A acquire Applicability Syntax Description Explicitly acquire data All systems except MERCURY and GEMINI 2000 acquire number_points sampling_interval double number_points points to acquire double sampling_interval dwell time in sec Acquire data points where the sequence of events is to acquire a pair of points for 200 ns delay for sampling_interval minus 200 ns then repeat for number_points 2 times For UN TYINOVA systems there are small overhead delays before and after the acquire The pre acquire delay takes into account setting the receiver phase with oph and enabling data overflow detection The post acquire delay is for disabling data overflow detection When using acquire statements within a hardware loop these overhead delays and the functions associated with them are placed outside the hardware loop When using multiple acquire statements outside a hardware loop in a pulse sequence setting the phase and enabling data overflow detection is done before the first acquire statement Disabling overflow detection is done after the last acquire so there is no overhead time between acquire statements If an acquire statement occurs outside a hardware loop the number of complex points to be acquired must be a multiple of 2
593. stems with the Output board there is an effective resolution of the phase shift for the type of board on your system see Types of Acquisition Controller Boards page 72 The implementation as provided gives phase steps of 0 36 Acquisition Controller board or Pulse Sequence Controller board or 1 44 Output board Thus for any particular phase shift there may be a roundoff of 0 18 Acquisition Controller board or Pulse Sequence Controller board or 0 72 Output board This is not a real error because you know exactly what the phase shift is but are not able to set it with any finer resolution On systems with an Output board only see page 72 for a list of boards a 0 2 us delay internally precedes the AP analog port bus statements xmt rphase dcplrphase and dcplr2phase The apovrride statement prevents this 0 2 us delay from being 01 999165 00 A0800 VNMR 6 1C User Programming 89 Chapter 2 Pulse Sequence Programming inserted prior to the next and only the next occurrence of one of the these AP bus statements Controlling the Offset Frequency Statements for frequency control are decoffset dec2offset dec30ffset dec4offset obsoffset offset and ioffset Table 12 summarizes these statements Table 12 Frequency Control Statements decoffset frequency Change offset frequency of first decoupler dec2offset frequency Change offset frequency of second decoupler dec30ffset frequency
594. structure are set as follows e nblocks is the number of data blocks present in the file 01 999165 00 A0800 VNMR 6 1C User Programming 285 Chapter 5 Parameters and Data e ntxraces is the number of traces in each block e np is the number of simple elements 16 bit integers 32 bit integers or 32 bit floating point numbers in one trace It is equal to twice the number of complex data points e ebytes is the number of bytes in one element either 2 for 16 bit integers in single precision FIDs or 4 for all others e tbytes is set to np ebytes e bbytes is set to ntraces tbytes nbheaders sizeof struct datablockhead The size of the datablockhead structure is 28 bytes e vers_id is the version identification of present VNMR e nbheaders is the number of block headers per data block e status is bits as defined below with their hexadecimal values All other bits must be zero Bits 0 6 file header and block header status bits bit 6 is unused 0 S_DATA Ox1 0 no data 1 data 1 S_SPEC 0x2 0 FID 1 spectrum 2 5 32 0x4 3 S_FLOAT 0x8 0 integer 1 floating point 4 S_ COMPLEX 0x10 0 real 1 complex 5 S_HYPERCOMP LEX 0x20 1 hypercomplex If S_FLOAT 0 S_32 0 for 16 bit integer or S_32 1 for 32 bit integer If S_FLOAT 1 S_32 is ignored Bits 7 14 file header status bits bits 10 and 15 are unused S_ACQPAR 0x80 0 not Acqpar 1 Acqpar S_SECND 0x100 0 first FT
595. sursssierveerseeir siess 174 Set quadrature phase of first decoupler esesseesseseeseeereeereresesrerererereee 174 Set quadrature phase of second decoupler ssseseeeseeeeeereesererereeeee 174 Set quadrature phase of third decoupler 0 0 0 ceeeesceeeeseeeeeeeeeeneeeees 174 Set quadrature phase of fourth decoupler eee eeeeeseeeeeeeeeneenees 175 Change first decoupler power level linear amp systems 175 Change second decoupler power level linear amp systems 175 Change third decoupler power level linear amp systems 176 Change fourth decoupler power level linear amp systems 176 End programmable decoupling on first decoupler eee 176 End programmable decoupling on second decoupler ee 177 End programmable decoupling on third decoupler eee 177 Start programmable decoupling on first decoupler 0 0 0 cece 177 Start programmable decoupling on second decoupler 0 177 Start programmable decoupling on third decoupler eee 178 Pulse first decoupler transmitter with amplifier gating 0 0 0 179 Set first decoupler high power level class C amplifier 179 Set first decoupler fine POWER ce eeeeesesecseeeeseeeeceteecesceeeeeeeeseeaees 179 Set second decoupler fine POWER eeesesesseseeseceeeeeeseeeeeeceeesaenees 180 Set third decoupler fine power 0 eeeeeesecseeceeseeseceteecescseeeeceeeneene
596. t a spectrum or 2D plane without displaying it ee 39 Input Output Tools seirinin inr ee hea E ETEO E OESE N a toned AE Ee EEEE Ear Ees 40 apa Plot parameters automatically 0 ec ee cee ceseeeeceseeeeseeeeeeeeeeeeeeees 40 banner Display message with large characters 0 0 eceeeeceseeeeeeeeeeeeeeeeeeeees 40 clear Clear a Window ssiestsossessesiatteabessacestescsseteasasvoestastesvenntans E ERE 40 confirm Confirm message using the MOUSE ce eeeeeeeeceeeeeteeeeeeseeeeaeseeeeeeee 40 echo Display strings and parameter values in text window eee 40 flip Flip between graphics and text window sessseseessreerreererreerrerereeesre 40 format Format a real number or convert a string for output eee 40 input Receive input from keyboard eee eee ceeceseeeeceseeeeeeeeeeeeeeeeeeeeae 41 lookup Look up and return words and lines from text file eects 41 nrecords Determine number of lines in a file ot eee ceeeeeeseeeeeeeeeeeaeneeeeeees 41 VNMR 6 1C User Programming 5 Table of Contents psgset Set up parameters for various pulse sequences vnmr_confirmer Display a confirmer window UNIX ce ceeeeseeseeceeseeseeeeeeeseeneeeeeees write Write output to various devices oo ee eee eee eeeecse cece caeeseeeeeeeaeeeeneees Repression and Curve Putin e ccs sececessieccssaseesseeasestspssvsaessopysoascepsetvaanss EEEE E EAEE EVEN ROURE EE EEEE analyze Generalized curve fitting eee eeeeeeeecsecee
597. t in order to function Many of these arguments are listed as real number Because of the flexibility of C a real number argument can take three different forms variable e g d1 constant e g 3 4 20 0e 6 or expression e g 2 0 pw 1 0 d2 Times whether delays or pulses are determined by the type of acquisition controller board used on the system listed on page 72 e On Data Acquisition Controller boards times can be specified in increments as small as 12 5 ns with a minimum of 100 ns e On Acquisition Controller boards and Pulse Sequence Controller boards times can be specified in increments as small as 25 ns with a minimum of 200 ns e On Output boards and the MERCURY VX MERCURY and GEMINI 2000 times can be specified in increments as small as 0 1 us The smallest possible time interval in all other cases is 0 2 us or 0 Any pulse widths or delays less than the minimum generate a warning message and are then eliminated internally from the sequence Note that time constants within a pulse sequence are always expressed in seconds A series of internal real time variables named v1 v2 v14 are provided to perform calculations in real time by the acquisition computer while the pulse sequence is executing Real time variables are discussed in detail later in this chapter For now note that all of the phases and a small number of the other arguments to the pulse sequence statements discussed here must be real
598. t lock while shimming Lock saturation while shimming A shim coil DAC limit hit while shimming 700 Autolock errors 701 702 703 704 705 User aborted ALKABORT Autolock failure in finding resonance of sample ALKRESFAIL Autolock failure in lock power adjustment ALKPOWERFAIL Autolock failure in lock phase adjustment ALKPHASFAIL Autolock failure lost in final gain adjustment ALKGAINFAIL 800 Autogain errors 801 Autogain failure gain driven to 0 reduce pw AGAINFAIL Hard errors 901 902 Incorrect PSG version for acquisition Sum to memory error number of points acquired not equal to np 76 VNMR 6 1C User Programming 01 999165 00 A0800 2 2 Overview of Pulse Sequence Programming Table 5 Acquisition Status Codes continued 903 FIFO underflow error a delay too small 904 Requested number of data points np too large for acquisition 905 Acquisition bus trap experiment may be lost 1000 SCSI errors 1001 Recoverable SCSI read transfer from console 1002 Recoverable SCSI write transfer from console 1003 Unrecoverable SCSI read transfer error 1004 Unrecoverable SCSI write transfer error 1100 Host disk errors 1101 Error opening disk file probably a UNIX permission problem 1102 Error on closing disk file 1103 Error on reading from disk file 1104 Error on writing to disk file 1400 1500 RF Monitor errors 1400 An RF monitor trip occurre
599. t permitted and will generate an error Depending on the pulse sequence additional code may be needed to trap for this condition and skip the starthardloop and endhardloop statements if the count is 0 Only instructions that require no further intervention by the acquisition computer pulses delays acquires and other scattered instructions are allowed in a hard loop Most notably no real time math statements are allowed thereby precluding any phase cycle calculations Also no AP table with the autoincrement feature set can be used within a hard loop The number of events included in the hard loop including the total number of data points if acquisition is performed must be as follows e 63 or less for Output boards e 1024 or less for Acquisition Controller boards e 2048 or less for the MERCURY VX and MERCURY STM Output board Pulse Sequence Controller board or Data Acquisition Controller board In all cases the number of events must be greater than 1 No nesting of hard loops is allowed For Output boards a hardware loop must be preceded by some timed event other than an explicit acquisition or another hardware loop If two hardware loops must follow one another it will therefore be necessary to insert a statement like delay 0 2e 6 between the first endhardloop and the second starthardloop With only a single hardware loop there is no timing limitation on the length of a single cycle of the loop With two hardware loops perhaps
600. tatesseuaceseascesesoten sucess 288 Storing Mul ple Traces aroieonor nipone te aare a E EE e ES 289 Feader and Data Display emieceie cau shes socesccssteccasaevstasescsotetesuivass gues E E EE E RERE 290 5 2 FDF Flexibl Data Format Piles ii eccccccssscasiecsccostccessccecsscs davee steed stecsstesisdontccssactecneci casencbdssdtncoseaieessntcas 290 File Structures and Naming Conventions esis ses sistecsnaniveatisnschdas ise deanvedeansviate 290 PVG Format sosoeie cfs vschesasssanes eent vaot PEE PER EEE REEE EE RETER EEE EEEE EE AEE EEEN EEE R E EE 291 Header Parameters cies ivesesseiaiaciiesecsaceectsabves vsaeecucesaead EEEE EOE EENE EEE E RTE 291 WHAMSTOPMABLONS H 55sczad0sesrecsdeszedeabevegecasssesouesuaepszacscabsepsdssadsasbahesaveodasesonhddeabeip cebvabstanavenageacsvarte 294 Creatine FDF Piles i cisietsssieeiiesctdadstie rE ES NEE TEETE EE EOE E A E siamese EEES VEKT TESTET EKTET 294 ELTE D PS sce E E E Wags tbesonies 295 5 3 Reformatting Data for Processing oo eee eccscsesseeecsecseeseesecaeceesscsaecessecsaeneeseesecseeseeseaesaeeeesaesaeeeteeeeaees 295 Standard and Compressed BO ats ecinic sutencnsey i e EEE e S e ENE EAEE EERE 295 Compressor Uncompress Data sonasiason orrien aeae a a A E E EE E aie 296 Moye and Reverse Data cercen erena eaea eE EEEE E A RERE EEEE EEE AOLE NE 296 Table Convert Data iineoa naines ri ea eE E E E E EEEE AEE aslo aS 298 Reformatine SPECA seer eorr inn neee Ee hc reS rE lived ahead n
601. tatus Menu page 68 to change the decoupler and receiver status at this point of the sequence Other Show prompt Enter Pulse Sequence Statement and use the information you enter Finish Close the pulse sequence file and compile the pulse sequence placing the output in the user pulse sequence directory Show Seq Display a listing of the pulse sequence in the text window Pulse Sequence Entry Delay Menu The Pulse Sequence Entry Delay Menu is typically entered by selecting Delay in the Pulse Sequence Entry Main Menu or by entering menu psg_delay After each button action is complete the Pulse Sequences Entry Main Menu see above is displayed Button Description D1 Add delay d1 at this point in the sequence D2 Add delay d2 at this point in the sequence automatically made the evolution time in 2D experiments D2 2 Add a delay d2 2 at this point in the sequence for split evolution times in 2D experiments D3 Add delay d3 at this point in the sequence MIX Add a delay mix at this point in the sequence Other Show prompt Input Name of Delay and add the name you enter as a delay at this point in the sequence Allow Homospoil Make the delay that follows start with a homospoil pulse of length hst Return You must use this button before selecting buttons 1 through 6 if that delay is to have a homospoil pulse Note that homospoil is not possible on the GEMINI 2000 Display Pulse Sequence Entry Main
602. te that the given value is the number of loops to be executed and that the values 0 and 1 cause the pattern to execute once Due to a digital hardware bug affecting looping patterns must be carefully constructed to achieve the desired results wait is a keyword either WAIT or NOWAIT that selects whether or not a delay is inserted to wait until the gradient is completed before executing the next element The total time it will wait is width Loops If Loops is supplied as 0 it will be counted as 1 when determining its total time getorientation Read image plane orientation rgradient Set gradient to a specified level shapedgradient Provide shaped gradient pulse to gradient channel shaped2Dgradient Generate arrayed shaped gradient pulse vgradient Set gradient to a level determined by real time math shapedvgradient Generate dynamic variable shaped gradient pulse Applicability Syntax Description Arguments Systems with WFG on imaging or PFG module shapedvgradient pattern width amp_const amp_incr amp_vmult channel vloops wait tag char pattern name of pulse shape text file double width length of pulse double amp_const sets amplitude of pulse double amp_incr sets amplitude of pulse codeint amp_vmult sets amplitude of pulse char channel gradient channel x y or tar codeint vloops variable for number of loops int wait WAIT or NOWAIT int tag unique n
603. template gt lt height gt write alpha printer line3 error template write reset file file lt template gt Displays strings and parameter values on various output devices VNMR 6 1C User Programming 41 Chapter 1 MAGICAL II Programming Regression and Curve Fitting analyze Syntax Description autoscale Description expfit Syntax Description expl Syntax Description pexpl Syntax Description poly0 Description rinput Description scalelimits Syntax Description 42 VNMR 6 1C User Programming Generalized curve fitting Curve fitting analyze expfit xarray lt options gt Regression analyze expfit regression lt options gt Provides an interface to the UNIX curve fitting program expfit supplying input data in the form of the text file analyze inp in the current experiment Resume autoscaling after limits set by scalelimits Returns to autoscaling in which the scale limits are determined by the exp1 command such that all the data in the exp1 input file is displayed Least squares fit to exponential or polynomial curve UNIX expfit options lt analyze inp gt analyze list A UNIX command that takes a least squares curve fitting to the data supplied in the file analyze inp Display exponential or polynomial curves expl lt lt options gt linel line2 gt Displays exponential curves resulting from T4 T gt or kineti
604. ter 4 This action produces a total phase cycle 16 transients long 4 for the basic cycle with the whole cycle repeated 4 times in successively incremented phases You are now ready to start programming the sequence Start with status A Select a delay d1 with homospoil Adding homospoil means that a homospoil pulse can occur at the start of this delay depending on your choice of parameters when the experiment is run 5 Click on Status gt A gt Delay gt Allow Homospoil gt D1 If you are using a GEMINI 2000 system no homospoil is possible however you can enter homospoil related statements and parameters without an error occurring Next consider status B Looking at Figure 2 we see that in status B we want the following elements 1 a pulse of phase x and length pw 2 adelay d2 2 because this experiment has a split evolution time 3 a pulse of length p1 whose phase cycles 0 3 2 1 during the course of four transients and 4 another d2 2 delay 6 Click on Status gt B gt Pulse gt X gt PW gt Delay gt D2 2 Then click on Pulse gt More gt 0321 gt P1 gt Delay gt D2 2 In status C we need only one action to select alternating receiver phase 7 8 Click on Status gt C gt Status gt Set Revr Phase gt The programming is finished Click on Finish 64 VNMR 6 1C User Programming 01 999165 00 A0800 2 1 Programming Pulse Sequences from Menus This closes the pulse sequence
605. ter gate control line that has been turned off in PSG at the end of the preceding delay to actually turn off in hardware before the AP bus instructions have been issued from the FIFO Otherwise any such high speed line would not be turned off in hardware until the end of the series of AP bus instructions This extra 0 2 us delay can be avoided with the apovrride statement Delays from Changing Status Other delays can be incurred with the status and set status statements The first occurrence of the status statement always incurs the full delay On subsequent occurrences of status the delay depends on values of the parameters dmm dmm2 and dmm3 There are three parts that contribute to this delay e Modulation mode On Y YINOVA if and only if the modulation mode changes 1 0 us is added to the delay and the first occurrence of s in the dm string or dm2 or dm3 adds an extra 1 0 us On systems with apinterface 3 or UNITYplus systems if and only if the modulation mode changes 2 3 us is added to the delay on UNITYplus 4 3 us on other systems On UNITYplus only if the mode is synchronous the first occurrence of the s in the dm string or dm2 or dm3 adds an extra 2 3 us when the modulation mode is switched from CW to synchronize the decoupling scheme Note that the waveform generator mode p needs CW modulation mode c Waveform generator Starting a waveform generator adds 1 25 us on UN TYINOVA 5 75 us on UNITYplus a
606. ter will be written For example set user rtoutput write alpha Suser label is label with Svalue If any variables are included in the value of the attribute the value must be enclosed in braces Sample Entry Control The exList field in the configuration files is used to specify files that contain excluded sample locations This is important for walkup automation where sample locations are reused The field is a list of file names The contents of the files are searched for location definitions For example if the line SAMPLE 33 is one of the files location 33 will be excluded This is also useful to exclude certain locations that contain reference samples The current exList is set to expl sampleinfo locQ Relative path names are relative to the automation directory Absolute path names can also be used The entry exp1 sampleinfo prevents the current location of the sample in the magnet from being used The locQ entry causes all locations to be used before they are reused Removing locQ from exList makes locations available for reuse as soon as all the experiments on that location are finished The locList is a single file that contains a list of locations that are submitted to an automation run This file is used to recycle used locations for walkup automation and should not be altered The difference between the files enter conf and auto conf 01 999165 00 A0800 VNMR 6 1C User Programming 321 Chapter 6 Customi
607. ternal_name can be any legitimate C variable name that has been defined at the beginning of the pulse sequence as type double J getval J acqtime getval at delay getval mix getstr Look up value of string parameter Generic delay routine All systems except MERCURY VX MERCURY and GEMINI 2000 G_Delay DELAY_TIME dl SLIDER_LABEL NULL SLIDER_SCALE ty SLIDER_MAX 60 SLIDER_MIN 0 SLIDER_UNITS 1 0 0 See the section Generic Pulse Routine page 121 Frequency offset routine All systems except MERCURY VX MERCURY and GEMINI 2000 G_Offset OFFSET_DEVICE TODEV OFFSET_FREQ tof SLIDER_LABEL NULL SLIDER_SCALE 0 SLIDER_MAX 1000 SLIDER_MIN 1000 SLIDER_UNITS 0 0 See the section Frequency Offset Subroutine page 122 Fine power routine All systems except MERCURY VX MERCURY and GEMINI 2000 G_Power POWER_VALUE tpwrf POWER_DEVICE TODEV SLIDER_LABEL NULL SLIDER_SCALE 1 4095 SLIDER MAX SLIDER_MIN 0 SLIDER_UNITS 1 0 0 See the section Fine Power Subroutine page 125 Generic pulse routine All systems except MERCURY VX MERCURY and GEMINI 2000 199 VNMR 6 1C User Programming Chapter 3 Pulse Sequence Statement Reference Syntax Description G_Pulse PULSE_WIDTH pw PULSE_PRE_ROFF rofl PULSE_POST_ROFF rof2 PULSE_DEVICE TODEV SLIDER_LABEL NULL SLIDER_SCALE Ly SL
608. text files such as macros menus and pulse sequences short text files such as those used to annotate spectra are usually edited in simpler ways Opening a UNIX Shell from VNMR Entering the she11 command from VNMR without any argument brings up a normal UNIX shell On the Sun a popup window is created On the GraphOn terminal the entire terminal is used Entering she 11 with the syntax shell command lt S filel file2 gt executes the UNIX command line given displays any text lines generated and returns control to VNMR when finished If return arguments filel file2 are present the results of the command line are returned to the files listed with each file receiving a single display line for example shell ls t grep May filelist On a terminal the command she11i command runs interactively the UNIX command line given as the argument No return or output variables are allowed Under window based VNMR shelli is identical to the she11 command To display information about who is on UNIX enter the w command from VNMR 4 4 Background VNMR Running VNMR commands and processing as a UNIX background tasks are possible by using Vnmr and vbg commands from UNIX 280 VNMR 6 1C User Programming 01 999165 00 A0800 4 4 Background VNMR Running VNMR Command as a UNIX Background Task VNMR commands can be executed as a UNIX background task by using the command Vnmr mback lt n gt command_string lt amp gt w
609. that the Loc and exp names are not arbitrary These two input selections have been given special characteristics that require specific attributes Setting the Content of the Output File On line 11 the out fields parameter specifies which items are written by enter into its output file and in what order they are written This output file contains all the information 314 VNMR6 1C User Programming 01 999165 00 A0800 6 1 Customizing the Sample Entry Form Window needed to run an experiment and is referred to as the ent erQ file even though at the time it is built its name is arbitrary When the output file is finally submitted as the set of experiments by the autogo command it is copied into the automation directory and named enterQ The default enter program requests nine selections named loc user exp solvent textfield userdir data stat and separator to be written into the enterQ file Some of the items in out fields match items in infields and some do not Also the order that the items are written does not need to match the order of the items in infields Setting Name Attributes The characteristics of each name used by infields and out fields needs to be defined Each name is defined by a series of attributes The attributes are fixed They include an id label menulabel style file numPerLine required output and duplicates There are also some attributes that depend on the value of other attributes These include min
610. the current value of ct performs the integer hlv operation and sets the variable v2 used for phases etc to that value On successive transients v2 has values of 0 0 1 1 2 2 etc Statements like these are called real time because they execute during the real time operation of the pulse sequence Run time statements then are statements that are evaluated and executed in the host computer by the pulse sequence program in seqlib when you enter go Real time statements are statements that are repeatedly every transient executed by the code program run in the acquisition computer Therefore it is not possible to include a statement like d2 1 0 0 33 ct The variable ct is a real time variable it is actually an integer pointer variable while C type mathematics are a run time operation Only the special real time statements included in this section can be executed on a transient by transient basis Manipulating Acquisition Variables Certain acquisition parameters such as ss steady state pulses and bs block size cannot be changed in a pulse sequence with a simple C statement The reason is that by the time the pulsesequence function is executed the values of these variables are already stored in a region of the host computer memory that will subsequently form the low core portion of the acquisition code in the acquisition computer These memory locations can be accessed and modified however by using real time math functions
611. the delay in seconds between gating the second decoupler off and gating the amplifier off dec2shaped_pulse gauss pl v9 rofl1 rof2 apshaped_dec2pulse Second decoupler pulse shaping via AP bus decshaped_puls Perform shaped pulse on first decoupler shaped_pulse Perform shaped pulse on observe transmitter sim3shaped_pulse Simultaneous three pulse shaped pulse dec3shaped_pulse Perform shaped pulse on third decoupler Applicability Syntax Description UNITYTNOVA and UNITY plus systems dec3shaped_pulse pattern width phase RG1 RG2 char pattern name of RF text file double width width of pulse in sec codeint phase real time variable for phase double RG1 gating delay before pulse in sec double RG2 gating delay after pulse in sec Performs a shaped pulse on the third decoupler If a waveform generator is configured on the channel it is used otherwise the linear attenuator and the small angle phase shifter are used to effectively perform an apshaped_dec3pulse statement 01 999165 00 A0800 VNMR 6 1C User Programming 185 Chapter 3 Pulse Sequence Statement Reference Arguments Examples Related decspinlock Applicability Syntax Description Arguments When using the waveform generator the shapes are downloaded into the waveshaper before the start of an experiment When dec3shaped_pulse is called the shape is addressed and started The minimum pulse le
612. the incdelay statement for the delay time index is DELAY1 DELAY2 DELAY3 DELAY4 or DELAYS and identifies which time increment is being initialized initdelay 1 0 sw DELAY1 initdelay 1 0 swl DELAY2 delay Delay for a specified time hsdelay Delay with possible homospoil pulse idelay Delay for a specified time with IPA incdelay Real time incremental delay vdelay Delay with fixed timebase and real time count Initialize parameters for spectroscopy imaging sequences Systems with imaging capability however this statement will be obsoleted in future versions of VNMR void initparms_sis Sets the default state of the receiver to ON so that the receiver is enabled for explicit acquisitions The original purpose of initparms_sis was to initialize the standard imaging parameters in imaging sequences but starting with VNMR 5 3 initialization of these parameters has been folded into PSG To upgrade older SIS sequences for Vnmr 5 1 insert initparms_sis after the variable declarations and update griserate variable EXTERNAL TRIGGER 01 999165 00 A0800 VNMR 6 1C User Programming 207 Chapter 3 Pulse Sequence Statement Reference initval Syntax Description Arguments Examples Related iobspulse Applicability Syntax Description Arguments Examples Related ioffset Applicability Syntax double revry hold initparms_sis
613. the slider when displayed in the Acquisition window acqi program ioffset tof OBSch tof offset Change offset frequency of transmitter or decoupler Pulse observe transmitter with IPA All systems except MERCURY VX MERCURY and GEMINI 2000 ipulse width phase label double width pulse length in sec codeint phase real time variable for phrase char label slider label in acqi Functions the same as pulse width phase statement except that ipulse generates interactive parameter adjustment IPA information when gf or go acqi is entered If go is entered ipulse is the same as pulse width specifies the duration in seconds of the pulse phase sets the phase of the pulse The value must be a real time variable v1 to v14 oph etc label1 is the short character string to be given to the slider when displayed in the Acquisition window acqi program ipulse pw v4 pulse ipulse pw v5 pw pulse Pulse observe transmitter with amplifier gating Change transmitter or decoupler fine power with IPA All systems except MERCURY VX MERCURY and GEMINI 2000 ipwrf power device label double power new fine power level int device OBSch DECch DEC2ch DEC3ch char label slider label in acqi Functions the same as rlpwrf statement except that ipwrf generates interactive parameter adjustment IPA information when gf or go acqi is entered If g
614. the time increment and delay The argument t ime_increment is the time increment that will be multiplied by the count a real time variable for the delay time and index is one of the indices DELAY1 DELAY2 DELAYS e g initdelay 1 0 sw DELAY1 or initdelay 1 0 swl DELAY2 2 Set the increment delay by specifying its index and the multiplier count using incdelay count index e g for incdelay v3 DELAY2 when v3 0 the delay is 0 1 sw1 Pulsing the Observe Transmitter Statements related to pulsing the observe transmitter are rgpulse irgpulse pulse ipulse obspulse and iobspulse Table 7 summarizes these statements Use rgpulse width phase RG1 RG2 as the main statement to pulse the observe transmitter in a sequence where width is the pulse width phase a real time variable is the pulse phase and RG1 and RG2 are defined according to system type e On the YNITYZNOVA and GEMINI 2000 RG1 is the delay during which the linear amplifier is gated on and then allowed to stabilize prior to executing the rf pulse and RG2 is the delay after the pulse after gating off the amplifier Thus receiver gating is VNMR 6 1C User Programming 01 999165 00 A0800 2 3 Spectrometer Control Table 7 Observe Transmitter Pulse Related Statements iobspulse string Pulse observe transmitter with IPA ipulse width phase string Pulse observe transmitter with IPA irgpulse width phase RG1 RG2 s
615. ther the decimal point or the E and the exponent may be missing Some examples are 1 37E 3 4e5 2E2 1 4 5 e A string constant is a sequence of characters surrounded by single quote characters or by backward single quote characters This is a string and This is a string are examples of string constants To include a single quote character in a string place a backslash character before the single quote character for example This string isn t permissible without the backslash To include a backslash character in the string place another backslash before the backslash such as This string includes the backslash Alternatively the two styles of single quote characters can be used If backward single quotes are used to delimit a string then single quotes can be placed directly within the string for example This isn t a problem Or the single quote styles can be exchanged for example This isn t a problem The single quote style that initiates the string must also terminate the string Operators Table 2 lists the operators available in MAGICAL Each operator is placed in a group and groups are shown in order of precedence with the highest group precedence first Within each group operator precedence in expressions is from left to right except for the logical group where the respective members are listed in order of precedence There are four built in special operators e sqrt
616. tical expression 35 mathematical functions 43 matrix arithmetic 31 matrix transposition 289 matrix window 328 maximum value of parameter 302 maxpk macro 37 MAXSTR dimension 73 maxvalue attribute 343 mean of data in regression inp 42 memory usage by VNMR commands 290 memory usage statistics 45 MEMS pulse sequence 96 memsize parameter UNIX 284 menu command 53 54 55 menu fields 326 menu files 53 54 menu system 52 menu system control 55 menu driven pulse sequence writing 63 menulib directory 53 54 57 menulibpath parameter 54 menus for pulse sequence programming 65 menuvi command 54 message confirmation by mouse 40 message display with large characters 40 metal objects warning 19 mf command 296 mfblk command 296 mfdata command 296 mftrace command 296 microimaging pulse sequences 152 minimum value of parameter 302 minvalue attribute 343 mkdir command UNIX 278 mlabel parameter 55 56 MLEV 16 modulation 243 mod2 statement 99 215 mod4 statement 99 215 modifying the instrument 20 modn statement 99 216 modulation frequency 243 modulation frequency change delay 143 modulation mode change delays 143 modulo 2 integer value 215 modulo 4 integer value 215 modulo n integer value 216 modulo number 99 mouse button 52 move data in FID file 296 move FID commands 296 moving files into a directory 279 MREV type sequences 129 msloop statement 1
617. time variables A real time variable must appear as a simple argument e g v1 and cannot be replaced by anything else including an integer a real number a regular variable such as d1 or an expression such as v1 v2 Any variables you choose to use in writing a pulse sequence must be declared Most variables will be of type double while integers will be of type int and strings such as dmm are of type char with dimension MAXSTR Table 4 lists the length of these basic types on the Sun computer Many variables that refer to parameters used in an experiment are already declared see Accessing Parameters page 110 Real time variables are of type codeint int on MERCURY VX and UN YINOVA 32 bits whose size is 16 bits you will probably not be declaring new variables of this type A framework including variable declarations of the main types might look like this include lt standard h gt pulsesequence double delta declare delta as double char xpolar MAXSTR declare xpolar as char 01 999165 00 A0800 VNMR 6 1C User Programming 73 Chapter 2 Pulse Sequence Programming 74 Table 4 Variable Types in Pulse Sequences Type Description Length bits char character 8 short short integer 16 int integer 32 long long integer 32 float floating point 32 double double precision floating point 64 Implicit Acquisition The hom2dj c pulse sequence listing in Listing 6 on page 69 has one notable om
618. tinuous walkup mode i e errormess is set to a null string when all sample locations are used e The usenext loc attribute is an initialization step only it is not customizable Button Definitions The buttons at the bottom of the ent er window are partially configurable The choices available are addExp saveExp saveAndExit addSaveAndExit and quit Choices appropriate to automation runs are autoSample autoSampleNoExit and prioritySample T e The addExp selection when pressed copies the currently defined experiments into a temporary file The user still has the choice of ending the session by pressing either the saveAndExit button or the quit button e The saveAndExit selection appends the temporary file created by pressing the addExp button to the enterQ output file deletes the temporary file and then causes the enter program to exit e The saveExp button when pressed copies the currently defined experiments into a temporary file appends the temporary file to the ent erQ output file and then deletes the temporary file e The addSaveAndExit button does exactly the same things as the saveExp button and then it causes the enter program to exit e The autoSample button submits the currently defined experiment directly to an automation run and then exits the enter program e The autoSampleNoExit button functions the same as the autoSamp1le button except autoSampleNoExit does not cause the
619. tive title at the selected grid rectangle The available characteristics are the following Label of element The text string to be displayed as the title While this field is optional the title element is invisible if it is empty The title item is useful to explore the effect of Row Extent and Column extent If you input a fairly long text line as the title and then press Refresh Display only a portion of the text is displayed Increase the value of Row Extent from the menu and more text is displayed Increase the Column Extent and the title can be positioned between rows of the grid Label Element The label element places a noninteractive label at the selected grid rectangle The label is different from a title in that the value of a parameter can be displayed and the display is updated in the parameter value changes However you cannot change the parameter directly with this item The available characteristics are the following Label of element Text string to be displayed to the left of the parameter value This field is optional Units Text string to be displayed to the right of the parameter value This field is optional Width of element Width of the field that the parameter value is displayed This field is optional but is automatically set to 8 if no value or an illegal value is entered Vnmr Variables List of VNMR variables that are used to construct a value to be displayed This can be zero or more parameter names Tcl
620. to6 3 to6 7to8 dec2rgpulse dec3rgpulse delay 1 lor2 lor2 1to5 lor2 hsdelay 1 lor2 lor2 1to5 lor2 1lk_hold 1 2 3 lk_sample obspulse 3to6 3to6 3to6 5to8 offset 9 latching 7 standard 72 7 11 latching power obspower 1 2 2 3 decpower dec2power dec3power pwrf obspwrf 1 4 3 E _ decpwrf dec2pwrf dec3pwrf pulse rgpulse 3 3 to6 3 to6 3 to6 5to8 simpulse 3to5 3 to 10 3 to 10 3 to 15 7 to 10 sim3pulse 3 to7 3 to 14 3 to 14 status 0 to 5 times 0 to 8 times 0 to 7 per 0 to 12 0 to7 number of number of channel channels channels txphase 0 0 0 0 0 xmtrphase 1 4 6 128 VNMR6 1C User Programming 01 999165 00 A0800 2 8 Hardware Looping and Explicit Acquisition Explicit Acquisition Closely related to hardware looping is the explicit acquisition feature the acquisition of one or more pairs of data points explicitly by the pulse sequence This feature not available on MERCURY and GEMINI 2000 lets you intersperse pulses and data acquisition and allows coding pulse sequences that acquire multiple FIDs during the course of a pulse sequence such as COCONOSY It also allows pulse sequences that acquire a single FID one or more points at a time such as MREV type sequences For Output boards any sequence that uses hardware looping or explicit acquisition must have parameter d1 greater than 0 or at least some delay prior to the start of the hardware loop or explicit acquisition For Data
621. tothe newpul macro after the psgset line 01 999165 00 A0800 VNMR 6 1C User Programming 119 Chapter 2 Pulse Sequence Programming Also see the cosyps c pulse sequence in vnmr psgl1lib section 2 14 Multidimensional NMR page 148 and the chapter on Multidimensional NMR in the User Guide Liquids manual 2 7 Using Interactive Parameter Adjustment 120 The section Spectrometer Control page 79 included statements for interactive parameter adjustment IPA Such routines start with the letter i e g idelay irgpulse For users who need added flexibility in programming this section explains IPA and these routines in more detail IPA is available on all systems except MERCURY VX MERCURY and GEMINI 2000 General Routines In addition to the statements previously described PSG has four general routines e G_Pulse for generic pulse control e G_Offset for adjustment of the offset frequency e G Delay for generic delay control e G_Power for fine power control Each of these is called with an argument list described below specified with attribute value pairs terminated by a mandatory zero The terminating zero is mandatory If the zero is left out the results are unpredictable and can include a core dump of PSG Each attribute has a default value a pulse can be specified simply as G_Pulse 0 which would produce a transmitter pulse of size pw with rofl and rof2 set the same as the experiment parameters and phase
622. tributes of that parameter to display the name and value of all parameters in a tree or to display the attributes of all parameters in a tree To Move Parameters Use groupcopy from_tree to_tree group to copy a set of parameters of a group from one parameter tree to another it cannot be the same tree group is the same keywords as used with set group The fread file lt tree lt reset value gt gt command reads in parameters from a file and loads them into a tree The keyword reset causes the tree to be cleared before the new file is read value causes only the values of the parameters in the file to be loaded The fsave file lt tree gt command writes parameters from a parameter tree to a file for which the user has write permission It overwrites any file that exists To Destroy a Parameter The destroy parameter lt tree gt command removes a parameter from a parameter tree while the dest roygroup group lt tree gt command removes parameters of a group from a parameter tree The group argument uses the same keywords as used with the set group command If the destroyed parameter was an array the array parameter is automatically updated To remove leftover parameters from previous experimental setups use prune instead The prune file command destroys parameters in the current parameter tree that are not also defined in the parameter file specified Format of a Stored Parameter To use the
623. tring Pulse observe transmitter with IPA obspulse Pulse observe transmitter with amp gating pulse width phase Pulse observe transmitter with amp gating rgpulse width phase RG1 RG2 Pulse observe transmitter with amp gating a misnomer RG1 and RG2 set amplifier gating as shown in Figure 3 The receiver is off during execution of the pulses and is only gated on immediately before acquisition On Transmitter gating Width Off Amplifier On i i gating RG1 4 RG2 4 Off Figure 3 Amplifier Gating e Onthe MERCURY VX MERCURY UNITYplus UNITY and VXR S the receiver and amplifiers are tied together such that when the amplifier is on the receiver is automatically turned off and when the receiver is on the amplifier is off Some further information about RG1 and RG2 e Typically RG1 is 10 us for 1H 19F and 40 us for other nuclei A typical value for RG2 is 10 to 20 us e The phase of the pulse is set at the beginning of RG1 The phase requires about 0 2 us to settle on UN TYINOVA and UNITYplus 10 us on GEMINI 2000 H 3C and broadband decouplers 1 0 us on MERCURY VX MERCURY and GEMINI 2000 broadband 0 5 to 1 0 us on other systems with direct synthesis rf and twice as long for rf types A and B e A transmitter gate is also switched during RG1 The switching time for this gate is 100 ns for YINOVA and UNITYplus systems or 1 to 3 us for GEMINI 2000 and UNITY systems For systems with linear
624. trolling Pulse Sequence Graphical Display ssieissiseccsisiiisiriecsisnsseseicustoiisrorisresesissesrisssrisess 104 Doar Real Time AP Tables scrima s5e ed da secesteses sa eoo E E A EE E REE ENEE SO EENE EEES 104 Loading AP Table Statements from UNIX Text Files 0 ssscsseccsoesseencestsetonssnesesensnsenenorenses 105 Table Names and Stale MINES i oiiire siorino E E E EERE E E O E RAEE 105 AP Table NOtanOn vereni nn REER A A ai anion anid 106 Handling AP TADES icenen re E eE ETEO E REEERE EEE ROEE E 107 Examples of Usina AP Tables crociere rine inea eE aE a ineo is arar REE E na Ce E EE 108 2 6 ACCESSING Parameters oseese ceb aena ET cists SE EEEE EERE E EEEE E EE SEERE EE 110 Gere e e E A leusBonetdesusesdusesnaste 110 Looking Up Parameter Values orisati osoetan seeno reses uta EKOE aE secs cabase ties EESE E SEE 117 Usine Parameters ma Pulse Sequence u scsscascisacessdsadeisceiecudectnsensn ti aea A RS Ea RREA 117 2 7 Using Interactive Parameter Adjustment oo eee ce cess eesceeeeeeceseeeeeeseeeaecaeecaecaaesaecsaesaeseeeeseeeeeesenseas 120 COTS TAU ou IE S 5 i cccd cde aae E E E E EE EE EE E O REE 120 Geneue Pulse ROUNDS cnioncoioni aonne EE EE A ae cine dies 121 Freguency Offset SU DTM xo jccs cscegdeces se ses cace sazscs dqevespestcosagnd sutsosseesonseoiceabasesuieaccetauseiaecscoeapeveneseed 122 Generne Delay RONUNE iss 6 ccavecdscases seesaieiesas taanesdbascazcennassabnasdabevavedbsasesouscasnscis cobapbsteaesanadauieaberts 12
625. ts 93 Gaussian pulse 139 gcoil parameter 153 generic delay routine 123 199 generic pulse routine 121 199 getarray statement 157 196 getelem statement 107 197 getfile command 47 getll command 38 getorientation statement 197 getreg command 38 getstr statement 72 117 198 getval statement 72 117 198 getvalue command 299 Ggroup 301 302 gilson conf file 322 glide directory 52 global file 299 global list 167 statements 157 global PSG parameters 111 global variables 32 global type parameter tree 299 go command 101 102 gradaxis parameter 154 gradient control 150 set to specified level 238 simultaneous shaped 213 variable angle 265 variable angle gradient pulse 266 variable angle shaped gradient 266 variable angle shaped gradient pulse 268 waveforms 132 134 zero all gradients 276 gradient function 203 gradient level set by real time math 270 gradient pattern file 206 gradient pulse 151 generation 248 on z channel 276 simultaneous shaped 214 gradient statement 155 01 999165 00 A0800 Index gradtables directory 153 gradtype parameter 144 150 graphical display of a sequence 70 graphical display of pulse sequences 104 graphical display of statements 190 191 graphics display status 47 graphics window 40 graphis command 47 GraphOn terminal 280 GRD file suffix 132 grep command UNIX 279 gripper abort 76 group of parameters 301 groupcopy command 301
626. ts are different from AP tables in that the lists are sent down to the acquisition console when the experiment starts up and are accessible until the experiment completes In working with arrayed experiments be careful when using a 1 in the 1ist_number argument because a list will be created for each array element In this case a list parameter can be created as an arrayed parameter with protection bit 8 256 set To read in the values of this type of parameter use the get array statement To ensure that the list is only created once check the global array counter variable ix and only call create_delay_list to create the list when it equals 1 An example is shown below list is a pointer to a list of delays nvals is the number of values in the list 01 999165 00 A0800 VNMR 6 1C User Programming 165 Chapter 3 Pulse Sequence Statement Reference Examples Related List_number l1 or a unique number from 0 to 255 for each list pulsesequence Declare static to save between calls Static int tisti Lrst2 int ip any double delay1 1024 delay2 1024 n 1024 if ix 1 for i 0 i lt n itt Initialize delayl amp delay2 arrays First listl is set to 0 listl create_delay_list delayl n 0 This is list 1 create_freq_list freqs nfreqs OBSch 1 This is list 2 create_offset_list freqs nfreqs OBSch 2 Next list2 is set to 3 list2 create_delay
627. typical real parameter file named a is interpreted the numbers in parentheses are not part of the file but are line references in the interpretation 1 a 31 1e 30 1e 30 00101 64 2 24 126400 3 0 This file is made up of the following lines 1 The parameter has the name a subtype is 3 delay basictype is 1 real maximum size is le 30 minimum size is le 30 stepsize is 0 Ggroup is 0 ALL Dgroup is 1 ACQUISITION protection is 0 cannot array the parameter active is 1 ON and intptr is 64 not used 2 Parameter a has 1 value the real number 24 126400 3 Parameter a has 0 enumerable values As another example here are the values in a file for the parameter tof 1 tof 517772 1 8202 1 64 2 1 1160 3 0 The tof file is made up of the following lines 1 The parameter has the name tof subtype is 5 frequency and basictype is 1 real To read the next 3 values we must jump to the protection field Because the protection word value is 8202 which is 8192 8 2 then bit 13 8192 bit 3 8 and bit 1 2 bitmasks are set Because bit 13 is set the maximum size minimum size and stepsize values each is 7 are indices into the 7th array value in the parameters parmax parmin and parstep respectively in the file conpar Because bit 3 is set this causes a macro to be executed The bit bitmask 2 is also set which means the active not active status of the parameter cannot be changed For the re
628. uals supplied with the magnet for the size of a typical 10 gauss stray field This gauss level should be checked after the magnet is installed WARNING Only qualified maintenance personnel shall remove equipment covers or make internal adjustments Dangerous high voltages that can kill or injure exist inside the instrument Before working inside a cabinet turn off the main system power switch located on the back of the console then disconnect the ac power cord WARNING Do not substitute parts or modify the instrument Any unauthorized modification could injure personnel or damage equipment and potentially terminate the warranty agreements and or service contract Written authorization approved by a Varian Inc product manager is required to implement any changes to the hardware of a Varian NMR spectrometer Maintain safety features by referring system service to a Varian service office WARNING Do not operate in the presence of flammable gases or fumes Operation with flammable gases or fumes present creates the risk of injury or death from toxic fumes explosion or fire WARNING Leave area immediately in the event of a magnet quench If the magnet dewar should quench sudden appearance of gasses from the top of the dewar leave the area immediately Sudden release of helium or nitrogen gases can rapidly displace oxygen in an enclosed space creating a possibility of asphyxiation Do not return until the oxygen level returns to no
629. ue gt Finds arc tangent of a number The optional return value is in radians Find arc tangent of two numbers atan2 y x lt value gt Finds arc tangent of y x The optional return argument value is in radians Calculate average and standard deviation of input averag num1 num2 average sd arguments sum sum_squares Finds average standard deviation and other characteristics of a series of numbers Find cosine value of an angle cos angle lt value gt Finds cosine of an angle given in radians Find exponential value of a number exp number lt value gt Finds exponential value base e of a number Find natural logarithm of a number in number lt value gt Finds natural logarithm of a number To convert to base 10 use logi9x 0 43429 1n x VNMR 6 1C User Programming 43 Chapter 1 MAGICAL II Programming sin Syntax Description tan Syntax Description Find sine value of an angle sin angle lt value gt Finds sine an angle given in radians Find tangent value of an angle tan angle lt value gt Finds tangent of an angle given in radians Creating Modifying and Displaying Macros crcom Syntax Description delcom Syntax Description hidecommand Syntax Description macrocat Syntax Description macrocp Syntax Description macrodir Description macroedit Syntax 44 VNMR 6 1C User Programming Cr
630. uitry might not be able to hold on to the lock When this is the case the correction added in the feedback loop that holds the lock can be held constant by calling 1k_hold Atsome time after the disturbance has passed how long depends on the type of disturbance the statement 1k_sample should be called to allow the circuitry to correct for disturbances external to the experiment Programming Microimaging Pulse Sequences The procedures for programming microimaging pulse sequences for UNITY and UNITYplus systems are the same as those used in the programming of spectroscopy sequences with the exception that additional pulse sequence statements have been added to define the amplitude and timing of the gradient pulses and the shaped rf pulses For example in the statement rgradient name value to set a gradient the argument name is either X Y or Z or alternatively with the connection through the parameter VNMR 6 1C User Programming 01 999165 00 A0800 2 16 Programming the Performa XYZ PFG Module orient gread gphase or gslice and value is the desired gradient strength in DAC units at the time the statement is to be implemented The basic imaging sequences included with the VNMR software are sequences for which the image data can be acquired processed and displayed with essentially the same software tools that are used with 2D spectra These sequences have been written in a form that provides a great deal of flexibility in adapting t
631. ular phase shift but also the less the precision in specifying the shift the smaller the shift the larger the time for a particular phase shift but the greater the precision in generating that shift The technique as described by Lallemand required a minimum time of 1 ms to perform the phase pulse the Varian implementation uses a time of 30 us and a resolution of 1 44 Use the statement phaseshift base multiplier device to implement the phase pulse technique on systems with rf type A or B for type C see the next section base is areal number expression or variable representing the base phase shift in degrees Any value is acceptable multiplier is the name of a real time variable ct v1 to v14 etc The value must be positive The phase shift will be base X multiplier mod 360 device specifies if the transmitter first decoupler second decoupler or third decoupler will be phase shifted Values can be OBSch DECch DEC2ch or DEC3ch respectively e g phaseshift 60 0 ct OBSch An important point to understand about using the phase pulse technique is that it is a cumulative technique That is a phase shift of 60 followed by another phase shift of 60 results in a total phase shift of 120 If one pulse requires a 60 phase and a subsequent pulse requires a 0 phase a 60 phase shift will need to be used after the first pulse Another important point is that the frequency that is shifted is the local oscillator L O
632. ulse 214 sin command 44 sine value of angle 44 single period notation UNIX 278 single quotes notation 27 30 size operator 31 33 SLI board 255 273 SLI lines set from real time variable 273 setting lines 255 sli statement 157 255 slider action 124 slider bars 327 SLIDER_LABEL attribute 120 124 small angle phase increment 87 small angle phase of decoupler 169 170 small angle phase of transmitter 275 small angle phase shifts 86 small angle phase step size 260 sn file 284 soft loop 125 141 solids high power amplifiers caution 22 solppm command 48 solvent resonances 48 sort command UNIX 278 sort files UNIX 278 source code 69 157 01 999165 00 A0800 sp off statement 97 256 sp on statement 97 257 SPARE 1 connector 97 spare line gating 256 257 spare lines 97 spectral analysis tools 38 spectrometer control statements 79 spectrometer differences 69 spectroscopy imaging sequences 207 spectrum gap 47 spectrum intensity at a point 39 spectrum selection without display 39 spell command UNIX 279 spelling errors check UNIX 279 spin lock control on transmitter 257 spin lock control statements 137 spin lock waveform control on decoupler 186 spinlock statement 137 144 257 spinner errors 75 split evolution time 64 sqrt operator 30 square brackets notation 33 square brackets notation 307 square root 30 square wave modulation 243 ss parameter 98 102 ss
633. umber for gradient element Operates the selected gradient channel to provide a shaped gradient pulse to the selected set of gradient coils This statement is tailored to provide a dynamic variable shaped gradient level controlled using the system AP math functions and real time looping The statement drives the chosen gradient shape to the level defined by the formula amplitude amp_const amp_incr amp_vmult The range of the gradient amplitude is 32767 to 32767 where 32767 is full scale and 32767 is negative full scale If the requested level lies outside this range it is truncated to the appropriate boundary value Note that the vloops argument is also controlled by a real time AP math variable Unlike the shaped rf pulses the shaped gradient leaves the gradients at the last value in the gradient pattern when the pulse completes name is the name of a text file without a GRD extension to describe the shape of the pulse The text file with a GRD extension should be located in Svnmrsystem shapelib or in the user s directory vnmruser shapelib 01 999165 00 A0800 VNMR 6 1C User Programming 249 Chapter 3 Pulse Sequence Statement Reference width is the requested length of the pulse in seconds The width of the pulse is affected by two factors 1 the minimum time of every element in the shape file must be at least 10 us and 2 the time for every element must be a multiple of 50 ns If width is less than 10 us time
634. umn e g math werr wexp The maximum number of columns is 4 each column can have 17 lines of output Since this includes the title s fewer than 17 parameters can be displayed in any one column The entire template is limited to 1024 characters or less As an alternative to a single string template which tends to be difficult to read a template can written as multiple strings each enclosed in double quotes The first number indicates the number of strings that follow Each string must start with a column number Figure 8 contains the display template for the parameter dg2 which is a typical example of a multiple string template 6 1 ist DECOUPLING dfrq 3 dn dpwr 0 dof 1 dm dmm dmf 0 dseq dres 1 homo 2 numrfch gt 2 2nd DECOUPLING dfrq2 3 dn2 dpowr2 0 dof2 1 dm2 dmm2 dmf2 0 dseq2 dr es2 1 homo2 2 numrfch gt 3 3rd DECOUPLING dfrq3 3 dn3 dpwr3 0 dof3 1 dseq3 dres3 1 homo3 3 ni2 3D ACQUISITION d3 3 sw2 1 ni2 0 phase2 0 3 ni2 3D DISPLAY rp2 1 lp2 1 4 ni2 3D PROCESSING 1b2 3 sb2 3 sbs2 sb2 3 ef2 3 gfs2 oef2 3 awc2 3 wtfile2 p roc2 fn2 0 Figure 8 Multiple String Display Template The conditional statement in this example e g numrfch gt 2 is covered below The title field can contain a string variable besides a literal If the variable is a real variable or not present or equal to the null string the variable itself is used as the title e g mystrvar 1 Example Col 1l andm
635. unction cancel Cancel Cmd Function menu Menu On Function mainmenu Main Menu Function help Help Function flip Flip Function resize Resize Using one of the actions usermacrol to usermacro8 sets the name to the macro called That macro then determines the action of the button For example to label the first button as Send Plot and make it the same as calling the page command use the following definition in the vnmrmenu file Function usermacrol Send Plot Then edit the macro usermacrol1 to contain the page command Customizing Menu Files and Help Files The standard system menu files are stored in the directory vnmr menulib For example the file vnmr menulib display_1D contains main choices for the 1D Data Display Menu Most often a menu is activated by selecting a button on a menu that involves switching to another menu Alternately a menu can be activated by pressing on a function key associated with menu switching button or by entering the menu command with the name of the menu as an argument An example of using the menu command would be entering menu display_1D to open the 1D Data Display Menu Every menu has associated with it a help file stored in the vnmr help system directory with the same name as the menu itself The help file for the current menu is displayed when the Help button in the upper menu is selected or the help command is entered For 01 999165 00 A0800 VNMR 6 1C User Programming 53 Chapter 1 MAGICAL II
636. unt number of times to loop int index real time variable to use during loop Description Starts a loop to execute statements within the pulse sequence The loop is ended by the endloop statement Syntax 1 is used with UNTYINOVA MERCURY VX MERCURY UNITY plus UNITY and VXR S systems Syntax 2 is used with GEMINI 2000 systems Arguments count is a real time variable used to specify the number of times through the loop count can be any positive number including zero index is a real time variable used as a temporary counter to keep track of the number of times through the loop The value must not be altered by any statements within the loop nis the same value 1 2 or 3 as used in the corresponding endloop statement Examples 1 initval 5 0 v1l set first loop count loop v1 v10 dbl ct v2 set second loop count loop v2 v9 rgpulse pl v1 0 0 0 0 endloop v9 delay d2 endloop v10 2 loop 2 5 0 v9 Related initval Initialize real time variable to specified value endloop End loop msloop Multislice loop magradient Simultaneous gradient at the magic angle Applicability Not applicable on MERCURY VX MERCURY and GEMINI 2000 Syntax magradient gradlvl double gradlvl gradient amplitude in G cm Description Applies a simultaneous gradient on the x y and z axes at the magic angle to B Information from a gradient table is used to scale and set values correctly The gradients are left at t
637. upling pattern is stored in the waveform generator e g VNMR 6 1C User Programming 01 999165 00 A0800 2 10 Pulse Shaping Table 28 Programmable Control Statements decprgoff End programmable decoupling on first decoupler dec2prgoff End programmable decoupling on second decoupler dec3prgoff End programmable decoupling on third decoupler decprgon Start programmable decoupling on first decoupler dec2prgon Start programmable decoupling on second decoupler dec3prgon Start programmable decoupling on third decoupler obsprgoff End programmable control of observe transmitter obsprgon Start programmable control of observe transmitter decprgon name 90_pulselength tipangle_resoln dec2prgon name 90_pulselength tipangle_resoln dec3prgon name 90_pulselength tipangle_resoln obsprgon name 90_pulselength tipangle_resoln obsprgon waltz16 pw90 90 0 The obsprgon statement returns the number of 50 ns ticks as an integer value in one cycle of the decoupling pattern Explicit gating of the observe transmitter with xmt ron and xmt roff is generally required To terminate any programmable phase and amplitude control on the observe transmitter under waveform generator control use obsprgoff Programmable Control of Decouplers The decprgon dec2prgon and dec3prgon statements set programming decoupling on the first second and third decouplers respectively The arguments for each statement are the same as o
638. urpose menus and help files reside in the same libraries as other menus and help files The manual Getting Started covers the VNMR 6 1C User Programming 01 999165 00 A0800 1 6 Customizing the Files Menus standard Files program menus as seen by the user In this section we look at programming these menus Starting the Program To start the Files program take one of the following actions e Enter the files command in the VNMR input window e Click on the File button in the Main Menu By default either action selects the menu files_main also called the Files Main Menu or the last active files menu You can also call up a particular menu by entering the command files file where file is the file name of the menu For example entering files files_main calls up the Files Main Menu Selecting and Accessing Files At startup the program reads the entries in the current directory and displays them on the screen To select a file click on each entry you want with the mouse Each name is highlighted in reverse video to show it has been selected You then click on the button with the desired function in the menu To deselect a file name click on the entry again Use the ilesinfo command to access the list of selected files This command expects at least one of the following input arguments e filesinfo number returns the number of selected files If no files have been selected it returns a value of 0 e filesinfo na
639. us apshaped_pulse Observe transmitter pulse shaping via the AP bus decshaped_pulse Perform shaped pulse on first decoupler dec2shaped_pulse Perform shaped pulse on second decoupler shaped_pulse Perform shaped pulse on observe transmitter apshaped_decpulse shape pulse_width pulse_phase power_table phase_table RG1 RG2 apshaped_dec2pulse shape pulse_width pulse_phase power_table phase_table RG1 RG2 apshaped_pulse shape pulse_width pulse_phase power_table phase_table RG1 RG2 decshaped_pulse shape width phase RG1 RG2 dec2shaped_pulse shape width phase RG1 RG2 dec3shaped_pulse shape width phase RG1 RG2 shaped_pulse shape width phase RG1 RG2 Controlling Attenuation This section describes how to configure and control the system attenuators Standard System with Two Attenuators On UNYTINOVA UNITY plus UNITY and VXR S systems with two attenuators connect the two existing attenuators in series leaving one channel without computer controlled attenuation This is often acceptable in homonuclear experiments while in heteronuclear experiments and some homonuclear experiments it may be desirable to insert a simple fixed attenuator in line in the channel that isn t being shaped 01 999165 00 A0800 VNMR 6 1C User Programming 141 Chapter 2 Pulse Sequence Programming If you take this approach the tpwr and dpwr parameters or equivalently the power 0BSch and p
640. us register 0 1 2 or 3 Sets one of the four 8 bit AP bus registers that provide an output interface to custom user equipment The outputs of these registers go the USER AP connectors J8212 and J8213 located on the back of the left console cabinet The outputs have a 100 ohm series resistor for circuit protection vi is an index to a real time variable that contains a signed or unsigned real number or integer to output to the specified user AP register register is the AP register number mapped to output lines as follows e Register 0 is J8213 lines 9 to 16 e Register 1 is J8213 lines 1 to 8 e Register 2 is J8212 lines 9 to 16 e Register 3 is J8212 lines 1 to 8 vsetuserap vl 1 readuserap Read input from user AP register setuserap Set user AP register Set SLI lines from real time variable Systems with imaging capability and the Synchronous Line Interface SLI board an option that provides an interface to custom user equipment vsli address mode var int address SLI board address int mode SLI_SET SLI_OR SLI_AND SLI_XOR codeint var real time variables for SLI lines Sets lines from real time variables on the SLI board It has no return value vs1i has a pre execution delay of 10 950 us but no post execution delay The delay is composed of a 200 ns startup delay with 5 AP bus cycles 1 AP bus cycle 2 150 us 01 999165 00 A0800 VNMR 6 1C User Programming 273 Chapter 3 Pulse Sequen
641. us section simple pulse sequences can be written completely using the menu system without any knowledge of C programming For example the hom2dj pulse sequence that we wrote in the step by step example is a simple text file similar to Listing 6 We will return in a moment to the specifics of what is included in this text file Spectrometer Differences This manual contains information on how to write pulse sequences for UNTYINOVA MERCURY VX MERCURY UNITYplus GEMINI 2000 UNITY and VXR S spectrometers Each class of spectrometer has different capabilities so not all statements may be executed on all platforms For example because MERCURY VX hardware differs significantly from YNTYZNOVA hardware sections in this manual covering waveform generators and imaging are not applicable to the MERCURY VX even though the pulse sequence programming language is the same Pay careful attention to comments in the text regarding the system applicability of the pulse sequence statement or technique Pulse Sequence Generation Directory Pulse sequence generation PSG text files like hom2dj c in Listing 6 are stored in a directory named psglib There are many such psg1ib directories including the system vnmxr psglib directory and a psglib directory that belongs to each user Listing 6 Text File for hom2dj c Pulse Sequence Listing VARIAN VNMR MENU GENERATED PULSE SEQUENCE hom2dj include lt standard h gt pulses
642. usr local fdf startup 01 999165 00 A0800 VNMR 6 1C User Programming 291 Chapter 5 Parameters and Data Data Set Dimensionality or Rank Fields These entries specify the data organization in the binary portion of the file e rank is a positive integer value 1 2 3 4 giving the number of dimensions in the data file e g int rank 2 e matrix isa set of rank integers giving the number of data points in each dimension e g for rank 2 float matrix 256 256 e spatial_rankisastring none voxel 1dfov 2dfov 3dfov for the type of data e g char spatial_rank 2dfov Data Content Fields The following entries define the data type and size e storage isastring integer float that defines the data type e g char storage float e bits is an integer 8 16 32 or 64 that defines the size of the data e g float bits 32 e type is astring real imag absval complex that defines the numerical data type e g char type absval Data Location and Orientation Fields The following entries define the user coordinate system and specify the size and position of the region from which the data was obtained Figure 6 illustrates the coordinate system Vectors that correspond to header parameters are shown in boldface a voxel in data set always displayed at upper left of screen origin span location 2 Data Slice aL Origi ar user onda te D stem e mid plane of
643. ut board and only on these systems by default r lpower statements are preceded internally by a 0 2 us delay see the apovrride statement for more details power Sets the power level by assuming values of 0 minimum power to 63 maximum power on channels with a 63 dB attenuator or 16 minimum power to 63 maximum power on channels with a 79 dB attenuator device is OBSch observe transmitter or DECch first decoupler For the UNITYINOVA and UNITYplus only device can also be DEC2ch second decoupler or DEC3ch third decoupler On systems with linear amplifiers be careful when using values of rlpower greater than 49 about 2 watts Performing continuous decoupling or long pulses at power levels greater than this can result in damage to the probe Use config to set a safety maximum for the tpwr dpwr dpwr2 and dpwr3 parameters 1 pulsesequence double satpwr satpwr getval Satpwr rlpower satpwr OBSch 2 rlpower 63 0 OBSch decpower Change first decoupler power linear amplifier systems dec2power Change second decoupler power linear amplifier systems dec3power Change third decoupler power linear amplifier systems 01 999165 00 A0800 VNMR 6 1C User Programming 239 Chapter 3 Pulse Sequence Statement Reference rlpwrf Applicability Syntax Description Arguments Examples Related rlpwrm Applicability Syntax Description Arguments Examples
644. uttons of type addExp saveExp addSaveAndExit autoSampleNoExit autoSample and priortySample can have a rtoutput attribute The value of the 01 999165 00 A0800 VNMR 6 1C User Programming 319 Chapter 6 Customizing Graphics Windows 320 rtoutput attribute is sent to VNMR for every sample added to the enter queue by the button The rt output attribute has access to all of the attributes of all the variables listed in the outfields variable In addition the value of each of the outfield variables is available as the val attribute For example loc val contains the value of Loc of the submitted experiment Similarly user val Sexp val solvent val etc will be set to the values selected by the user A variable filename is the name of the file where the output from the enter program will be written A second real time output attribute can be specified by the rtoutput2 attribute which has access to all the same variables as the rt out put attribute The distinction is that the action specified for rt output occurs for each sample submitted A single press of the addExp button can cause many experiments to be submitted if for example multiple experiments and or multiple locations were specified The rt out put will occur once for each submitted experiment The rtoutput2 action happens after all the rtoutput actions and only once for the entire group of samples submitted by a single button press An example is as follows
645. variable is an array the mathematical operators try to do simple matrix arithmetic If two matrices of the same size are equated added subtracted multiplied divided or one matrix is taken as a modulus each element of the first matrix is operated on with the corresponding element of the second If two matrices of the same size are compared with an and operator the resulting Boolean is the AND of each individual element If two matrices of the same size are ORed together the resulting Boolean is the OR of each individual element If the two matrices have unequal sizes an error results An arrayed variable cannot be operated on added multiplied etc by a single valued constant or variable For example if pw is an array of five values pw 2 pw does not double the value of each element of the array Separators and Comments Blanks tabs new lines and comments serve to separate tokens and are otherwise ignored Characters between double quote marks are comments except when the double 01 999165 00 A0800 VNMR 6 1C User Programming 31 Chapter 1 MAGICAL II Programming 32 quotes are in a literal string such as The word and is a reserved word Comments can appear anywhere at the beginning middle or end of a line but may not span multiple lines At the end of a comment place a second double quote otherwise the comment is automatically terminated when the end of a line occurs Variable Types As wit
646. ver along the way Tcl gets a look at the string and may well do some evaluation and substitution As an example in the simple case where Vnmr Cmd is something like tof SVALUE Tcl substitutes the contents of VALUE a Tcl variable in the string for VALUE Thus the final string is something like tof 493 5 assuming that the value entered was 493 5 More complex mixtures of MAGICAL and Tcl can be used For example if vnmrSize pp then pp SVALUE vnmrUnits pp endif The effect of this command is discussed later An issue that arises is where to use a local MAGICAL variable such as a Unless something special is done Tcl intercepts a and looks to substitute it by the contents of a Tcl variable a This will probably fail The solution is to escape the by using the syntax a instead of Sa The is then passed to MAGICAL What TCL Sees For Tcl Cmd the string is eventually evaluated and the results displayed So we can think of this as the value being displayed as being dgTemp1 ate once it is evaluated by Tcl The value displayed normally comes from VNMR Consider the situation where you might enter a negative value for spectral width You can type a negative value and it shows until you either press Return or move the mouse focus At this point the negative number is sent to VNMR MAGICAL catches this and will 01 999165 00 A0800 VNMR 6 1C User Programming 339 Chapter 6 Customizing Graphics Windows correct the err
647. versing of data within a spectrum and the reformatting of arbitrarily ordered 2D spectrum by using an AP table These commands do not change the original FID data and they may provide some speed improvement over the similar commands that operate on FID data For 2D data an ft 1d command should be applied to the data followed by the desired reformatting and then an t 2d command to complete the processing Listing 13 Example of Command Reversing Data Order Wk KK KKK KK KKK KKK KKK KK KKK KKK KKK KKK KKK KK KKK KKK KKK KKK KKK KKK KKK KKK KKK epirf lt blkno gt macro to reverse every other FID block amp trace indicies start at 1 for rfblk rftrace rfdata WK KKK KKK KKK KKK KKK KKK KKK KKK KKK KK KKK KKK KKK KK KKK KKK KKK KKK KKK KKK KKK mfopen i 2 while i lt nv do rftrace 1 i Si i 2 endwhile mfclose 5 4 Creating and Modifying Parameters 298 VNMR parameters and their attributes can be created and modified with the commands covered in this section The parameter trees used by these commands are UNIX files containing the attributes of a parameter as formatted text Parameter Types and Trees The types of parameters that can be created are real string delay frequency flag pulse and integer default is real In brief the meaning of these types are as follows for more detail refer to the description of the create command in the VVMR Command and Parameter Reference
648. vi dg to use the vi text editor or enter paramedit dg to use the text editor set by the UNIX environmental variable vnmreditor Users can also create a new template parameter e g newdg and then display it with the command dg newdg Display Template A display template can have a single string or multiple strings The first number on the second line of a stored parameter indicates the number of string templates If the number is 1 the display template is a single string otherwise a value greater than 1 indicates the template is multiple strings Figure 7 shows an example of a single string display template actually the parameter dg and the resulting display dg 22 1023004161 64 1 L ACQUISITION sfrq 3 tn at 3 np 0 sw 1 fb 0 bs 0 ss 0 pwil pl 1 d1 3 d2 3 tof ri nt 0 ct 0 2 SAMPLE date solvent file 2 DECOUPLING dn dof 1 dm dmm dmf dhp 0 d lp 0 homoz 2 nid 2D ACQUISITION swi 1 ni 0 3 PROCESSING cf nf 0 1b6 2 sb 3 sbs sb d 3 ef 3 gfs ef 3 awc 3 lsfid 0 phfid 1 wtfile proc fn 0 math werr wexp wbs wn t 4 nid 2D PROCESSING 1b1 2 sb1 3 sbsi sb1 3 efl 3 gfsil gf1 3 awcl 3 wtfilel p roci fn1 0 4 FLAGS il in dp hs 4 SPECIAL temp 1 0 ACQUISITION SAMPLE PROCESSING FLAGS sfrq 399 952 date March 6 lb not used il n tn H1 1993 sb not used in n at 2 305 solvent cdcl3 gf not used dp y np 29952 file exp awc not used hs nn sw 6497 7 DECOUPLING lsfid not used SPECIAL fb 3600 dn H1 phfid not used temp not used bs not us
649. w surprises such as at the acquisition time the pulse sequence does not know this The statements getval and get str are provided for this category Looking Up Parameter Values The statement internalname getval parametername allows the pulse sequence to look up the value of any numeric parameter that it otherwise does not know parametername and introduce it into the pulse sequence in the variable internalname internalname can be any legitimate C variable name that has been defined as type double at the beginning of the pulse sequence even if it is created as type integer If parametername is not found in the current experiment parameter list internalname is set to zero and PSG produces a warning message For example double j j getval j The getstr parametername internalname statement is used to look up the value of the string parameter paramet ername in the current experiment parameter list and introduce it into the pulse sequence in the variable internalname internalname can be any legitimate C variable name that has been defined as array of type char with dimension MAXSTR at the beginning of the pulse sequence If the string parameter parametername is not found in the current experiment parameter list internalname is set to the null string and PSG produces a warning message For example char coil MAXSTR getstr sysgcoil coil Using Parameters in a Pulse Sequence As an example of using parameters in a
650. window see Figure 15 is used to define the interaction elements At the top of this window the Panel File entry identifies the configuration file associated with the current dg pane Below that is the Panel Title and the Geometry of the DG window This 01 999165 00 A0800 VNMR 6 1C User Programming 329 Chapter 6 Customizing Graphics Windows z a fear 7 9 2 gt BREE JE 10 9 j 11 9 2 6 12 7 2 8 12 9 T A 6 3 15 9 An 10 Display Groups Panel File Panel Title cquisitior Geometry of DG window 925x350 0 0 Rows 16 Colums 10 Current element Type of element Row extent Colum extent Justify Label of element Choices Value of choices Units Color of label Width of element Scale Tcl pars Yumr Variables W s2pul Specific Save Display Figure 15 Interaction Elements Window dg Program 330 VNMR 6 1C User Programming 01 999165 00 A0800 6 3 Customizing the Interactive dg Window information comes from the dg conf file At the bottom of the window are several buttons The Refresh Display button causes any changes you may make to be displayed in the Dg pane However those changes are only temporary and will go away when the configuration window goes away either by pressing the Exit button or by selecting another tab from the Dg pane To save changes the only way is to press the Save Display button in the lower right hand conner of the window To the left of this button is a selection to s
651. wing syntax G_Offset OFFSET_DEVICE OFFSET_FREQ SLIDER_LABE 1 IDER_SCALE IDER_MAX IDER_MIN S S S S 0 122 VNMR 6 1C User Programming TODEV NULL 0 1000 1000 IDER_UNITS 0 01 999165 00 A0800 2 7 Using Interactive Parameter Adjustment The following table describes the attributes used with G_Offset Attribute Type Default OFFSET _DEVICE int none OFFSET_FREQ double SLIDER_LABEL char NULL SLIDER_SCALE int 0 SLIDER_MAX int i SLIDER_MIN int 7 SLIDER_UNITS double 1 0 Description Device or rf channel to receive frequency offset This is required Thus G_Offset 0 not allowed TODEV for transmitter channel or DODEV for first decoupler channel On UNITYplus DO2DEV for 2nd decoupler channel or DO3DEV for 3rd decoupler channel Offset frequency for selected channel Default is offset frequency parameter tof dof dof2 dof3 of associated channel If no slider label selected offset cannot be changed in acqi Otherwise becomes the label 1 6 characters in acqi Number of decimal places displayed in acqi Default is 0 because default range is 2000 Hz so a resolution finer than 1 Hz is not necessary Maximum value on the slider Default is 1000 Hz more than the offset frequency Minimum value on the slider Default is 1000 Hz less th
652. with respect to phase setting it must be set The remaining decoupler transmitter pulse related statements are variations of decpulse and decrgpulse 01 999165 00 A0800 VNMR 6 1C User Programming 83 Chapter 2 Pulse Sequence Programming 84 e To pulse the decoupler the same as decpulse or decrgpulse but generate interactive parameter adjustment IPA information when gf or go acqi is entered use idecpulse width phase string or idecrgpulse width phase RG1 RG2 string respectively where string is used as a label in acqi If go is entered instead the IPA information is not generated For details on IPA see Using Interactive Parameter Adjustment page 120 IPA is not available on MERCURY VX MERCURY and GEMINI 2000 systems e To pulse the second decoupler use dec2rgpulse width phase RG1 RG2 To pulse the third decoupler use dec3rgpulse width phase RG1 RG2 To pulse YN TYTNOVA systems with a deuterium decoupler installed as the fifth channel use dec4rgpulse width phase RG1 RG2 The width phase RG1 and RG2 arguments have the same meaning as used with decrgpulse and rgpulse The homo parameter has no effect on the gating on the second decoupler board On UNITYTNOVA and UNITY plus systems only homo2 controls the homodecoupler gating of the second decoupler homo3 does the same on the third decoupler and homo4 does the same on the fourth decoupler when it is used as a deuterium channel on the MERCURY VX ME
653. words or lines options is one or more keywords file seek skip read readline count and delimiter and other arguments Determine number of lines in a file nrecords file S number_lines Returns the number of records or lines in the given file Set up parameters for various pulse sequences psgset file paraml param2 paramN Sets up parameters for various pulse sequences using information in a file from the user or system parlib Display a confirmer window UNIX vnmr_confirmer message lt label value gt lt x posx gt lt y posy gt lt fn name gt Displays a confirmer window consisting of a message a single line multicharacter string and one or more buttons The default window location and font can be changed by the arguments posx posy and name Each button has a unique label a short string and value a number or string that are set by arguments label and value When the user clicks on one of the buttons vnmr_confirmer returns a value Because it is a UNIX command vnmr_confirmer cannot be called directly from VNMR it must be accessed using the VNMR shell command e g shell vnmr_confirmer This is a test Label 1 1 Label 2 2 Label 3 3 Sret displays the message This is a test and makes three buttons available returning 1 2 or 3 respectively Write output to various devices write graphics plotter lt color pen gt lt reverse gt x y lt
654. xecutes the command The text lines usually displayed as a result of the UNIX command given in the argument can be returned to filel file2 etc Return ppm and peak width of solvent resonances solppm chemical_shift peak_width Returns information about the chemical shift in ppm and peak spread of solvent resonances in various solvents for either H or C depending on the observe nucleus tn and the solvent parameter solvent This macro is used internally by other macros only 01 999165 00 A0800 substr 1 4 Using Dialog Boxes from a Macro Select a substring from a string Syntax substr string word_number substring substr string index length substring Description Picks a substring out of a string If two arguments are given substring textis returns the word_number word in string If three arguments it returns a substring from st ring where index is the number of the character at which to begin and length is the length of the substring Return the current text display status Syntax textis command Syes_no textis Sdisplay_command Description Determines what command currently controls the text window If no argument unit is supplied the name of the currently controlling command is returned Define conversion units Syntax unit lt suffix label m lt tree gt lt mult div gt b lt tree gt lt add sub gt gt Description Defines a linear relationship that can be used to enter para
655. xperiment data contains the once transformed spectra This is equivalent to the interferograms if the data is properly reorganized see fj and f2 traces below If a display is done now phasefile contains phased or absolute value half transformed spectra or interferograms e After the second FT in a 2D experiment data contains the fully transformed spectra and after a display phasefile contains the equivalent phased or absolute value spectra Storing Multiple Traces Arrayed experiments are handled in VNMR by storing the multiple traces of arrayed experiments in one file To allow this the file is divided into several blocks each containing one trace Therefore in an arrayed experiment the files fid data and phasefile typically contain the same number of blocks The number of traces in an arrayed experiment is identical to the parameter arraydim The only complication when working with such data files in arrayed experiments might be that there are holes in such files in the UNIX version of VNMR only The holes occur if not all FIDs are transformed or displayed They do not present a problem as long as a user program just uses a seek operation to position the file pointer at the right point in the file and does not try to read traces that have never been calculated One can look at 2D experiments as a special case of an arrayed experiment however the situation is complicated by the fact that the data often has to be
656. y vscan rtvar codeint rtval AP math variable Provides a dynamic scan capability for compressed compressed image sequences It uses an AP real time variable as a counter This real time variable must be supplied by the user but need not be initialized since the init_vscan statement provides the initialization vscan uses the standard nt parameter to determine the number of scans it performs Since it is a real time variable it is limited to 32K scans When vscan is used system supplied scan functionality is disabled similar to the use of the acquire statement vscan has no return value rtvar is an AP math variable v1 to v14 Its range is 1 to 32767 pulsesequence char gphase gread gslice int amplitude igpe stat double gpe initval nv v10 272 VNMR 6 1C User Programming 01 999165 00 A0800 Related vsetuserap Applicability Syntax Description Arguments Examples Related vsli Applicability Syntax Description Chapter 3 Pulse Sequence Statement Reference initval nf v9 loop v10 v6 init_vscan vll np nf loop v9 v5 acquire np 1 sw endloop v5 vscan v11 endloop v6 acquire Explicitly acquire data init_vscan Initialize real time variable for vscan statement Set user AP register using real time variable UNITYTNOVA systems vsetuserap vi register codeint vi variable output to AP bus register int register AP b
657. y of doubles double upss 256 declare array upss int uns uns getarray upss upss get values from upss poffset_list upss gss uns vl2 create_delay_list Create table of delays create_freq_list Create table of frequencies er ate_offset_list Create table of offsets poffset_list Set frequency from position list position_offset_list Set frequency from position list VNMR 6 1C User Programming 01 999165 00 A0800 getelem Applicability Syntax Description Arguments Examples Related Chapter 3 Pulse Sequence Statement Reference Retrieve an element from an AP table All systems except the GEMINI 2000 getelem table AP_index AP_dest codeint table table variable codeint AP_index variable for index to element codeint AP_dest variable for destination Gets an element from an AP table The element is identified by an index table specifies the name of the table t 1 to t 60 AP_index is an AP variable v1 to v14 oph ct bsctr or ssctr that contains the index of the desired table element Note that the first element of an AP table has an index of 0 For tables for which the autoincrement feature is set the AP_index argument is ignored and can be set to any AP variable name each element in such a table is by definition always accessed sequentially AP_dest isan AP variable v1 to v14 and oph into which the retrieved table element is placed getelem t25 ct vl loa
658. ype C or D decphase Set quadrature phase of first decoupler stepsize Set small angle phase step size rf type C or D xmtrphase Set small angle phase of obs transmitter rf type C Set small angle phase of 2nd decoupler rf type C or D Systems using a second decoupler with rf type C or D dcplr2phase multiplier codeint multiplier real time phase step multiplier Sets second decoupler phase in step size units set by the st epsize statement The small angle phaseshift is a product of multiplier and the step size If stepsize has not been used the default step size is 90 If the product of the step size set by the stepsize statement and multiplier is greater than 90 the sub 90 part is set by dcp1lr2phase Only on systems with an Output board are carryovers that are multiples of 90 are automatically saved and added in at the time of the next 90 phase selection such as at the time of the next pulse or dec2pulse On systems with a Data Acquisition Controller board a Pulse Sequence Controller board or an Acquisition Controller board this is done by dcplr2phase see the description section of the acquire statement for further information about these boards Unlike dec2phase dcplr2phase is needed any time the second decoupler phase shift is to be set to a value that is not a multiple of 90 dec2phase sets quadrature phase shift only which is rarely need 01 999165 00 A0800 VNMR 6 1C User Programming 169 Chapter 3
659. ystem without gradient waveshaping hardware e shapedincgradient x i illegal RT variable xior shapedincgradient no match is displayed if the requested shape cannot be found or if a width of zero is specified channel selects the gradient coil channel desired and should evaluate to the characters x y or z Be careful not to confuse the characters x y or z with the strings x y or z pattern is the name of a text file without a GRD extension to describe the shape of the pulse The text file with a GRD extension should be located in Svnmrsystem shapelib or in the users directory Svnmruser shapelib width is the requested length of the pulse in seconds The width of the pulse is affected by two factors 1 the minimum time of every element in the shape file must be at least 10 us and 2 the time for every element must be a multiple 248 VNMR 6 1C User Programming 01 999165 00 A0800 Related Chapter 3 Pulse Sequence Statement Reference of 50 ns If the width of the pulse is less than 10 us times the number of steps in the shape a warning message is generated The shapedincgradient software will round each element to a multiple of 50 ns If the requested width differs from the actual width by more than 2 a warning message is displayed a0 al a2 a3 x1 x2 x3 are values used in the calculation of level loops is a value from 1 to 255 that allows the user to loop the selected waveform No
660. ystrvar 2 Example Col 2 Default Display Templates The settcldefault lt lt default gt lt sequence gt gt macro selects the display templates to use as the default for a pulse sequence 01 999165 00 A0800 VNMR 6 1C User Programming 305 Chapter 5 Parameters and Data 306 e Without any arguments settcldefault prompts for the name of a set of display templates to use for the default displays for the current pulse sequence The current pulse sequence is defined by the parameter seqfil e Ifa single argument is given it is used as the name of the display templates for the default displays of the current pulse sequence e g settcldefault cosy uses the cosy display templates as the default displays for experiments using the pulse sequence defined by seqfil e Ifa second argument is given it is used in the place of seqfil to define which pulse sequence will use the default displays of the first argument e g settcldefault default2d HMOC8 uses the default 2d display templates for HMQC8 experiments In general 1D experiments do not need to define a default set of templates because a set already exists A good default set for GLIDE style 2D experiments is default 2d These experiments generally have capital letters in their names e g HSQC NOESY A good default set for older style 2D experiments is defaultold2d These experiments generally do not have capital letters in their names e g mqcosy tocsy C
661. zing Graphics Windows files is the selection of the button at the bottom of the window and the setting of the exList and locList parameters Adding a New Field If you want to add a new field to the enter program editing the enter conf file is required Suppose you want to have the users input a notebook number If you have a list of possible notebook numbers you could use a xcheck or xradio style of window pane Alternatively you could have the user type in a notebook number using the textentry style Adding the a lines defines the window pane using the textentry style set notebook notebook set notebook ene Note book Number set notebook style textentry set notebook col 40 set notebook required 1 set notebook output NOTEBOOK set infields loc user solvent exp notebook textfield i set notebook file set outfields loc user exp solvent notebook textfield userdir data stat separator Adding notebook to infields causes the notebook pane to appear in the enter program Adding notebook to outfields causes its value to be written to the file when an entry is added Note that in the example the notebook entry is specified as required The specifications in the enter conf file can be multiply defined The last definition in a top to bottom model is the definition that is used Therefore adding the above lines to the button of the default enter conf file has the effect of adding the n

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