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Acquisition commands and parameters - Pascal-Man

1. Prosol Parameter Names Description of the Standard Hard Prosol Parameters Pulse Length Power Level Mixing Time 90 degree tranmitter decoupler P90 PL90 a cpd PCPD PLCPD bilev second cpd PLCPD2 tocsy spin lock PTOC PLTOC TTOC roesy spin lock PROE PLROE TROE cw irradiation PLCW LaS NOE diff irradiation PLNOE aes Homo decoupling zs PLHD T Band homo decoupling aa PLHC 5 Table 1 6 Prosol Parameters for the Standard Hard Pulses 1 3 6 2 The edprosol Command Using the edprosol command you can define one prosol parameter set govern ing the 90 degree pulse length power level for the transmitter power level for the presaturation etc for any particular nucleus and link all this information to any existing logical channel F F2 Fx This information may then be used accord ing to the relations file described later to set individual pulse lengths power lev els in the acquisition data set The prosol parameter set can also be saved either for all solvents or for individual solvents When starting edprosol a window pops up displaying the standard hard pulse length and power levels of two prosol parameter sets for nucleus NUC1 read from the current dataset On the left side are the prosol parameters for NUC1 on the logical channel F1 routed to the amplifier Ax On the right side are the prosol parameters for NUC1 on channel F2 routed to the amplifier Ay
2. A 236 Commands to start data acquisition s s 0 0 cee eee eee eee A 237 Working with acquisition memory buffers 0 000000 A 245 Writing memory buffers to disk 01 0 0 cece cee eee eee A 247 A shortcut for acquisition in higher dimensions using the mc command A 249 The mc command in 3D 0 2 ee eens A 253 Enhancements for the mc command 0 00 e sees eee eee A 255 Overview over the mc command sssssusrnunrrurrn nenene A 256 Multiple E EVES r a a e A a E A 259 Real time outputs 2 0 0 cece A 259 Gradients iio Ose a Ea eek Ea EA Boo astels Anao A 261 Miscellaneous commands 0 eee eect eee ee eee A 267 Chapter 1 The Acquire Menu 1 1 General XWIN NMR provides the following data acquisition commands 1 zg and go Used to execute a NMR experiment based on acquisition parameters set up with the command eda The commands gs helps with the interactive adjustment of the acquisition parameters by real time displaying the fid or spectrum zg and go may be invoked in AU programs to control several experi ments 2 iconnmr You should use ICON NMR for routine spectroscopy based on stand ard experiments and for automation using a sample changer ICON NMR is described in its own manual The following two commands serve the same pur pose but are historically older They are just maintained for compatibility rea sons a run Used to execute a serie
3. 1 ph CETEL Figure 1 4 edlock parameter dialog box for a BSMS unit In the following lines for a desired solvent you may enter the BSMS lock parame ters LPower LGain LTime LFilt and LPhase valid for the current probehead These are the parameters stored in the param file The parameters are loaded into the hardware by the commands lock lopo and lopoi XWIN NMR also provides the 1 3 The configuration suite config P 25 SAVE Store current setting in their files and quit BSMS FIELD Read current value from BSMS and update top line Select new nucleus Equivalent to clicking on a NU nucleus button in the dialog window NEW SOLVENT Insert new entry at table end Initialize it with the last selected solvent click on a solvent to select it Click on this button to activate delete mode Then DELETE click on a solvent to remove an entire solvent entry or click on a nucleus to remove only this nucleus for the corresponding solvent ABORT Discard any changes and quit Discard the current settings and load standard values LOADSTAN from the file XWINNMRHOME exp stan nmrlist 2Hlock Increment the LPower values of all solvents by the specified amount POWER Print the lock parameters on the device given by the LIST parameter CURPRIN Set it up with edo e g CURPRIN hplj4p COPY_VALUE automatically set the selected value for all solvents HELP P
4. 1 Depending on the current color setup 2 7 BSMS panel bsmsdisp P 127 2 7 3 6 The Left Right Display Field 2 7 3 7 2 7 3 8 The left display field contains as a reminder the initial value of the current func tion e g the value at the time the current function was selected The right display field contains the actual value as currently set and confirmed by the BSMS device Once a value function has been selected their values are going to be displayed in the left display field and right display field Both value fields show the current function value set on the BSMS device When changing now that value as described below the new current value is displayed in the right value field and the left field remains unchanged The actual value set on the BSMS device is always displayed in the right value field emphasized by the label ACTUAL above The left value field only changes when switching to another function so you can find there the old function value indicated by the label PREVIOUS above Changing a functions value is allowed only within the functions range which is displayed above the slider The function minimum and function maximum Figure 2 11 show the functions smallest resp largest value allowed to be set Methods to Change the Current Value of a Function There are different methods provided to change the current function value 7 Using
5. The Acquire Menu P 58 probe head and solvent dependent parameters see command prosol are then inserted according to the setting of SOLVENT and the current probe head Finally any parameter changes the user possibly requested are applied PROBHD probehead A status parameter stored at the end of an experiment according to the current probehead set with edhead PROSOL update probehead solvent dependent parameters This parameter may take on the values true or false If set to true the following will happen in eda The pulse lengths and power levels of the current data set depending on the solvent and probehead will be overwritten by the values defined with prosol or solvloop The pulses or powers e g P1 PLO concerned may be taken from the AU program pulsesort which describes the prosol parameters and their associated eda parameters EXP experiment performed Reserved to be updated by quicknmr and run with the experiment peformed RO spinner rotation frequency in Hz The AU command ro will set sample rotation to the frequency RO The command will wait for 15 seconds and check if the desired rate could be achieved If this is not the case an error message is printed If you enter the command ro on the key board you may disable or enable sample rotation and specify the desired rate TE temperature in Kelvin The command teset sets the Eurotherm temperature unit according to TE teset may be entered on the keybo
6. The right display field can accept values entered from the computer keyboard Click with the left mouse button in the right display field A frame is drawn around that field and a cursor is placed after the value Clear the current value enter the new value and press lt return gt Enter key The new value is set now Values out of the function range will not be accepted and the current value is redis played in the right value field The Windows Menu P 130 2 7 3 11 2 7 3 12 2 7 4 2 7 4 1 Function Sensitivity Two of the three methods to change the current function value use an offset for incrementation decrementation the button and the slider method This off set is displayed next to the label Step When clicked on the 2 2 button with the left mouse button the current step size is approximately halved when clicked with the middle mouse button approx imately doubled Change that step size and the current value either with the slider or the button Incrementation resp decrementation will follow the new step size now This size is useful for constant adjustment of function values and can be seen as some kind of function sensitivity a large step size will change the value faster when using for example the button held down for a certain time while a lower step size will be less sensitive Each value function has assigned an own step size S
7. 4 22 4 sgrad sin save index stack with depth 1 rgrad sin restore index As mentioned in the chapter Shaped gradients the length of an internal gradient function or shape should be specified at the beginning of the pulse program e g Igrad sin 100 sine function with 100 values Internal Gradient Functions As described in the chapter Shaped gradients a gradient function is either a gradi ent shape read from a gradient file or an internal function calculated during pulse program compilation The following internal functions are supplied plusminus which always contains the 2 values 1 and 1 rld r2d and r3d which are linear ramps from 1 to 1 where the final value is never reached step which is a linear ramp from 0 to 1 and the final value will always be reached sin which is a sine function from 0 to 7 excluding 7 The angle increment depends on the length of the function see above cos Which is a cosine function from 0 to 7 excluding 7 sinp which is a sine function from 0 to 7 including 7 gauss lt truncval gt which is a gaussian function with truncation level e g gauss2 5 for 2 5 truncation level rnd which is a random function Multiplication of rectangular or shaped gradients Example 1 300m gron2 0 5 plusminus 4 22 Gradients P 265 4 22 5 pl gpl sin 100 cnstO igrad plusminus igrad sin lo to 1 times 100 Gradients specified with gron0 gron
8. include lt limits h gt include lt ShapelO ShapeIOC h gt define MAX_ANZ20 char result PATH MAX char filename PATH_MAX char singleResult int i numbOfParams double retValue MAX_ ANZ double bandWidthFactor read gaussian shape and call analyze command bandw2 void sprintf filename slists wave Gauss getstan 0 0 numbOfParams analyzeShapeC filename bandw2 90 amp result 0 if numbOfParams lt MAX_ANZ i 0 singleResult strtok result scan resultstring for results retValue i atof singleResult while singleResult strtok 0 retValue i atof singleResult if i gt numbOfParams break bandWidthFactor ret Value 0 do further calculations with bandWidthFactor 3 7 APPENDIX P 179 In this example the call analyzeShapeC reads a gaussian shape stored in XWINNMRHOME Yexp stan nmr lists wave and applies the command bandw2 with the parameter total rotation 90 degree and stores the result of the calculation into the char result The return value of analyzeShapeC is the number of results cal culated In the case of bandw2 only one result the bandWidthFactor Aw AT is returned Now the bandWidthFactor can be used for further calculations in the AU program Most of the analyze commads return more than one result In this case the results are separated by semicolons in the returned char result The while loop in the exam
9. locallist locallist this executes twice the same list entry so executing twice a 10 micsec pulse locallist the increment above becomes valid only in this line resulting in a 20 micsec pulse locallist 2 locallist 3 this will execute locallist 3 twice this is not what you expected Note Names for user defined items may consist of up to 19 characters where only the 7 first are significant i e Pulselist and Pulselist2 are legal names but would address the same symbol and thus must not appear in different definitions Manipulating pulse durations The operator A pulse duration can be manipulated by the operator if appended to the pulse command Examples of legal commands p1 1 5 p30d1H 3 33 p3 oneThird vp 3 10mp 0 33 would be illegal since 10mp is a fixed pulse The operator must be placed behind the pulse command not before oneThird is the name of a macro which was defined at the beginning of the pulse program by means of a define statement e g define oneThird 0 33 Manipulating pulse durations Changing p0 p31 by a constant value Each pulse command p0 p31 has been assigned an acquisition parameter INPO INP31 containing a duration in microseconds The pulse program commands Writing Pulse Programs P 192 4 5 1 8 ipu0 ipu31 add INPO INP31 to the current value of p0 p31 respectively Likewise dpu0 dpu31 subtract INPO INP31 from the current value of p0 p31 The com mands r
10. Scale Amplitude scale Scales the amplitude of a shape to a given percentage Add constant Phase addphase Adds a constant phase to the shape Time Reversal trev Time reverse a shape Add Shapes This command allows to add several shapes up to 10 The filename can be selected by means of a file selection box showing the content of the relevant directory see File menu for details Each shape can be scaled with the scaling factor being between 0 and 100 The final amplitude will be rescaled according to the number of shapes added 3 5 6 The Options Menu The entries in the Options menu may be used to customize Shape Tool commands Using the Set Path to Shape Directory command the default directory can be changed Then all file related commands as Open and Save work on the specified directory The Define Parameter Table Figure 3 13 command relates shape tool parame ters to XWIN NMR acquisition parameters For instance the acquisiton parame ter SP1 may be related to the power level of the shaped pulse etc 3 6 Examples P 175 Parameter Table Length of hard pulse Power Level of hard pulse Length of shaped pulse Power Level of shaped pulse Name of shaped pulse Name of frequency list Figure 3 13 Define Parameter Table This table is evaluated both to read parameters from the current dataset of XWIN NMR as well as to store parameters with the Update Parameters command 3 6 Examples
11. The syntax of cpd sequences is demonstrated by examples Table 4 8 shows the realization of Broadband and Garp decoupling by means of cpd sequences Each sequence is an infinite loop indicated by the last command jump to 1 A pulse width may be specified in the form of a fixed pulse e g 850up as indi cated from pulse programs or as a command p0 p31 also indicated from pulse programs The Garp sequence shows the usage of the lo loop command The Garp sequence as well as the sequences in Table 4 9 make use of the com mand pcpd to generate pulses This facilitates the executiion of the same sequence for different nuclei on different channels For example if executed on channel f2 f3 the pulse duration of pcpd is given by the parameter PCPD2 PCPD3 This allows you to specify the 90 degree pulse width for two different nuclei in PCPD2 and PCPD3 and decouple both nuclei within the same pulse program using the Writing Pulse Programs P 224 po p31 10up Smp 2 5sp pepd Generate pulses with durations PO P31 Generate pulses in micro milli and seconds Generate a pulse with duration according to PCPD1 PCPD8 depending on the channel where the cpd sequence is executed use eda to set PCPD do d31 Generate delays with durations DO D31 10u 5m 2 5s Generate delays in micro milli and seconds 3 5 Multiplier Can be appended to p0 p31 or d0 d31 135 5
12. Then the command compTime would execute a delay whose name is defined by the user and whose duration is determined by an arithmetic expression The define line must be placed some where at the beginning of the pulse program before the beginning of the actual pulse sequence Note The defining expression of a user defined delay must occur before the actual start of the pulse sequence It is evaluated at compile time of the pulse program not at run time Legal names for user defined delays consist of alphanumeric char acters where the first character must be an alphabetic character The maximum length of the name is 11 characters Of course it must not be identical to any of the reserved words like adc go pulse etc Variable list delays The command 4 6 Delay generation commands P 213 vd executes a delay whose duration is given by the current value of a delay list A delay list is a text file containing one delay per line Delay lists are set up with the command edlist described in the chapter The File Menu The command vd uses the list file given by the acquisition parameter VDLIST When the pulse program is started the first duration in the list is valid The pulse program command ivd must be used to advance the list pointer to the next duration If the end of the list is encountered the pointer is reset to the beginning The command ivd must be spec ified behind a delay for internal reasons Examples dl
13. Trouble shooting part 2 Some of the units controlled via serial port e g ACB board HPPR 3 channel SE451 are addressed during cf to read their internal configuration During this procedure the following error message appears Error during open of lt unit gt no such device or address There are several reasons leading to this error e The lt unit gt is connected to a serial port other than the one entered by the opera tor e The lt unit gt is switched off e The lt unit gt is connected with a wrong or broken cable e The lt unit gt is defective e The SCSI type cables from the CCU to the RS232 panel are interchanged e One or both of the SCSI type cables from CCU to the RS232 panel is broken e The RS232 driver chip on the CCU is defective This can happen if a unit has been connected to this device with a wrong cable Temperature unit configuration cfte This command may be used to configure the temperature unit if this has not yet been done during cf cfte asks for the RS232 device to which the temperature unit 1 3 The configuration suite config P 13 is connected Device for Temperature Unit tty06 The RS232 device configuration is stored in the file XWINNMRHOME conjf instr lt instrument name gt rs232_device temp 1 3 3 Sample changer configuration cfbacs This command may be used to configure the sample changer if this has not yet been done during cf First cfbacs asks for the RS232 devi
14. turned off For example in Figure 2 12 the SPIN ON OFF function is turned on highlighted and the LIFT ON OFF and SPIN CALIB functions turned off To change a toggle function just click on the corresponding button and it s state will toggle clicking on a button turned on will turn it off and vice versa unless the BSMS currently does not allow a change of that function in which case a short beep is emitted Value Functions Value functions have assigned a value which is displayed in the two display fields in the lower part of the control panel see left display field and right display field in Figure 2 11 This means only one value function can be displayed and controlled in a panel at a time To change a functions value select that function by clicking on the correspond ing function button The function values are going to be displayed in the two value fields In Figure 2 12 the value function SPIN RATE has been selected as the current function indicated above the two display fields the function button SPIN RATE is highlighted The current function values can be changed with the control elements in the lower area described in the following paragraphs Each control panel can have a current function once there is clicked on a value function button The current function name appears above the two display fields and its corresponding function button is highlighted
15. 1 3 15 3 1 3 15 4 1 3 15 5 XWINNMRHOME exp stan nmr lists cpd Install and compile AU programs modules The XWIN NMR release media include AU programs and modules for a number of special applications You may inspect the source code of AU programs after their installation using the edau command Usually the function of an AU program is described in its header AU programs and modules are written in the C language and must be compiled before they can be executed with one of the command xau xaup xaua expinstall copies the C source files from the directories XWINNMRHOME prog au src exam XWINNMRHOME prog au modsrc exam to the working directories XWINNMRHOME exp stan nmr au src XWINNMRHOME exp stan nmr au modsrc Then they are compiled and the excutable files are stored in the directories XWINNMRHOME pro g au bin XWINNMRHOME prog au modbin Recompile all user AU programs AU programs a user wrote himself using the edau command are also stored in the directory XWINNMRHOME exp stan nmr au src They are not deleted if a new XWIN NMR version is installed unless they happen to have the name of a Bruker AU program please avoid this You must however recompile your own AU pro grams in order to make them compatible with the new program version Install library gradient files On the release media gradient files for a number of applications are delivered for various types of instruments in own directories accordin
16. Contents Part2 Data acquisition Chapter 1 Phe Acquire Menu o e h ocisee 5b so sveve ser esas a she sis ele seVer8 lors ses A 1 1 1 General sinas ete code eee E a T BRR aa ee ey ee Meee E a A 1 1 2 Preparing for data acquisition 0 cee cece eee eee eens A 2 1 3 The configuration suite config o nno 00 0 cece eee eee eee A 2 1 4 Defining the acquisition data set new edc 0 0 cee eee eee A 41 1 5 Setting up acquisition parameters 00 eee eee eee A 42 1 6 Interface control commands 0 0 cee eee cee eee A 85 1 7 Starting and stopping data acquisition 0 0 cee eee eee A 97 Chapter 2 The Windows Menu cc cece cece eee cence eee eeees A 103 2 1 Interactive plot editor xwinplot 0 0 00 cee ee eee eee A 104 2 2 Routine Spectrometer operation iconnmr 0000 A 104 2 3 Lock lockdisp ero ri ha oe eae eke Regione wed eae A 104 2 4 Amplifier control acbdisp 0 0 cece eee eee ee eee A 105 2 5 Pulse program pulsdisp 0 0 0 e cee cee eee eee eee A 107 2 6 Pulse and Gradient Program Display 0 00 e eee e ee eee A 111 2 7 BSMS panel bsmsdisp 0 0 0 e eee eee eee eee eee A 121 2 8 Temperature monitor temon 2 0 cece ee eee A 134 2 9 MAS rate monitor masrmon n nnan 000 0c cc teens A 134 Chapter 3 Th Shape Tool oisceseisepssescue state Fi ds ee wi h
17. and the correct process ID The latter can be found with the UNIX ps and grep command ps grep bsmsdisp will display something like 2010 ttyq6 0 00 bsmsdisp The first number here 2010 is the process ID The tool can be killed with the command kill 2010 If that doesn t terminate the application enter kill 9 2010 and the BSMS display tool disappears Turn the Display Tool On Off The display tool can be turned off when access to the BSMS is not needed for a while Use the menu entry Turn Off from the Display pulldown menu in the main panel to switch the display tool off This menu entry changes to Turn On when the tool has been turned off and all control panels are closed as they are not needed when the display tool is off line You will see that the control panel but tons are disabled dimmed in the off line state when reopening any control panel Accessing the BSMS is not possible until the tool is turned on again with the same menu entry which has changed now to Turn On If the tool turned on is iconified it turns off automatically during the iconified state To prevent any interference of the BSMS display tool with other applications it is The Windows Menu P 132 recommended to turn the BSMS display tool off if not in use As long as a dialog with a BSMS error message is open no other application can access the BSMS 2 7 4 3 2 7 4 4 Save Pan
18. ning rate in Hertz Furthermore variable rotation may be selected In this case the rotation frequency is randomly varied by a few Hertz in order to eliminate sol vent side bands In AU programs the command ro will set the rotation speed according to the acquisition parameter RO without variation After turning on rotation the command will wait for 15 sec and check whether the selected rate was reached Otherwise an error message is sent The command ij inserts the sample into the magnet by switching off the pneumat The Acquire Menu P 90 ics ej ejects it from the magnet 1 6 9 Set preemphasis setpre 1 6 9 1 Introduction Using this standard XWIN NMR control feature it is possible to modify or reload the current settings of gradient preemphasis in any plane on the fly The setpre command is the standard adjustment tool required for the various different types of preemphasis units which Bruker currently offers Previously installed values may also be loaded and stored as required Figure 1 10 setpre adjusting of pre emphasis parameters 1 6 9 2 Features GREAT BGU II and Acustar features such as Gradients generation Preemphasis bypass BO compensation Amplifier modules and Protection switches if available 1 6 Interface control commands P 91 for the actual hardware equipment may be accessed from the setpre control win dow For the BGU II and Acustar units the Gradient coil temperature is also dis played and u
19. play of the preamplifier is set accordingly 1 wobb reads most parameters from the current data set with the exception of few parameters needed by the wobble pulse program which are read from either acqu_go4 Avance or acqu_go2 AMX ARX ASX located in XWINNMRHOME prog wobble 2 wobb uses the pulse program XWINNMRHOME prog wobble pulsprog_X which is linked to any of the pulse programs pp_amx_X pp_arx_X pp_dmx_X or pp_drx_X by cf depending on the type of instrument The Acquire Menu P 72 1 5 4 5 Trouble shooting guide a The wobble curve shows no dip There are two possible reasons b c d x wm wa eThe probe is heavily mistuned and mismatched Just turn the tune knob and check the wobble curve for changes This works best when watching the screen instead of the preamplifier display Often a tiny change some where in the curve indicates the dip The dip is outside the wobble sweep range This happens especially on broadband probes which previously were tuned for another X nucleus Increase WBSW e g 10 to 20 MHz and try again The wobble curve moves periodically although the tune and match knobs are not touched The sample is spinning either ignore the movement or switch off the spin ning After starting acquisition one of these error messages appears wobble signal too weak with RG or Error changing RG maximum RG reached The rf signal received from the preamplifier is too low to
20. ze labell d1 p1 f1 lo to labell times myCounter go label1 This example defines the variable myCounter to represent a loop counter An arithmetic expression assigns a value to it the parameter AQ divided by 10 milliseconds plus 1 The compiler truncates the quotient aq 10m to give an integer The expression may include any of the parameters shown in Table 4 3 on page 193 4 11 Conditional pulse program execution 4 11 1 Conditions evaluated at precompile time Consider the pulse program at the left part of Table 4 11 It combines two experi ments in one pulse program a simple Cosy and a Cosy with presaturation during relaxation The required pulse program statements to select or deselect presatura tion are define aFlag 4 11 Conditional pulse program execution P 231 define PRESAT define PRESAT 1 ze 1 ze 2 dll 2 d11 3 0 lu 3 0 1lu ifdef PRESAT include lt Presat incl gt d12 pl9 f1 pl phl dl cw fl do d13 do f1 pO ph2 d12 pl1 f1 go 2 ph31 endif d11 wr 0 if 0 idO zd pl phl lo to 3 times td1 do exit pO ph2 go 2 ph31 d11 wr 0 if 0 idO zd lo to 3 times td1 exit Table 4 11 Using define ifdef include ifdef aFlag ifndef aFlag endif and correspond to C language pre processor syntax The name of aFlag can be chosen by the user in our example aFlag PRESAT The identifier aFlag is con sidered to be defined in the pulse program if the statement define aFlag is present otherwise it is con
21. 0 exit Table 4 18 The same pulse program based on go adc rcyc and adc eosc Table 4 19 shows how homodecoupling during data acquisition can be realized using adc Homodecoupling requires the receiver to be turned off at regular inter vals This can be achieved with the option e appended to a pulse or delay com mand It disables the receiver for the duration of the respective pulse or delay Please note If e does not occur between the commands adc and rceyc eosc but elsewhere in the pulse program its sense is reversed i e the receiver is enabled rather than disabled The receiver phase In pulse programs based on the adc command the receiver phase must be specified behind adc e g adc ph31 This construction sends an interrupt signal to the RCU telling it to account for the receiver phase setting Interrupt handling on the RCU is a time consuming procedure which must be carried out during the recycle time of an experiment For certain applications e g some imaging experiments it may be necessary to keep the recycle time as short as possible Table 4 20 shows how receiver phase setting can be moved outside the recycle loop command recph ph31 allowing for a shorter aq or rcyc However then it is not possible to set the receiver phase differently for consecutive scans Only after NS scans the command ip31 in Table 4 20 right column will the phase which is activated by recph ph31 change 4 13 Commands to
22. Afterwards all units controlled via serial port are configured A window see Fig Figure 1 2 Configuration of RS 232 devices 1 3 The configuration suite config P 7 ure 1 2 appears which contains all installed units and allows to set the device name of each unit If an unit is not in use or has not been used before the device name shows no On none Avance spectrometers which are equipped with a triple housing preampli fier you should set the preamplifier device to no If the spectrometer is equipped with a BSMS and a sample changer then cf asks whether the sample changer or the BSMS should control the LIFT function Should the Sample Changer control the lift no If the spectrometer is equipped with a sample changer then cf aks for the delay between the change sample command sx and the next command This delay is needed to allow for the sample to settle in its position Delay between SX and next command sec 10 Typical values are 5 to 30 seconds depending on the magnet cf then connects to the sample changer to get the number of sample holders As soon as all configurator questions have been answered the nucleus table stored in the file XWINNMRHOME exp stan nmr lists nuclei all is displayed in a dialog win dow see Table 1 1 This table may now be modified according to your needs nuclei table 1H 500 13 2H 76 77 3H 533 46 4He 380 55 SAVE ADD RESTORE QUIT Table 1 1 Nuclei ta
23. Answer Return to all question until the list of allowed users is shown Remove all users with the backspace key and type Return Now you will be asked whether the experiment should be deleted n SAMPLES Click on this button and enter a number n The program will automatically set up the next n free holder entries with the same parameters The data set NAME parameters are assigned in the following way Assume the NAME parameter of the current holder is June 5 The next holders will get the names Junel5 1 June15 2 assigned If NAME of the current holder is June 5 the next holders will get the names June 5 2 June15 2 assigned You may further modify the parame ters of a particular holder by clicking on its number Change User The data set parameters for a XWIN NMR data set are NAME EXPNO PROCNO DU and USER NAME and EXPNO may be specified in the corrsponding holder entry fields and PROCNO is usually 1 USER is initilized with the current login name You may however change user by clicking on this button You will get a table of users displayed set up with eduser These are the users owning permission files Select the desired table entry enter the requested password From now on the entries of this user s permission file experiments data set names various permis sions are valid and the USER parameter for the data sets will be set to the login name of this user Holder Click in this field and enter a number The
24. Delete a shim file vish vish lt filename gt View the shim values stored in the specified file lish lish lt filename gt List the shim values stored in the specified file on the current printer CURPRIN which can be set using the command edo setsh Display a table of shim gradients In this table you can set shim values which are immediately loaded into the shim hardware 1 6 2 2 Automatic shimming XWIN NMR provides the command tune to start autoshimming Its syntax is described in Table 1 20 The autoshim procedure is controlled by the parameters tune Select tune file from a dialog box and start autoshim procedure using the parameters stored in the tune file tune lt filename gt Start autoshim procedure using the parameters stored in the specified tune file In AU programs use the syntax tune filename tune lt gradient gt Start autoshim procedure for the specified gradient only e g tune z1 Uses XWIN NMR internal parameters In AU programs use the syntax tune gradientname Table 1 20 tune command contained in a tune file which can be set up using the command edtune edtune may also be invoked with a tune file as an argument A tune file is a text file stored in the directory XWINNMRHOME exp stan nmr lists group 1 6 Interface control commands P 87 It contains two example tune files example and example_bsms suitable for BSN18 and B
25. HADC HRD16 16 bits 2 5 microsec SADC 16 bits 3 325 microsec HADC 16 bits 3 325 microsec SADC 16 bits 3 325 microsec IADC 16 bits 0 1 0 05 microsec Table 1 18 Digitizer types The receiver control unit RCU of all Avance instruments is equipped with two digital signal processors DSP which can perform digital filtering during the acquisition The digitizer will sample with a dwell time DWOV which is related to the conventional dwell time by DW DWOV DECIM The DSP will decimate the sampled points by a factor DECIM and at the same time perform digital filtering The oversampling dwell time DWOV must be in the range 2 5 5 usec for HADC HRD16 and FADC and in the range 3 3 6 6 usec for a SADC For homodecoupling the oversampling dwell time must be between 25 and 50 usec The decimation factor DECIM is chosen so that after the Fourier trans form the spectrum will have a spectral width as close as possible to the chosen SW parameter The factor DECIM is stored as an acquisition status parameter in the file acqus It is required to calculate a correct baseline correction of the fid and the first order phase correction during the Fourier transform for the standard DSP firmware the parameter DSPFIRM may be set to used defined if non standard firmware should be used In this case the firmware file in ASCII must be located in XWINNMRHOME exp stan nmr lists DSPFIRM Digital filtering enhances the digitizer resolution by
26. assigned by the relations file lt filename gt getprosol copies the contents of the relations file lt filename gt that is used to the current dataset in the file DU data USER nmtr lt dataset name gt EXPNO relations 1 3 The configuration suite config P 21 The user will therefore know which relations are used for this experiment 1 3 7 Setting up user permissions eduser Execute the command eduser to define which experiments a XWIN NMR user may execute You may skip this command if you do not intend to use the acquisition commands run or quicknmr You may also skip eduser for now and execute it at a later time but before invoking run or quicknmr First a list of installed users is displayed After selecting the desired one a permis sion file XWINNMRHOME conjf instr lt instrument name gt users lt login id gt is created for this user if not yet existing e g XWINNMRHOME conf instr dmx3 00 users guest It is a copy of the default permission file XWINNMRHOME exp stan nmr lists sam_users_exam provided by XWIN NMR The file is displayed by a text editor and you may modify it Figure 1 3 shows an example Comment lines begin with a character Data set names In the section Data set names you may predefine a list of data set names These will be the only names which may be given a data set during experiment set up with the command set The special name DATE will be converted to the cur
27. go and rga Type in a name or click on the down arrow button right of the entry field to get a list of available pulse programs Click on the desired one to store it in PULPROG The first list entry is EDIT CURRENT a command which displays the text of the The Acquire Menu P 46 current pulse program The pulse program list is generated according to the con tents of the directory XWINNMRHOME exp stan nmr Nists pp It contains the Bruker pulse programs according to the expinstall installation and the pulse programs created by yourself or your system administrator by means of the command edpul A special chapter in this manual Writing Pulse Programs describes the pulse pro gram language The command pulsdisp displays a graphical representation of the current pulse program You will find a description of pulsdisp in the chapter The Windows Menu AQ_mod acquisition mode The acquisition mode with the possible settings gf gseq qsim standard setting DQD e gf single channel detection Only one detector is used e qseq quadrature detection sequential mode Two detectors with a reference phase shifted by 90 degrees are used In the resulting fid two successive data points originate from different detectors Their acquisition time difference is given by the dwell time parameter DW e qsim quadrature detection simultaneous mode Two detectors with a refer ence phase shifted by 90 degrees are used In the result
28. while editing nuclei you may also change the default routing i e assign a different amplifier or preamplifier to a channel The edit NUCLEI button in fact invokes the command edasp You may therefore set up nuclei not only from eda but directly from the keyboard by entering this command See also the description of edasp to find out further details For AMX ARX type spectrometers the nucleus names for the channels 1 3 are designated NUCLEUS DECNUC and DECNUCB respectively rather than NUC1 NUC3 Channel 4 which is a special hardware accessory for these instru ments has no nucleus parameter assigned TL DL DBL low power levels in db for square pulse transmitters AMX ARX type instruments with 3 channel interface MCI only These are 3 parameter arrays of size 8 TL 0 7 DL 0 7 and DBL 0 7 one array for each channel The square pulse low power level may be set in a pulse program with the commands tl0 tl7 dl0 d17 dbl0 db17 For example tl3 sets the power value TL 3 in channel 1 dbl6 sets the value DBL 6 in channel 3 Low power mode for the 3 channels is activated with the pulse program commands tlo dlo dblo Correspond ingly high power mode is activated with the commands thi dhi dbhi channel 1 transmitter channel 2 decoupler channel 3 second decoupler CPDPRG1 CPDPRG 8 cpd programs Avance type instruments only These parameters must contain the names of com posite pulse decoupling cpd progr
29. 0 X BB HR 2 X QNP HR 8 X BB HP 10 X QNP HP QNP QNP selection An integer number 1 4 is required HL1 HL4 ecoupler high power levels in db FL1 FL4 F19 decoupler high power levels in db XL YL BSV 0 X BSV 0 X power level ZL1 ZL4 4th channel low power levels in db 1 5 Setting up acquisition parameters P 55 AMX ARX type instruments only The pulse program commands hl1 hl4 and fl1 fl4 may be used to enable the respective high power level of the ecoupler or 19F decoupler The default power which is set if power is not explicitely switched with hl1 hl4 is HL1 and FL1 for F19 If the spectrometer is equipped with a 4th channel the pulse program commands zll zl4 may be used to set the low power according to the parameters ZL1 ZL4 The command zlo switches the 4th channel decoupler to low power mode zhi to high power mode There is no possibility of controlling the high power PLO PL31 32 power levels in db Avance type instruments only The pulse program commands pl0 pl31 may be used to set power levels pl0 takes the power value from the PLO parameter etc The frequency channel must be specified behind the command E g the pulse pro gram command pl1 f2 sets the power level of channel f2 to the value PL1 Chan nels f1 to f8 are legal and require the corresponding hardware equipment The default power setting for channel n which is used if power is not explicitely switched with pl0 pl31 is PLn The parameters
30. 1 ze in0 in 2 2 d1 0 5 3 d1 0 5 4 pl phl do pO ph2 go 2 ph31 Writing Pulse Programs P 252 d1 0 5 wr 0 if 0 id0 ip1 zd lo to 3 times 2 d1 0 5 rp1 lo to 4 times 13 exit FnMODE States cosy in States mode 13 td1 2 1 ze 2 d1 0 5 3 d1 0 5 4 pl phl do pO ph2 go 2 ph31 d1 0 5 wr 0 if 0 zd ip1 lo to 3 times 2 d1 0 5 idO rp1 lo to 4 times 13 exit FnMODE TPPI cosy in TPPI mode 1 ze 2 dl 3 pl phl do pO ph2 go 2 ph31 d1 wr 0 if 0 idO zd ip1 idO lo to 3 times tdl exit FnMODE States TPPI cosy in States TPPI mode 1 ze 2 d1 0 5 4 17 The mc command in 3D P 253 3 d1 0 5 4 pl phl d0 pO ph2 go 2 ph31 d1 0 5 wr 0 if 0 zd ip1 lo to 3 times 2 d1 0 5 idO lo to 4 times 13 exit You will notice that the mc command will take care of the following actions for you In QSEQ States States TPPI and Echo Antiecho mode the loop is split into two parts delays and labels are calculated accordingly In QSEQ and TPPI mode the value for the delay increment is divided by 2 dur ing runtime The parameter NDO will have the same value for each value of FnMODE counting the number of delays dO within the loop s th relations will set values for spectral width and dwell time correctly In QSEQ and States mode a reset command rp1 is added in the outer loop for the phase change In QSEQ and TPPI mode the delay increment is done in the inner loop In the other cases in the outer loop
31. 3 6 1 Preparing a Shaped Pulse for Multiple Solvent Suppression using WET e In XWIN NMR prepare a frequency list containing the frequencies to be sup pressed Store this frequency list as a f1 list in the directory XWINNMRHOME exp stan nmrlists fl e Under the Shape Menu select a Sinc shape e Enter the following parameters in the parameter editor Figure 3 14 and then click the OK button The Shape Tool P 176 Dee Dea Mee Figure 3 14 Editor for Sinc Shape e Under the Manipulate Menu select Phase Modulation acc to Offset Freq Figure 3 15 Figure 3 15 Editor for offs Command 3 6 Examples P 177 e In the first radio button box choose Beginning at Phase 0 e Inthe second radio button box choose Reference O1 from current Data Set e Check the box entitled Frequencies taken from Frequency List Enter 10000 for the Length of Pulse e Enter freqlist for the Name of Frequency List e Click the Apply button to view the frequncy list entries Figure 3 16 Figure 3 16 Editor for Frequency List e Click the OK button to accept these frequencies and to observe the modulated shape e Click the OK button to exit the Phase Modulation window e Save the new shape by selecting Save As from under the File Menu and entering a name for the shape The Shape Tool P 178 3 6 1 1 Using Shape Tool commands in AU Programs include lt stdio h gt include lt stdlib h gt include lt strings h gt
32. GPZ the gradient strength multipliers for the 3 spatial dimensions and a file name containing the gradient strength values File name File name is the name of a gradient file A gradient file can be generated using the command st The file formats of gradient shape files are described in the Chapter File Formats Since Xwin nmr release 2 5 the gradient compiler accepts ASCII format The specified file must be located in the directory XWINNMRHOME exp stan nmr lists gp Note If you specify an internal gradient shape you don t need a shape file how ever you should define the length of the shape as described below GPX GPY GPZ These are multipliers with values from 0 to 100 They are applied to the gradient strength values which range from 1 0 to 1 0 in the shape file to obtain the final gradient field strength You can access the table entries not only from eda but also from the keyboard For example the command gpnam5 would display the file name corresponding to table entry 5 while gpx15 would display the strength value for the x dimension of entry 15 4 22 3 Gradient Functions You can use gradient shapes as gradient functions Then the current function value is used to calculate the gradient You can manipulate the function index via special index manipulation commands zgrad sin zero index gt use Ist function value igrad sin increment index dgrad sin decrement index Writing Pulse Programs P 264
33. Gradient Program Display P 117 2 6 2 3 Redraw program display re displays the ppg information without re reading it or recompiling the ppg This can be useful to recover after some errors for example if the complete program could not fit in the too small window Regenerate program display re reads the compiled information and re displays its contents without recompiling the ppg This can be useful to return to the original display after opening a number of loops see later Export Export a pull down submenu containing the following items Export window contents exports the contents of the window in the PostScript format The name for the export file is requested via the usual file selection dialog The produced PostScript file can be sent directly to a PostScript printer viewed with a PostScript previewer edited with the freeware ivtools package imported into XWIN PLOT under Unix only and so on The PostScript output looks almost exactly as on the screen Export unzoomed picture exports the whole unzoomed ppg drawing in the PostScript format The name for the export file is requested via the usual file selection dialog If the ppg was expanded too much the resulting drawing could be packed too tightly so that the text annotations could become hardly readable Otherwise the properties of the exported picture are similar to the preceding menu item Multipage window based exports the whole ppg drawin
34. Phase in degrees Can be appended to pulses spO sp31 Shaped pulse selectors Can be appended to pulses pl Power specifier see example in Table 4 9 pl 5 in dB pl sp13 according to shaped pulse parameters SPO 15 pl pl25 according to PLO 15 fq Frequency change fq 2357 in Hz relative to SFO1 for channel 1 SFO2 for 2 fq cnst25 from the parameters CNSTO 31 fq fq2 from the frequency list specified in FQ2LIST gt Begin of a comment until end of line lo to label times n jump to label Loop to label n times Branch to label Usually the last statement addphase setphase Special phase control commands Table 4 7 Commands available to build cpd sequences same cpd program Table 4 9 shows two cpd sequences based on shaped pulses Shapes are selected in the same way as described earlier in this chapter using the sp0 sp15 pulse selector options The examples demonstrate the order in which duration multiplier shape selector and phase must be specified The sequences in Table 4 8 do not contain a power setting command Therefore the current power setting of the main pulse program for the respective channel is valid In the right column of Table 4 9 the command pl sp15 switches the power of the channel where the sequence is executed to SP15 which is the power given 4 9 Composite pulse decoupling cpd P 225 1 90up 0 1 pepd 0 339 0 160up 180 pcepd 0 613 1
35. SFO1 8 nuclei frequencies These parameters are setup within edsp edasp or eda All nuclei specified in the experiment whose rf signals pass through a HPPR preamplifier module can be wobbled If more than one nucleus is defined wobb starts with the nucleus having the lowest frequency The selected frequency SFOx specifies the center of the wobble window e WBSW wobble sweep width in MHz This parameter sets the frequency range of the wobble sweep which is from SFOx WBSW 2 to SFOx WBSW 2 The lower limit for WBSW is at 0 001 MHz the default value being 4 MHz It can be set within eda or by typing WBSW via the keyboard e WBST number of wobble steps This parameter determines the number of single frequencies measured by wobb and can be set within eda or by typing WBST via the keyboard The allowed range is between 256 and 4096 the default being 256 However as the preci sion of the wobble curve displayed on screen is limited by the number of pixels it is of no use to set WBST higher than the horizontal pixel number On the other hand the display refresh rate decreases with higher WBST Now enter the acquisition window by clicking Acquire gt Observe fid window and start the wobble routine by clicking on Acquire gt Acquisition parameter setup gt Tune probehead Alternatively enter acgu and then wobb via the keyboard The acquisition is started and after a few seconds the wobble curve see Figure 1 7 is displayed and refreshed c
36. Whenever a loop has to be split the delay belonging to the jump label is split in equal parts in order to keep the timing for the loop constant 4 17 The mc command in 3D It is straightforward to extend the use of the mc command to 3D experiments In the same way as F1 loops the F2 loop can be described by F2PH F2EA F2QF parameters Our initial example can easily be extended to a 3D experiment just writing the mc command as d1 mc 0 to 1 FIQF rd10 id0 F2PH ip10 id10 Writing Pulse Programs P 254 This makes sense when another delay d10 is varied as well The FnMODE can be set independently in F1 and F2 With settings FnMODE 1 QF FaMODE 2 TPPI this will expand to ze d1 0 5 d1 0 5 3 pl d0 go 1 d1 0 5 wr 0 if 0 zd id10 ip10 lo to 2 times td2 d1 0 5 rd10 idO lo to 3 times td1 Ne The aqseq 312 command will be evaluated and will cause the order of acquisition to be reversed With aqseq 312 specified in the pulse sequence the above program would expand to aqseq 312 ze 1 d1 0 5 d1 0 5 3 pl d0 go 1 d1 0 5 wr 0 if 0 rd10 id0 lo to 2 times td1 d1 0 5 id10 ip10 lo to 3 times td2 So the reset of the delay for the inner loop is placed at the wrong place and you would have to specify the command as d1 mc 0 to 1 FIQF id0 F2PH ip10 rd0 id10 in order to obtain the intended result 4 18 Enhancements for the mc command P 255 Especially for large data sets it is desirable to test
37. XWIN PLOT under Windows NT only or into other applica tions supporting this format The Enhanced Metafile format is very Microsoft Win dows specific absolutely unportable and therefore can hardly be used on other computer platforms then that of Microsoft Another lacks of this format are that it cannot be printed directly and does not exactly represent the screen layout because Microsoft Windows has no exact equivalents to the standard PostScript fonts used internally by the ppgDisplay Unzoomed enhanced metafile exports the unzoomed ppg drawing in the Microsoft Windows Enhanced Metafile format Otherwise this command is similar to the preceding one The latter two menu items exist only in the ppgDisplay version under Microsoft Windows NT 2 6 Pulse and Gradient Program Display P 119 2 6 2 4 2 6 2 5 2 6 2 6 Zooming and scrolling the ppg At the bottom of the ppgDisplay window there are two sliders controlling the off set in pixels of the left most window corner from the start of the whole ppg draw ing this slider controls ppg scrolling and the width in pixels of the whole ppg drawing if it is bigger than the window width then the ppg drawing is zoomed Additionally there is a button with which the scrolling and zooming can be neglected and the whole ppg drawing brought completely into the window Mousing inside the Display Frame e Left button press drag display the cross hair cursor if the cursor points t
38. a shape Since shapes are often optimized for a particular rotation e g Iz gt Iy excita tion reversing the rotation ly gt Iz flipback will only work reliably if the 3 3 Manipulate existing Shape P 153 shape is time reversed as well e Syntax trev needs no additional parameters e Example st manipulate HalfGauss trev 3 3 9 command add Add two existing shapes to form a new shape e Syntax st add lt input1 gt lt input2 gt lt result gt lt inputl gt filename of first shape to be added lt input2 gt filename of second shape to be added lt result gt result of the addition If the two input files are different in size the smaller one is taken and the align ment will be with respect to the beginning of the shapes A different scaling of the input shapes is not implemented If needed use the command scale to do the scal ing before adding the shapes This behaviour is different to the interactive add procedure e Example st add Gauss 1 Gauss 2 Gauss result Input files are taken from XWINNMRHOMEYLexp stan nmr lists wave Output file is written back to XWINNMRHOMEYSexp stan nmr lists wave The Shape Tool P 154 3 4 Analyze existing Shape Syntax st analyze lt shape type gt lt analyze command gt lt further parameter gt The shape is loaded from XWINNMRHOME exp stan nmrNists wave The following analyzing commands are implemented bandw2 calculate bandwidth fo
39. acquisi tion data in the data set corresponding to the current pointer position The com mands ifp and dfp increment or decrement the pointer by 1 rfp resets it to the beginning of the list See command edlist in The File Menu how to set up data set lists VCLIST variable loop counter list file The pulse program command lo to x times c executes a loop to the label x in the pulse program The number of times the loop is performed is taken from the cur rent position in the loop counter list file In order to proceed to the next list posi tion the command ive for Avance vc for AMX ARX must be used e g d1 ivc See command edlist in The File Menu how to set up loop counter lists VDLIST variable delay list file The pulse program command vd executes a delay whose length is taken from the current position in the variable delay list file In order to proceed to the next list position the command ivd for Avance vd for AMX ARX must be used e g d1 ivd or vd ivd See command edlist in The File Menu how to set up variable delay lists VPLIST variable pulse list file The pulse program command vp executes a pulse whose length is taken from the current position in the variable pulse list file In order to proceed to the next list position the command ivp for Avance ip for AMX ARX must be used e g d1 ivp You may append the usual pulse and phase program options to vp e g vp ph1 f2 See command edlist in The File Me
40. amp G Bodenhausen J Magn Reson 97 135 148 1992 3 2 2 4 HalfGauss Shapes Syntax st generate HalfGauss lt size gt lt trunclevel gt or st generate HalfGauss lt size gt false lt trunclevel gt In the second case only amplitude data are generated int lt size gt shape size in number of points double lt trunclevel gt truncation level in Example st generate HalfGauss 256 10 Literature J Friedrich S Davies amp R Freeman J Magn Reson 75 390 395 1987 3 2 2 5 Hermite Shapes Syntax st generate Hermite lt size gt lt trunclevel gt lt quadcoeff gt or st generate Hermite lt size gt false lt trunclevel gt lt quadcoeff gt In the second case only amplitude data are generated int lt size gt shape size in number of points double lt trunclevel gt truncation level in double lt quadcoeff gt coefficient of quadratic term 4 0 6 0 Example st generate Hermite 256 10 1 0 Literature W S Warren J Chem Phys 81 5437 5448 1984 3 2 Generate a new shape P 141 3 2 2 6 Seduce Shapes Syntax st generate lt shape type gt _ lt size gt int lt size gt shape size in number of points The following Seduce lt shape types gt are implemented Seducel Seduce3 Example st generate Seduce 1000 If only amplitude data are needed The call is st generate Seducel 1000 false Literature M A McCoy amp L Mueller J Magn Reson A
41. be used for the wobble curve In most cases the rf signal path has been interrupted some where Checking the rf signal path usually helps After starting acquisition the error message appears wobble signal too strong despite of smallest receiver gain The rf signal received from the preamplifier is too high to be used for the wobble curve Unplug the TUNE IN cable at the preamplifier put in a 10dB attenuator and reconnect the cable If this does not fix the problem a hard ware fault may be the reason e The DC voltage of one or both of the receiver outputs is so high that the acquired data always fall outside the valid range of the automatic receiver gain adjustment Get Bruker service to check and adjust the DC voltages of both receiver outputs 1 5 Setting up acquisition parameters P 73 1 5 5 1 5 5 1 e There are unwanted signals at the digitizer input e g spikes or oscillat ing signals from the stages before Get Bruker service to check the receiver outputs or the digitizer inputs and fix the problem e Errors in the preamplifier controller If an error occurs in the preamplifier controller an error message appears on screen showing the type of error After confirmation the error is cleared in the preamplifier controller and wobb is cancelled Depending on the type of error wobb can be restarted without errors However in most cases a thor ough investigation and correction of the error is necessary Interactive adj
42. because the same nucleus is used for channel 2 as that one which was used in experiment 1 for channel F1 If an inverse experiment would be done next it is possible to interchange the nuclei for F1 and F2 from experiment 2 with the command edsp Amplifiers The frequency output of each FCU is hardwired to a router input and each router output is hardwired to a specific amplifier The edsp display shows in the first col umn the logical assignment of channels F1 F8 to the FCUs in the second column the connections of the FCUs to the amplifiers which is done by the router The third column of connections shows the so called switchbox which can connect the output of the first X amplifier and of the 1H amplifier to different preamplifiers by means of relays or diode switches Preamplifier Up to 5 preamplifier modules can be installed in the HPPR They are connected directly to switch box outputs X 19F H or to optional High Power Transmitters which may also be connected to these outputs Note and rules for manual routing After each nucleus selection the default routing will be set It can be accepted or The Acquire Menu P 34 1 3 15 may be changed by the user This should be done only after the complete set of nuclei has been selected All changes in the routing are made by moving from the left to the right through the display Connections between two units may be created or cut by two mouse clicks on the corresponding two buttons T
43. branch commands such as go label lo to label times n goto label You may also use labels for numbering the lines of a pulse program Labels need not necessarily be num bers You can also use an alphanumeric string followed by a comma e g first label ze The command ze serves the following purpose To reset the scan counter displayed during acquisition to 0 To enable the execution of dummy scans This will cause the pulse program command go label to perform DS dummy scans before accumulating NS data acquisition scans If you replace ze with zd go label will omit the dummy scans To reset phases to the beginning of phase programs phase lists 8 d11 pll4 f2 Execute a delay whose duration is given by the acquisition parameter D11 Behind any delay command you may specify further actions to be executed during the delay provided the duration chosen was sufficiently large In this example the power level of channel f2 is switched to the value given by the acquisition parameter PL14 9 d11 cw f2 Execute a delay whose duration is given by the acquisition parameter D11 and at the same time turn on continuous wave cw decoupling on frequency chan nel f2 Decoupling will remain active until explicitly switched off with the command do f2 This delay and cw decoupling will begin immediately after the end of the delay specified in item 5 above Items 5 and 6 illustrate a general feature of pulse programs The actions spe
44. combined e Example st manipulate Gauss offs m f s 100 50 75 freqlist st manipulate Gauss offs e f p 100 90 180 freglist The manipulation command offs reads the shape file from XWINNMRHOME exp stan nmr lists wave and writes the manipulated file back to XWINNMRHOME exp stan nmr lists wave If the manipulated shape should have another filename a new one may be specified using filename lt new filename gt as last parameter e Example st manipulate Gauss offs e s 100 2 2000 50 3000 75 filename Gauss new command sinm2 Calculates an amplitude modulation such that the pulse excites at two symmetric sidebands offset with opposite phase e Syntax st manipulate lt shape type gt sinm2 lt pulDur gt lt offset gt double lt pulDur gt length of shaped pulse in us double lt offset gt offset frequency in Hz e Example st manipulate Gauss sinm2 1000 3000 3 3 Manipulate existing Shape P 151 3 3 3 command cosm2 Calculates an amplitude modulation such that the pulse excites at two symmetric sidebands offset with the same phase Syntax st_manipulate lt shape type gt cosm2 lt pulDur gt lt offset gt double lt pulDur gt pulDur length of shaped pulse in us double lt offset gt offset frequency in Hz Example st manipulate Gauss cosm2 1000 3000 3 3 4 Modulation according to Frequency Sweep 3 3 4 1 command sweep Calculates a phase modulation according to a linea
45. control commands P 95 1 6 9 6 the cancel request If confirmed then all preemphasis parameters which were in the preemphasis unit before starting setpre will be reloaded back into the unit and then setpre will exit The Edit pulldown Grad calib const Hz cm enter the gradient calibration constant in Hz cm Hz cm are the primary units for this constant same as in the ParaVision package and this constant is read and saved along with the preemphasis parameters by the Read and Write commands Grad calib const G mm enter the same gradient calibration constant in G mm These units are supported for compatibility with microimaging AU programs writ ten by Dr Dieter Gross This constant is automatically and instantly written to the file conf instr gradient_calib required by these AU programs and it is also read from there on startup Gradient scaling factor enter the gradient scaling factor for the current gradient direction Ideally all gradients should have scaling factors of 1 0 Using these parameters it is possible to correct inaccuracies in the gradients The scaling fac tors are read and saved by the Read and Write commands in the conf instr gradient_calib file Rate to measure temperature enter how often in seconds the setpre module should measure the gradient coil temperature and update the setpre window title bar It cannot be guaranteed that rapid changes in the coil temperature will
46. d1 pl lo to lab1 times 12 0 lu iul count number of scans 0 lu iu2 sincrement 12 if 11 lt 3 goto lab2 if scancounter lt 4 0 lu ru2 sreset 12 to L2 lab2 go lab1 This example repeats the sequence d1 p1 L2 times before scan 1 L2 1 times before scan 2 and L2 2 times before scan 3 Then 12 is reset to its initial value L2 Before all remaining scans the sequence d1 p1 is gener ated L2 times L1 must be set to 1 before starting the sequence 4 12 Commands to suspend the pulse program execution XWIN NMR allows to stop the pulse program execution at specified points in the pulse program The program execution can be continued by the command resume The suspension can be done always autosuspend calcautosuspend or conditionally if the command suspend has been given by the user Since the program which is executed on the TCU is precalculated the precalculated program parts may be invalid if a parameter has been changed before the command resume is executed Therefore the possibility to prevent the precalculation has been implemented calcsuspend calcautosuspend When program execution is resumed after such a command enough time must be left to precalculate a large enough portion of the pulse program before the program is resumed 4 13 Commands to start data acquisition P 237 4 13 4 13 1 suspend stop execution if command suspend has been given autosuspend stop execution always
47. directly in squared brackets counting from 0 i e the command Pliist 1 would execute a pulse of 20microseconds with the above definition Lists can be executed and incremented at the same time using the caret postfix operator The command Pllist is equivalent to Pllist P1list inc Finally you can set the index directly in an arithmetic expression within double quote characters appending idx to the list name The following example summarizes all list processing features list definitions define list lt pulse gt locallist 10 20 30 40 define list lt pulse gt fromfile lt mypulselist gt define list lt pulse gt fromvarfile lt VPLIST gt locallist locallistinc pulse of 10 micsec change index from 0 to 1 locallist locallistres pulse of 20 micsec set index to 0 locallist 2 pulse of 30 micsec independent from index setting locallist locallist dec pulse of 10 micsec after index reset change index from 0 to 3 locallist pulse of 40micsec locallist idx 3 set index to 3 locallist pulse of 40micsec move index on to 0 locallist pulse of 10 micsec 4 5 Pulse generation commands P 191 4 5 1 6 4 5 1 7 Note there are some restrictions on the multiple use of lists within the same line Any index operations on pulse lists will take effect only in the next line Further more you cannot access two different entries of the same list in the same line of code as illustrated in the following example
48. during runtime the newly generated labels have names like LBLF1 in order not to interfere with already existing labels You cannot use these labels by your own The lines are generated by the preprocessor program in order to allow refer ences to the line numbers of the original pulse program Here is an example of the pulseprogram generated from the cosyph sequence with PARMODE 2 and FnMODE 1 TPPI d0 3u 1 mc_line 14 file expanding definition part of mc command before ze dimension 2 aq mode F2 undefined F1 TPPI define delay MCWRK define delay MCREST MCWRK dl MCREST d1 d1 14 1 ze 1 mc_line 14 file expanding definition of mc command after ze inO inO 2 15 1 mc_line 15 file expanding start label for mc command 2 MCWRK LBLFI1 MCREST 16 we 4 20 Multiple receivers P 259 3 pl phl do pO ph2 go 2 ph31 1 mc_line 20 file expanding mc command in line MCWRK wr 0 if 0 zd ipl idO lo to LBLFI times td1 21 exit phl 02201331 ph2 0 2021313 ph31 02201331 4 20 Multiple receivers If a spectrometer is equipped with multiple receivers the number of the receiver 1 8 from where data should be acquired can be appended to the following com mands e g go5 label if no number is present 1 is assumed e g go is equivalent to gol go gonp gosc goscnp adc rcyc rcycnp eosc eoscnp ze zd st st0 aq dw dwov recph wr if Paramet
49. enable the intermediate frequency command syrec XWIN NMR provides the special delay generation commands del de2 de depa derx deadc dw dwov and aq to facilitate the handling of these items del DE1 de2 DE2 de DE depa DEPA derx DERX deadc DEADC dwov DW DECIM and the loopcounter item decim DECIM Any pulse program employing adc must contain one of the commands eosc eoscnp rcyc or rcycnp to ensure a correct end of scan handling You may use several adc commands in con junction with for example a single eosc command Table 4 18 shows the same pulse program realized via go label adc in conjunction with rcyc and adc in conjunction with eosc For an explanation of the macros DE1 DE2 etc used for the generation of the pre scan delay sequence see Table 4 21 As an example of how the go macro can be written explicitly the pulse pro gram zgadc is delivered with the pulse program library This program will pro duce exactly the same result as the program zg The command adc will send a command to start the digitizer The digitization doesn t start immediately with this command but only after a delay DE DE1 In this way the sampling starts exactly with the beginning of aq Writing Pulse Programs P 242 ze e 2dl 2d1 p1 ph1 f1 SANA p1 ph1 f1 i DE1 DE2 DEPA DERX DEADC DE3 eee DE1 DE2 DEPA DERX DEADC DE3 go 2 ph31 aq aq rare A reyc eosc wr 0 AET T lo to 2 times ns exit wr 0 TME ete el th exit wr
50. execute as d1 0 5 id9 lo to 2 times tdO d1 0 5 wr 0 if 0 zd id0 As loop counter the parameter TDO is evaluated In order to be able to switch dimensions timing of commands within the loops must be controlled by the mc command So delays or pulses must not be used as argument to the FO FIPH clauses of the mc command But in some cases commands must be separated by an delay Precautions have been taken for this case the amp symbol used within an argument of F0 will be substituted by an equal fraction of the delay with which the mc command was specified e g d1 mc 0 to 1 FO ip1 amp ip3 will expand to d1 x ipl d1 x ip3 lo to 3 times tdO where x is a value depending on the number of loops generated 4 19 Overview over the mc command The syntax for the mc command is lt delay gt lt options gt mc lt buffer gt to lt label gt FO lt cmds gt F1I lt cmds gt lt loopcounter gt F1PH lt phaseinc gt lt delayinc gt F1QF lt phaseinc gt lt delayinc gt F1EA lt phaseinc gt lt delayinc gt 4 19 Overview over the mc command P 257 F21 lt cmds gt lt loopcounter gt F2PH lt phaseinc gt lt delayinc gt F2QF lt phaseinc gt lt delayinc gt F2EA lt phaseinc gt lt delayinc gt Following rules hold The lt label gt must be followed by a single delay in its definition The lt delay gt in the definition of the lt label gt must be bigger or equal the delay in the mc comm
51. is defined the word CURHEAD is used instead Therefore each probehead has its own default preemphasis file The off set loop and impedance parameters of the GREAT as well as the gradient calibra tion constant scaling factors and rates to measure temperature and to check status are also contained in these preemphasis parameter files Read from read preemphasis parameters from the file defined by the user via the standard file selection dialogue and load them into the preemphasis unit The file exp stan nmr parx preemp lt CURHEAD gt default is proposed as the default Convert read preemphasis parameters in the old format convert them to the native format and load into the preemphasis unit The file to convert is selected by the user via the file selection dialogue default being exp stan nmr lists preemp default The offset loop and impedance parameters of the GREAT and GREAT 3 can not be converted and therefore will not be changed Write default write current preemphasis parameters to the default file exp stan nmr parx preemp lt C URHEAD gt default Write to write current preemphasis parameters to the user defined file the default filename is proposed Exit exit setpre If the parameters have been changed and not yet written to disk a warning message is shown asking if the user really wants to exit Cancel cancel adjustment The user is asked via the warning dialogue to confirm 1 6 Interface
52. is in progress and the lock and the amplifier control windows are open the contents of all three windows are refreshed at the same time and the user may at any time move the mouse into one of the windows and execute a command 2 1 Interactive plot editor xwinplot The command xwinplot opens an interactive plot editor which allows you to set up plots interactively on the screen and plot data on a variety of printers or store data in ecapsulated PostScript or other formats for inclusion in documents The layouts created with xwinplot may be used for plotting of other data sets Particularly the XWIN NMR command autoplot plots the current data set using the layout file whose path name is defined by the parameter LAYOUT This parameter must be set up using the command edo The following path name conventions are valid If the path name begins with a character the specified path will be relative the the login user s home directory If it begins with a sign the path will be relative to WXINNMRHOME plot layouts xwinplot is described in detail in its own manual which is also accessible on line 2 2 Routine Spectrometer operation iconnmr The command iconnmr opens a special user interface designed for easy spectrome ter operation in a routine environment Please refer to the ICON NMR manual for details 2 3 Lock lockdisp The command lockdisp opens a new window and displays the spectrometer s lock signal Paramet
53. label cf the previous section The eoscnp command executes only steps 5a and 5b Writing Pulse Programs P 240 4 13 4 4 13 5 These commands are provided for pulse programs with data acquisition based on adc In contrast to rcyc the user must add the appropriate loop commands You must not specify phase programs behind eosc and eoscnp However decou pling commands are legal although it is not meaningful to use them here Table 4 18 displays an example of an acquisition loop based on eosc The eosc commands may also be specified behind a delay e g 100u eosc In this case they are executed during the specified delay instead of the default 3 millisec onds The delay must not be shorter than 100 microseconds The commands ze and zd Both commands perform the following actions 1 They set the scan counter visible during real time fid display to 0 or DS Neg ative values indicate that dummy scans are in progress 2 They set a flag which informs the next go gonp gosc goscnp or ade command that the fid digitized by the respective command should replace any existing data in the acquisition memory All NBL memory buffers are concerned If ze or zd are placed outside an acquisition loop the replace mode will only be valid for the first scan performed by the loop The fids of all the scans that follow will be added to the data present in the memory buffer 3 The difference between ze and zd is that zd inhibits the
54. log file name is masRateLog Chapter 3 The Shape Tool 3 1 Introduction XWIN NMR 3 0 provides a number of utilities for the creation of pulse shapes e The command stdisp opens a new display that allows to view shapes and to interactively create and manipulate shapes using various parameters e The command st lt parameters gt allows to generate or manipulate shapes from the XWIN NMR command line The main purpose of this syntax is that the com mand can easily be included in AU programs to produce shapes automatically e Once created or changed a shape is stored in a text file in JCAMP DX format suitable to be displayed with stdisp and to be executed by the Xwin nmr acquisition commands There are some commands in Shape Tool that utilize parameters from the current dataset of XWIN NMR These parameters are defined in the Options menu See Chapert 3 5 6 and default to p1 pl1 p11 sp1 spnam1 and fq1list Besides these intrng and o1 are evaluated in some routines P 135 The Shape Tool P 136 The st command is available in the following forms stdisp provides the analogue functions in its menus for display interactive work cf Chapter 3 5 1 st generate lt further parameters gt Generates new shapes 2 st manipulate lt further parameters gt Manipulates existing shapes 3 st analyze lt further parameters gt Analyze existing shapes 3 2 Generate a new shape e Syntax st generate lt shape type gt
55. of channel f1 f8 are set according to PL1 PL8 Power lists In addition to the PLO PL31 parameters you can use user defined power lists on AVANCE spectrometers A user defined power list is defined and initialized in a single define clause e g define list lt power gt pwl 6 0 3 0 0 The define list lt power gt key is followed by the symbolic name under which the list can be addressed further on The name is followed by an equal sign and an initiali zation clause which is a list of concrete high power values scaled in dB included in braces Entries are separated by whitespace You can refer to a power list the same way you use the PLO PL31 parameters just by writing its name e g dl pwl f1 would set the amplitude of channel f1 to 6 0 dB when used for the first time To move within the list there are increment decrement und reset suffix operators inc dec res So you might switch to the next entry of the above list by writing pwl inc In analogy to the syntax for phase programs you can use the carret operator to execute a power setting command and increment the list pointer at the same time dl pwl f1 is equivalent to d1 pwl f1 pwl inc You can also access the list index directly in a relation appending idx to the sym bolic name e g pwl idx pwl idx 1 The above expression is equivalent to the list increment Furthermore it is possible to access a specified list element randomly writing i
56. of the counter if a loop is duplicated several times the loop s text is printed only once The loop s counter and loop s type are printed for a gp loop RF pulse lines For lines containing RF pulses for F1 F2 F3 depending on how many RF channels are actually in use real pulse shapes are displayed with real attenuation values The optional vertical arrows show the points of fql fq8 for ABX 01 02 03 switching or of trigpe trigpl trigne trignl for ABX trigp trign triggering The rectangle drawn with broken lines denotes the area where the receiver gate is opened The sinusoidal FID or echo denotes the area where digitizing is in progress However in the case of ADC triggering as with x or c13 pulse chan nels the acquisition is shown as a spike For RF pulses the tpn or tln channel the attenuation value the name of the shape file and the decoupler status if any is displayed The default condition is to display hard cw pulses Gradient pulse lines If gradients are used actual gradient shapes are shown The gradient functions are shown with 6 lines one below the other the highest and the lowest representing the whole area over which the gradient values are varied The vertical dotted lines show the gradient point switching events i e the occurence of ngrad pulses All gradient base values and gradient functions are printed If the trim numbers are available they are shown together with their values separ
57. phase list to be specified behind the pulse It is defined at the end of the pulse program in our example ph1 0 2 2 0 1 3 3 1 The phase of the pulse varies according to the current data acquisition scan For scan 1 p1 will get the phase 0 90 degrees for scan 2 2 90 for scan 3 2 90 for scan 4 0 90 etc After 8 scans the list is exhausted With scan 9 the pulse phase is cycled i e it restarts with the first phase in the list Phase cycling is a method of artefact suppression in the spectrum to be acquired Cycling the pulse phase requires the receiver phase to be cycled accordingly to ensure that coherent sig nals of subsequent scans will accumulate rather than cancel This is achieved by the receiver phase program ph31 in our example 12 go 2 ph31 Execute 1 data acquisition scan then loop to the pulse program line with label 2 until NS scans have been accumulated NS being an acquisition parameter The NS scans are preceded by DS dummy scans because the command ze is used at the beginning of the pulse sequency rather than zd A dummy scan does not acquire any data but requires the same time given by the acquisition parameter AQ as a true scan Dummy scans are used to put the spin system of the sample into a steady state before acquisition starts The receiver phase is changed after each scan as described above for the pulse phase Phase cycling is based on the phase program ph31 Phase cycling is also employed during the executi
58. pulse program example in Table 4 1 at the beginning of this chapter Any pulse program may contain up to 32 phase programs ph0 to ph31 Phase cycling When a pulse program begins to execute the first phase of each phase program will become valid as soon as the pulse sequence is followed by data acquisition scans rather than dummy scans The next phase will become valid with the next scan or dummy scan cf the section Commands to start data acquisition for Writing Pulse Programs P 200 4 5 3 5 4 5 3 6 details If the end of a phase program is encountered it will be repeated from the beginning phase cycling Phase pointer increment It is possible to explicitly switch to the next phase in a phase program Consider the two commands p1 f2 ph8 p2 f2 ph8 pl is executed with the currently active phase of ph8 then p2 is executed with the next phase in p8 If you had omitted the carret sign in the first line p2 would have been executed with the same phase as p1 A carret sign appended to a phase program will increment the phase pointer to the next phase in the list This phase will become valid with the next pulse program command including this phase pro gram this can be the same command if included in a loop The following two commands have the same effect as the previous example p1 f2 ph8 ipp8 p2 f2 ph8 In this case the command ipp8 is used to increment the pointer in the phase pro gram ph8 Please note t
59. see that the slider button follows your mouse pointer and the actual value ACTUAL will change accord ingly When the slider button has reached the left edge of the slider the function is set to the minimal value allowed compare right display field with function minimum they should be equal At the right sliders edge the function is set to its maximum where function maximum and the right display field should show the same value 2 7 BSMS panel bsmsdisp P 129 Setting Values by Positioning the Slider Button Directly The slider button can be placed immediately by a click with the middle mouse but ton on the estimated spot within the slider The button jumps to that position with out the dragging behaviour Value changes accordingly The slider button jumps to the new position 2 7 3 10 Figure 2 14 Usage of the Slider Continuous Adjustment of Values The slider can be used for continuous adjustment of the current value in a way that maps to the behaviour of the key using the left mouse button a click in the slider area on the right of the slider button not on the button itself will increment the value by the displayed step size Holding down the button for a while will adjust the value continuously In turn when clicking on the left of the slider button but still within the slider the value is going to be decremented Changing the Current Value Using the Right Display Field
60. set from the parameters CNSTO 31 or from any number d1 fq cnst20 SFOn MHz cnst20 Hz d1 fq 3000 SFOn MHz 3000 Hz These two commands set the frequency as specified in CNST20 or directly in the pulse program Additional frequency lists For AVANCE hardware there is another type of frequency lists in addition to the known fql fq8 frequency lists user defined frequency lists can be added The name can be choosen freely by the user at definition time with the define list lt fre quency gt command e g define list lt frequency gt username 200 300 400 In fact the list must be initialized at definition time specifying a list of frequency offsets separated by whitespace in braces As Default the entries are taken as fre quency offsets in Hz to the SFOx frequeny of the channel for which the list is used If the first entry of the list is the capital letter O like offset followed by an absolute reference frequency in MHz values are calculated absolutely Writing Pulse Programs P 196 Alternatively lists can also be specified in a file in the xWINNMRHOME exp stan nmrNists f1 directory For this substitute the braces by angled brackets including a filename e g lt afqlist gt If you specify as a filename a term FQxLIST the filename will be read from the FQxLIST parameter where x is a digit varying from 1 to 8 Note up to 32 different user defined frequency lists may be defined within a pulse program
61. space character must be specified in front of the deg and db units Example 2 pulse 30 deg pl2 auto f2 ph1 Generate a 30 degree pulse using the power given by the acquisition param eter PL2 The program calculates the required pulse width and executes the pulse on channel f2 using the phase program ph1 In general you may use pl0 p131 for the second argument referring to the parameters PLO PL31 Example 3 pulse 45 deg auto 5u f2 ph1 Generate a 45 degree pulse using a pulse width of 5 microseconds The pro gram calculates the required power and executes the pulse on channel f2 using the phase program ph1 You may append u m or s to the number in the third argument to designate microseconds milliseconds or seconds Example 4 pulse 45 deg auto p1 f2 ph1 Generate a 45 degree pulse using a pulse width defined by the acquisition parameter P1 The program calculates the required power and executes the pulse on channel f2 using the phase program ph1 Please note that you may Writing Pulse Programs P 210 specify PO P31 as the third argument but no pulses defined by means of the define pulse statement Example 5 pulse 90 deg auto 10m sp1 f1 ph1 Generate a 90 degree shaped pulse using a pulse width of 10 milliseconds The program calculates the required power and executes the pulse on chan nel f1 using the phase program phl Please note Power calculation uses the same formula for rectangular
62. stO makes the first buffer the current buffer The first buffer will also become the current buffer if st is executed more than NBL times The commands st and stO must be specified behind a delay which must not be shorter than 10 microseconds e g 10u st Table 4 23 shows an example the 1 ze d11 pl14 f2 d11 fq2 f2 st0 2 d1 3 d20 cw f2 d13 do f2 pl phl go 2 ph31 d1 fq2 f2 st lo to 3 times 14 d11 wr 0 if 0 exit Table 4 23 Illustrating st and st0 noedif pulse program noedif pulse program of the Bruker library The fids acquired with different decou pling frequencies are stored in subsequent memory buffers The size of NBL is limited by the constraint that NBL times TD must not exceed the available RCU memory For example an RCU equipped with 4 Mbytes DRAM allows for about 3 8 Mbytes fid data to be stored the remainder is needed by the acquisition parameters Additional memory is available as an option 4 15 Writing memory buffers to disk P 247 4 15 Writing memory buffers to disk Any pulse program must contain at least one disk write command to transfer the acquired data to disk since the data acquisition commands go label gonp label gosc goscnp and adc put the digitized data into a memory buffer but do not store them persistently Table 4 24 shows the pulse program commands provided by XWIN NMR to access wr 0 Transfer the acquisition buffer to the file fid or transfer NBL acquisition
63. standard composite experiments A sequence of standard experiments may be composed to build a new standard experiment called a composite experiment see also set command Such experi ments may be selected for execution in the dialog windows opened by set or quick nmr These routines locate composite experiments in the file XWINNMRHOME conjf instr lt Instrument Name gt users pool If you enable this expinstall item this file is created by making a copy of the stand ard composite experiments provided by Bruker in the file XWINNMRHOME exp stan nmr pp 300 pool The pool file of composite experiments is common to all users With the set com mand you may define own composite experiments and define which user is allowed to execute a particular experiment Install standard scaling region files The directory XWINNMRHOME exp stan nmr lists scl exam includes files whose names are composed of a nucleus and a solvent name e g 3C Acetic The files contain spectral regions usually around the solvent and reference which are to be excluded when the program scales a plot or during sweep width optimization with commands such as getlim If this expinstall item is enabled the sample region files will be copied to their working directory XWINNMRHOME exp stan nmr lists scl where they are accessed by the respective commands If you need solvent nucleus combinations other than those provided by Bruker you may create own suitable files
64. start data acquisition P 243 1 2 define delay dw1 define delay dw2 define pulse pw3 define delay dw4 define delay dw5 define loopcounter tdov dw1 0 1u dw2 2u dw4 2 5u pw3 2 dwov 5 20 dwell dw5 2 dwov dw1 dw2 pw3 dw4 tdov td decim 2 ze d1 pl ph31 DE1 DE2 DEPA DERX DEADC DE3 dwl dw 2 e pw3 f2 e dw4 e dw5 lo to 10 times tdov 50u rcyc 2 wr 0 exit ph30 0 ph31 02201331 Table 4 19 Homodecoupling during data acquisition 4 13 6 External dwell pulses The go and adc commands instruct the digitizer to acquire a desired number of data points with a rate given by the dwell time The dwell pulses which activate the digitizer in regular time intervals are generated internally on the RCU so that the detection of a complete fid is automatically accomplished once initialized via go or adc This is the reason for the waiting time aq in the two rightmost columns of Table 4 18 Certain experiments however require that the user can control the detection of each individual data point of an fid The pulse program in Table 4 22 Writing Pulse Programs P 244 jee 2d1 10u adc ph31 aq rcyc 2 10u ip31 lo to 1 times 11 1 2u recph ph31 2d1 10u adc aq d2 reyc 2 10u ip31 lo to 1 times 11 Table 4 20 Receiver phase setting without with recph define DE3 de define delay rde1 define delay rde2 define delay rdepa define delay rd
65. subtracts the next two gp uses a more complicated procedure If the transmitter pulses in the pulse program do not have phases assigned explic itely their phases are shifted automatically during the corresponding scan to ensure accumulation of the scans WBST number of wobble steps WBSW wobble sweep width in Mhz Parameters required by the command wobb probehead tuning See wobb for more information V9 variation width of random delay in per cent In a pulse program any of the delay commands d0 d31 may get appended the option 7 e g dl r The result will be that each time this command is encountered the delay will get a different randomized value The maximum variation with respect to the original value may be specified in V9 AUNM acquisition AU program The AU program specified in this parameter is executed by the command xaua xaua is most often used in an AU program to start another AU program which may depend on the current acquisition parameters POWMOD power mode Possible settings low high and linear Power mode selection for spectrometers equipped with a high power accessory HPPRGN gain for HPPR preamplifier Possible settings normal and plus Amplifier selection for spectrometers equipped with the respective accessory PRGAIN high power preamplifier gain Possible settings low and high Gain selection for spectrometers equipped with a high power accessory INO IN31 increment values for the delays
66. sweep width will be adjusted but not NDO The Acquire Menu P 50 in10 to change the increment IN10 in F2 of a 3D data set the sweep width will be adjusted but not ND10 1 SWH 1 SW to change the sweep width in Hz ppm in F1 of a 2D or 3D data set the increment INO will be adjusted but not NDO 2 SWH 1SW to change the sweep width in Hz ppm in F2 of a 3D data set the increment IN10 will be adjusted but not ND10 Note 2 SWH 2 SW on a 2D data set will change the sweep width in F2 and 3 SWH 3 SW on a 3D data set will change the sweep width in F3 Therefore incre ments and NDO or ND10 values will NOT be effected because the changes are made in the acquisition dimension and not in one of the indirect detected dimen sion If you want to change the parameters in an AU program use storeparl NDO value changes the sweep width in F1 of a 2D data set if NDO is changed value must be a INTEGER variable storepar3 NDO value changes the sweep width in F1 of a 3D data set if NDO is changed value must be a INTEGER variable storeparl ND10 value changes the sweep width in F2 of a 3D data set if ND10 is changed value must be a INTEGER variable storepar1 INO value to change the increment INO in F1 of a 2D data set value must be a FLOAT variable storepar3 INO value to change the increment INO in F1 of a 3D data set value must be a FLOAT variable storeparl IN10 value to change
67. than the max interval If they exist they are made equal to the max interval Step 5 Distributes lines with information pertaining to gradients RF acquisition and time scale around the screen Calculates the heights of these lines depending upon how many lines are to be drawn If the heights are larger than the max height the max height is taken Step 6 Calculates intensities of all RF pulses depending on their attenuations in pixels Checks if there are pulses smaller than the min height If they exist they are made as high as the min height The user can adjust these values for an optimal ppg display Default display parameters resets all adjustable parameters see previous menu item to their default values The default values depend on the current font size see later Select drawing area font This command opens the font selection dialog where the user can choose a font style from a number of supported styles presented in the combo box control Addi tionally it is possible to adjust the font size via the slider similar to the sliders used in the Adjust display parameters menu item The combo box and the slider con trol the font appearance independently The ppgDisplay uses only scalable vector and PostScript fonts Default drawing area font resets the font size see previous menu item to its default value The default value depends on the current window dimensions The font style is not altered 2 6 Pulse and
68. the amplitude of the fid signal before it is fed into the digitzer It must be adjusted to maximum amplitude without causing overflow of the digitizer in this case signal cutoff would occur generating artefacts in the transformed spectrum The values depend on the receiver system of your spec trometer You may use the command rga for automatic determination of the opti The Acquire Menu P 52 mum RG value rga performs some scans using the pulse program specified in PULPROG and sets RG to the found value You may then further adjust RG to fit your special requirements DW dwell time in microseconds The dwell time is the time difference between two data points of the fid It is calcu lated from the sweep width according to DW 10e6 2 SW SFO1 If you change DW SW is recalculated according to SW 10e6 2 0 05 DW SFO1 The mini mum dwell time corresponding to the maximum possible sweep width depends on the digitizer type installed in the spectrometer see also DIGTYP parameter Table 1 18 DWOV oversampling dwell time For spectrometers equipped with digital filters Avance only It is displayed as an information for the user and is related to the dwell time DW according to DW DWOV DECIM DWOV is the actual sample rate of the digitzer if digital filtering is enabled The decimation factor DECIM is chosen so that after the Fou rier transform the spectrum will have a spectral width as close as possible to the chosen SW paramet
69. the pulse program Writing Pulse Programs P 194 4 5 2 4 5 2 1 4 5 2 2 not at run time In fact any expression containing user defined names cannot be evaluated during runtime Pulse frequency Frequency channels The RF frequency of a pulse is selected via the spectrometer channel number f1 f8 the actual number of channels in your instrument depends on its type and equipment Executing a pulse on a particular channel means executing it with the frequency defined for this channel The commands p1 f2 p2 0 33 f2 p30d1H 3 33 f2 vp f2 would execute pulses with the duration P1 P2 0 33 p30d1H 3 33 VPLIST respectively on channel f2 The pulse frequency is that assigned to f2 namely SFO2 which is an acquisition parameter in MHz units If the channel is omitted f1 is assumed as default Generally the frequencies of the channels f1 f8 are given by the parameters SFO1 SFO8 cf SFO1 NUCLEI and edasp for more information about defining frequencies for a particular channel These parameters are loaded into the synthesizer s before the pulse program starts rather than at the time a pulse is executed This gives the hardware time to stabilize before the experiment begins Changing the frequency It is possible to change the frequency of a channel within a pulse program XWIN NMR provides the commands fq1 fg8 for this purpose They refer to frequency lists from where the new frequency will be taken A frequency list
70. there was not enough time to execute the whole shaped pulse the phase is still loaded as required for the shaped pulse namely with the phase cycle of the shaped pulse and not with the phase correction value for the power pl channel DE1 DE2 DEPA DERX and DEADC The acquisition parameter DE is the waiting period between the last pulse and the The Acquire Menu P 30 begin of data acquisition digitizer start to avoid pulse feed through You may change DE by entering a new value For analog acquisition mode DIGMOD this value is automatically recalculated when SW SWH or DW are changed such that the Ist order phase distortion is near 0 in the resulting spectrum For digital mode this value remain unchanged in these cases During DE several actions will be exe cuted the timing of which may be controlled by the following parameters DEPA after this time the preamplifier HPPR is switched to open the receiver channel default is 0 5 us DEI after this time the frequency is switched from the transmit to the receive frequency DRX DPX and DQD only see also SYREC default value is 1 0 us DE2 after this time the phase is switched to 0 default value is 0 5 us The parameter PHASPR which will pull forward the phase setting is taken into account automatically such that the true phase setting occurs after DE2 This may lead to the situation where the program prints the error message DE too small although DE2 is smaller than DE
71. to adjust P5 It is asked for by the program Alternately this parameter may be typed in after clicking the PARAMETER field e g type P5 Alternatively enter gschan lt Parameter gt via the keyboard to select this new param eter for manipulation by mouse Changing the mouse sensitivity Below the label mouse are the four buttons 2 2 8 and 8 The sensitivity of the mouse for the variation of parameters is increased or decreased by the appropriate factor by activating these buttons Save adjusted parameter In order to save the current parameter adjusted by mouse for a later data accumula tion with go or zg activate the save button Alternatively enter gsstore via the keyboard Reset adjusted parameter In order to reset the parameter currently adjusted by mouse to the last saved value activate the DEF button 1 5 Setting up acquisition parameters P 77 Alternatively enter gsres via the keyboard 1 5 6 Acquisition parameter setup with set 1 5 6 1 Please note that you should use ICON NMR for routine spectroscopy based on standard experiments and for automation using a sample changer rather than the command set run quicknmr which are historically older and are just maintained for compatibility reasons The acquisition command run allows you to start a series of experiments run is most often used to work with an automatic sample changer but may also be used if samples are changed manually Please refer to t
72. to write lengthy phase programs in a compact form For phase programs with less than 16 phases the explicit forms 1 and 2 are usually easier to read The operator n with n 2 3 must be specified behind a list of phases enclosed in braces It repeats the contents of the braces n 1 times The operator m with n 1 2 3 must be specified behind a list of phases enclosed in braces or behind a previous m or operator Each m repeats what is in the braces exactly one time In addition the repeated phase list will be incremented by m module 4 The following lines display the phase programs 3 9 in their explicit form after 4 5 Pulse generation commands P 199 4 5 3 3 4 5 3 4 applying these rules 3 phl 00002222 4 phl 0213 5 phl 02132031 6 phl 13203113 7 phl 020213132020 8 phl 0022331122001133 9 phl 5 121220 In 10 phase programs are combined by multiplication with an integer constant and by addition This is illustrated by the following example Let ph2 0213 ph3 11113333 We want to calculate ph5 ph2 2 ph3 At first we build ph2 2 ph2 2 0022 We have to extend ph2 to the same size as ph3 before we can evaluate the equa tion ph2 00220022 ph3 11113333 Then we can calculate the result phl 11333311 Position of phase programs Phase programs must be specified at the end of the pulse program cf the
73. true 1 Literature M R Bendall amp D T Pegg J Magn Reson 67 376 381 1986 3 2 3 3 SmoothedChirp Shape Syntax st generate SmoothedChirp lt size gt lt SW gt lt length gt lt smoothed gt lt sweepDir gt int lt size gt shape size in number of points double lt SW gt Total Sweep Width in Hz double lt lenght gt length of pulse in usec double lt smoothed gt to be smoothed int lt sweepDir gt Direction of sweep 1 high to low 1 low to high field The Shape Tool P 144 Example st generate SmoothedChirp 256 40000 0 1500 0 10 0 1 If only amplitude data are needed The call is st generate SmoothedChirp 256 false 40000 0 1500 0 10 0 1 Literature J M Boehlen amp G Bodenhausen J Magn Reson A 102 293 1993 3 2 3 4 CompositeSmoothedChirp Shape Syntax st generate CompositeSmoothedChirp lt size gt lt SW gt lt length gt lt smoothed gt lt sweepDir gt int lt size gt shape size in number of points double lt SW gt Total Sweep Width in Hz double lt lenght gt length of pulse for basic element in usec double lt smoothed gt to be smoothed int lt sweepDir gt Direction of sweep 1 high to low 1 low to high field Example st generate CompositeSmoothedChirp 256 40000 0 375 0 10 0 1 If only amplitude data are needed The call is st generate CompositeSmoothedChirp 256 false 40000 0 375 0 10 0 1 Literature T L Hwang P C M va
74. tty 1 tty16 on the Ist SIB tty21 tty26 on the 2nd SIB tty3 tty36 on the 3rd SIB and tty41 tty46 on the 4th SIB Note To be able to use the RS232 devices on the 3rd and 4th SIB the file etc inittab on spect has to be modified manually by the operator 1 3 1 5 Trouble shooting part 1 While cf is checking the spectrometer hardware after entering the 1H frequency the following error message appears lt iiconf gt connection to lt Instrument Name gt aqport0 failed startd demon active on CCU This error message may be caused by several reasons There is no startd demon running on the CCU To check this use telnet to login onto spect e g telnet spect as user root in a unix shell and execute the follow ing command ps ef grep startd grep v grep If the last commands does not list any running startd it can be started manually with etc startd or by rebooting the CCU with 1 Serial Interface Board The Acquire Menu p 12 1 3 1 6 1 3 2 etc init 6 e The operating system on the host does not know the name of the spectrometer This happens if lt nstrument Name gt is a newly chosen name which has never been used before To solve this problem the superuser must add the new name to the hosts file Unix etc hosts Windows NT CA Winnt System32 drivers etc hosts directly behind the name spect e g for the name drx300 149 236 99 99 spect drx300
75. which are valid The Acquire Menu P 18 Prosol Parameter Names Prosol Parameter Pulse Length Power Level Shape Names Phase Alignment Standard PSH1 PLSHI1 PNSHI PASHI1 SoftPulses PSH16 PLSH16 PNSH16 PASH16 PUSER1 PLUSERI1 User defined Hard PUSER2 PLUSER2 Pulses PUSER3 PLUSER3 PUSER4 PLUSER4 PSH1U PLSH1U PNSH1U PASH1U User defined Soft PSH2U PLSH2U PNSH2U PASH2U Pulses PSH3U PLSH3U PNSH3U PASH3U PSH4U PLSH4U PNSH4U PASH4U Table 1 7 Prosol Parameters for the Standard Soft user defined Soft Pulses and User defined Hard Pulses for the current probe head and the solvent of the current dataset You can edit the prosol parameters by modifying the values of the corresponding entry fields Once the 90 degree power level and pulse length for the transmitter or for the decoupler are defined the buttons calc calculate the power level of the corresponding parameter if the pulse length is defined Or the calc routine can calculate the pulse length if the power level of the parameter is defined To set up the prosol parameters for another probe nucleus or solvent Select any probe of your system with the entry Probe name on the top of the window and a nucleus with the entry Nucleus With the entry Solvent s you can setup prosol parameters either for all solvents or for individual solvents If your system consists of more logical channels than j
76. wpar When you click on the experiment field a table of the available experiments is displayed The first column shows one of the character 0 1 2 or C referring to experiments requiring 0 1 or 2 preparation experiments or indicating composite C experi ments Experiments of type 1 or 2 require one or two preparation experiments to be performed before the experiment itself can start e g a 1D preparation experiment determining the optimized sweep width for a subsequent 2D experiment 1 5 Setting up acquisition parameters P 79 1 5 6 2 1 5 6 3 Priority Clicking on this field will toggle on or off urgent mode During sample changer operation such a sample will get priority Up to 10 samples may be declared urgent and will be processed in the order they were set up You must have the per mission to use this field see eduser The title entry field Enter the plot title for the experiment you are currently setting up You may seper ate lines in a title text by the 2 character sequence n Plots generated by composite experiments may have two titles one common to all plots and a particular one for each component experiment The common title is the one entered in the main set dialog window the other titles are taken from the title entries of the component experiments See EditPar button Command buttons at the bottom of the set window n EXPERIMENTS Opens a dialog window where you may specify up to 9 additional experi
77. 0 12 5ns 12 5us When you use different step sizes then the values will be rounded This may result in truncation or spikes Writing Pulse Programs P 208 4 5 4 4 4 5 5 Attention When varying the length of a shape pulse then the corresponding com mand must be specified within a delay The delay must have a length of at least 4us for each channel the shape appears on Note that relations may also affect the length of a shape so the relation which changes the length of the shape must follow a delay of appropriate length as well in case of list commands inc res dec these commands will cause a reload only within the next duration and thus must be followed by a delay of sufficient length Example luipul incorrect as pl occurs in pulse ipul must be specified in delay gt 4u pl pl 0 5m this is true for relations as well pl sp0 8uipul correct here the ipu command and the relation need 4u each pl pl 0 5m dellist inc 4u the inc command must be followed by the delay If timing change commands relevant for shaped pulses are specified within too short commands the TCU will print a warning during runtime of the experiment Another side effect is that varying the length of a shape with non zero offset fre quency will change the offset frecquency as the frequency shift is obtained via phase shifting This phase shift won t be recalculated during execution so the off set will be changed inverse pr
78. 0 F1 The Acquire Menu P 20 P 2 P90 F1 2 P 31 PROE F2 PL 1 PL90 F1 PL 6 PL90 F3 SPNAMO PNSH3 F2 SPNAM4 PNSH2U F3 D 16 D_grad If the current pulse program contains a line relations lt filename gt then get prosol uses lt filename gt as the relations file Otherwise getprosol uses the default relations file provided by Bruker All relations files have to exist in the following directory lt XwinNmrHome gt conf instr spect prosol relations To determine the prosol parameter filenames lt Nuc F x Ay gt getprosol reads the routing for each nucleus of the current dataset Nuc is the nucleus NUC1 or NUC2 or NUC8 of the current dataset Fx the channel where Nuc is con nected and Ay is the currently routed amplifier of Nuc on channel Fx First getprosol looks for the prosol parameter filename found in the directory lt XwinNmrHome gt conf instr spect prosol lt current probe Id gt lt current solvent gt If the prosol parameter file hasn t been created for the individual solvent lt current solvent gt getprosol looks for the prosol parameter file created for all solvents in the directory lt XwinNmrHome gt conf instr spect prosol lt current probe Id gt If no prosol parameter file is found getprosol prints a warning message After setting the acquisition parameters to the values of the prosol parameters
79. 0 Loop commands The general form of a loop command is lo to label times n Example 1 labell d1 p1 f2 lo to label1 times 10 p2 f2 Remember that a label can be an arbitrary string such as label1 followed by a comma or a number such as 2 without a comma appended The lo com mand in this example although specified on an extra line does not intro duce an extra delay between the last p1 pulse and p2 Example 2 label1 p1 f1 label2 d1 p1 f2 lo to label2 times 10 lo to label1 times 5 p2 f2 The first lo command in this example does not introduce an extra delay in the pulse program However any further lo command will add a delay of 2 5 microseconds XWIN NMR will display a respective message when the pulse 4 10 Loop commands P 229 program compiler is invoked i e when entering one of the commands gs Zg go or pulsdisp The lo command exists in a number of variations shown in Table 4 10 lo to label times 5 The loop counter is a constant lo to label times td The loop counter is TD the time domain size in the acquisition dimension to be defined with the command td or in the left column in eda lo to label times td1 The loop counter is TD F1 command 1 td for 2D parameter sets right column in eda lo to label times nbl The loop counter is the parameter NBL cf wr st st0 lo to label times 10 lo to label times 131 The loop counter is L
80. 1 5 2 3 1 5 2 4 temporary parameters into a format file by generating a corresponding new entry in the format file similar to the entries of DW AQ etc Invoking eda from the keyboard or from set or quicknmr Now the parameters displayed are not those contained in the acqu files of the currently displayed data set Instead they correspond to the experiment selected in the set or quicknmr dialog window and are valid only for the data set currently selected in these dialog windows See also command set for more details eda command buttons Table 1 4 lists the command buttons available in the eda dialog box SAVE Save modifications and quit Change eda display such that the parameters are arranged in a single column including their description 1 COL only 1D 2 COL Change eda display such that the parameters are only 1D arranged in two columns omitting their description Search An entry field where you may specify the name Parameter or some inital characters of a parameter After typing Return the cursor is auto positioned to the parameter NEXT Continue search to next parameter matching the string ABORT Discard any changes and quit Table 1 17 Command buttons in eda dialog window The acquisition parameters The acquisition parameters are described in the standard eda order PULPROG pulse program The pulse program to be executed by the acquisition commands gs zg
81. 101 122 130 1993 3 2 2 7 Sinc Shape Syntax st generate Sinc lt size gt lt cycnum gt int lt size gt shape size in number of points int lt cycnum gt cycnum nunber of cycles to calculate Example st generate Sinc 256 8 If only amplitude data are needed The call is st generate Sinc 256 false 8 Literature A J Temps Jr amp C F Brewer J Magn Reson 56 355 372 1984 3 2 2 8 Sneeze Shape Syntax st generate Sneeze lt size gt int lt size gt shape size in number of points Example st generate Sneeze 256 If only amplitude data are needed The call is st generate Sneeze 256 false Literature J M Nuzillard amp R Freeman J Magn Reson A 110 252 256 1994 The Shape Tool P 142 3 2 2 9 Snob Shapes e Syntax st generate DSnob lt size gt int lt size gt shape size in number of points The following Snob Shapes are implemented ESnob ISnob2 Snob3 RSnob DSnob e Example st generate DSnob 256 If only amplitude data are needed The call is st generate ISnob2 256 false e Literature E Kupce J Boyd amp I D Campbell J Magn Reson B 106 300 303 1995 3 2 2 10 Vega Shapes e Syntax st generate lt shape type gt lt size gt int lt size gt shape size in number of points The following Vega lt shape types gt are implemented EVegal EVega2 Vega e Example st generate EVegal 256 If only amplitude data are needed The cal
82. 215 4 6 7 4 6 8 Note there are some restrictions on the multiple use of lists within the same line Any index operations on delay lists will take effect only in the next line Further more you cannot access two different entries of the same list in the same line of code as illustrated in the following example locallist locallist this executes twice the same list entry so executing twice a 0 1sec delay locallist the increment becomes valid only in the following line resulting again in a 0 2 sec delay locallist 2 locallist 3 this will execute locallist 3 twice this is not what you expected Note Names for user defined items may consist of up to 19 characters where only the 7 first are significant i e Delaylistl and Delaylist2 are legal names but would address the same symbol and thus must not appear in different definitions Special purpose delays These are the delay commands del de2 de3 dw and aq of Table 4 4 They are provided to facilitate the construction of pulse programs which must use the com mand adc rather than go abel to start data acquisition Manipulating delays The operator A delay can be manipulated by the operator if appended to the delay com mand Examples of legal commands d1 1 5 compensationTime 3 33 d3 oneThird vd 3 10m 0 33 would be illegal since 10m is a fixed delay The operator must be placed behind the delay command not before oneThird is the
83. 31 or gp0 gp31 may be multiplied by a function or a constant In case of gron the function must be specified without parameters e g sin instead sin 100 in case of gp the function may or may not be specified with parameters General Gradient Statements Since the XwinNmr gradient software is also used by ParaVision it has features that support imaging in a medical environment With gradient statements of the form delay grad lt Ist dim gt lt 2nd dim gt lt r3d dim gt you can use these features even without ParaVision but in a restricted manner e You can specify Object Oriented Gradients that are converted into Physical Gradients This allows for Acquisition of images with different slice orientation while using the same pulseprogram The gradients may be specified in spatial coordinates other than x y and z The pulsprogram compiler multiplies the gradients with a rotation matrix see below to get x y and z Acquisition of images with different slice thickness and field of view every spatial dimension may be multiplied by a scaling factor e The gradients are defined as a precentage of maximum_gradient strength as scalar values or functions which may be combined by addition and multiplica tion e The functions are either Internal functions which are handled accordingly by the compiler or gradient files containing the function values see above e Scaling and rotation can be suppressed with s
84. 4 13 4 2 Pulse program library Routine users of a spectrometer usually do not need to write their own pulse pro grams Instead they can make use of the Bruker pulse program library provided with XWIN NMR covering the most useful experiments The edpul command dis plays a list of these experiments and allows you to view the pulse program text which includes a description of each Please refer to the description of edpul for details Viewing the library pulse programs requires that the expinstall command was executed by the administrator which copies the pulse programs suitable for your spectrometer into the appropriate working directory When writing your own pulse programs it is often helpful to start with a Bruker pulse program and apply modifications rather than beginning from scratch 4 3 Pulse program display A graphical representation of a pulse program for Avance type spectrometers may be obtained using the command pulsdisp which is described in its own section of the XWIN NMR manual After writing your own pulse program pulsdisp will not only check its syntax but will also allow you to visualize any fine timing detail before you try a real experiment 4 4 Basic syntax rules Table 4 1 shows a simple example from the Bruker pulse program library It is used to demonstrate some of the most important programming rules 4 Pulse programs are line oriented Each line specifies an action to be executed by the acquisition hardw
85. 80 240up 0 pcepd 2 864 0 AREEN pcpd 2 981 180 570up 0 pcepd 0 770 0 680up 180 eee 810up 0 pcepd 0 593 0 960up 180 lo to times 2 1140up 0 2 pepd 0 339 180 1000up 180 pcepd 0 613 0 850up 0 eee 710up 180 pepd 2 843 180 es pcepd 0 729 0 200up 0 pcepd 0 593 180 110up 180 lo to 2 times 2 jump to 1 jump to 1 Table 4 8 Broadband and GARP cpd sequences 1 pepd 2 sp15 0 1 pepd 14 156 sp15 60 pl sp15 pepd 2 sp15 0 pepd 14 156 sp15 150 pepd 2 sp15 180 pepd 14 156 sp15 0 pepd 2 sp15 180 pepd 14 156 sp15 150 pepd 2 sp15 180 pepd 14 156 sp15 60 pepd 2 sp15 0 2 pepd 14 156 sp15 240 pepd 2 sp15 0 pepd 14 156 sp15 330 pepd 2 sp15 180 pcepd 14 156 sp15 180 pepd 2 sp15 180 pepd 14 156 sp15 330 pepd 2 sp15 180 pepd 14 156 sp15 240 pepd 2 sp15 0 lo to 2 times 2 pepd 2 sp15 0 3 pepd 14 156 sp15 60 pepd 2 sp15 0 pepd 14 156 sp15 150 pepd 2 sp15 180 pepd 14 156 sp15 0 pepd 2 sp15 180 pepd 14 156 sp15 150 pepd 2 sp15 0 pepd 14 156 sp15 60 jump to 1 jump to 1 Table 4 9 MLEVSP and MPF7 cpd sequences in entry 15 of the shaped pulse parameter table which can be displayed in eda Writing Pulse Programs P 226 The following section of a pulse program starts a cpd program on channel f2 but keeps the f2 transmitter output disabled command cpdngs2 except for the periods given by p2 The p2 pulse actually serves as a gating pulse for cpd decoupling and should not have a phase program assigned to prevent overwriting the cpd
86. DO D31 in seconds The Acquire Menu P 60 See earlier description of DO D31 and of INO and IN10 INP0 INP31 increment values for the pulses PO P31 in microseconds See earlier description of PO P31 L0 L31 loop counter parameters The pulse program commands lo to x times 10 lo to x times 131 execute a loop to label x LO L31 times respectively Outside the loop you may use the pulse program commands iu0 iu31 and duQ du31 which increase or decrease the values given by LO L31 by 1 Assume the command iu0 is the next statement after lo to x times 10 and both lo to x times 10 and iu are contained in larger loop Then the first time the lo to x times 10 command is executed it will loop LO times the second time LO 1 times etc SEOUT SE 451 receiver unit output to be used Possible settings HR and BB The BB channel is used for special experiments only S0 S7 ecoupler power 1 in db Only for AMX ARX type spectrometers The pulse program commands s0 s7 set the Ecoupler power values according to the parameters SO S7 We recommend however to use hl1 hl4 instead which provide a faster power switching using the 4 fast ecoupler registers parameters HL1 HL4 PH_ref reference phase in degrees The pulse program command go n implicitly sets the receiver reference phase to 0 degrees The value PH_ref is added to this implicit receiver phase You can control the receiver phase explicitly with the command go n p
87. II text consisting of a number of lines Each line may contain one or more pulse program commands which specify actions to be per formed by the acquisition hardware and software You set up a pulse program by means of the XWIN NMR commands edpul or edcpul The chapter The File Menu describes their syntax and in which disk directories pulse programs are stored The XWIN NMR acquisition commands gs go and zg execute the pulse program defined by the acquisition parameter PULPROG to be set up with eda or pulprog Pulse program execution is a two step process When typing gs go or zg the pulse program compiler is invoked and translates the pulse program text into an internal binary form suitable to be executed During this stage syntax errors are reported acquisition will not be started if there are any If compilation is success ful the compiled pulse program is loaded into the acquisition hardware and the measurement begins This chapter describes the pulse program language for AVANCE type instruments Many of the features are also valid for AMX ARX ASX type spectrometers but we recommend that you cross check with the UxNMR User s Guide 910901 for differ ences P 181 Writing Pulse Programs P 182 Please note A few features described in this chapter are not implemented in XWIN NMR 2 0 but are planned for revision 2 1 These features are printed in grey rather than black letters e g the section 4 9 4 and the bottom of Table
88. IN10 respectively INO IN10 increments for delays DO and D10 in seconds The pulse program commands id0 and id10 increment the delays DO and D10 by INO and IN10 respectively See also description of DO D31 If you change INO during the setup of a 2D experiment the sweep width in the dimension F1 is recal culated according to SW 10e6 SFO1 DR INO If you change INO during the setup of a 3D experiment the sweep width in the dimension F1 is recalculated according to SW 10e6 SFO1 DR INO If you change IN10 during the setup of a 3D experiment the sweep width in the dimension F2 is recalculated according to SW 10e6 SFO1 DR IN10 Features a changing ND10 on a 3D data set in eda results in a correct calculation of IN10 SW and SWH b if the parameter INO or IN10 is changed by typing for instance inO or in10 from the XWIN NMR command line then the sweep width in ppm is updated cor rectly as well as the sweep width in Hz c changing the sweep width by typing 1 SWH or 3 SWH from the XWIN NMR command line will change the increment d Setting the parameters in an AU program with STOREPAR is possible If you want to change the parameters from the XWIN NMR command line type nd0 to change the sweep width in F1 of a 2D or 3D data set the increment INO is NOT changed nd10 to change the sweep width in F2 of a 3D data set the increment IN10 is NOT changed in0 to change the increment INO in F1 of a 2D or 3D data set the
89. It is a dialog window where you define the data set for the acquired data the solvent the experiment and a plot title Then acquisition may be started Please note that you should now use iconnmr rather than quicknmr which is a newer product It is the responsibility of the spectrometer administrator to assign permissions to the users of quicknmr with the command eduser The allowed data set names experiments right to modify parameters and to exit from quicknmr Displaying the lock and fid window e Open the acquisition window by selecting the command Observe fid window from the Acquire menu In this window the acquisition data fid may be observed in real time either in the time domain as an fid or in the frequency The Acquire Menu P 102 domain as a spectrum This window will also show the wobble curve during the probehead tuning procedure e Execute the command lockdisp type it in or call it from the Windows menu The lock signal will be displayed for locking shimming or vising Chapter 2 The Windows Menu The Windows menu contains XWIN NMR commands which generate new windows Figure 2 1 The Windows menu independent of the main XWIN NMR window They may remain on screen simulta neously with other windows of this type and with the main XWIN NMR window Since XWIN NMR is a multi tasking program the commands are executed in paral P 103 The Windows Menu P 104 lel For example if a data acquisition
90. O L31 to be defined with the keyboard commands 10 131 or L array in eda The pulse program commands iu0 iu31 increment the counters 10 131 by 1 du0 du31 decrement them and ru0 ru31 reset them to LO sa L31 lo to label times c The loop counter is taken from the list file given by VCLIST cf commands velist and edlist The pulse program command ivc advances the list pointer by 1 The list pointer position can also be calculated by an equation e g vcidx 5 lo to label times myCounter The loop counter is defined at the beginning of the pulse program by means of a define statement and an expression e g define loopcounter myCounter myCounter aq 10m 1 The result must not have a dimension Table 4 10 The lo commands Example 3 Ze Writing Pulse Programs P 230 labell d1 p1 f1 lo to labell times 12 lu iu2 p2 f2 go label1 Assume the parameter L2 is set to 1 using the keyboard command 12 or by setting L2 2 in eda Then before scan 1 d1 p1 f1 would be executed once before scan 2 twice etc The lo command does not introduce an extra delay in the sequence The increment command iu2 is executed during the specified 1 microsecond delay You could replace the loop counter 12 with c in this example and iu2 with ivc to use the number of loops specified in a list file Example 4 define loopcounter myCounter myCounter aq 10m 1
91. OLDER number Only experiments of type 0 no preparation experiments required or C composite experiments are allowed Table 1 19 summarizes all legal keywords Features 1 2 3 Up to 9 different experiments per holder The first experiment on a holder can be a composite experiment Each experiment can have an individual title This applies also for the individ ual experiments of a composite experiment see the example below Titles can have more than one line The line seperator is the n sequence The Acquire Menu P 84 comment line SETUPNAME name of destination setup file USER data set USER parameter SAMPLES start of holder definitions section HOLDER holder number NAME data set NAME parameter optional EXPNO data set EXPNO parameter optional SOLVENT solvent EXPERIMENT experiment name of type 0 or C TITLE rest of line is the plot title optional END end of holder definitions section Table 1 19 extset ASCII file keywords If several experiments are defined for one holder each experiment can have an individual name NAME and experiment number EXPNO The following example ASCII text file summarizes the above points Example in 1 column means comment SETUPNAME mikel USER eng SAMPLES HOLDER 8 NAME Junel5 EXPNO 10 SOLVENT CDCI3 EXPERIMENT sw_cosy45 TITLE This is a title nwith two lines TITLE This is a sec
92. SMS hardware respectively and show how to control auto shim ming using special commands and parameters that are discussed now Note that lines in a tune file starting with a character are treated as comments USE_FIDAREA The auto shim procedure will maximize the area under the fid USE_LOCKLEVEL The auto shim procedure will maximize the lock level LOCKDWELL n Determines a mean value of the lock level by measuring it n times 3 lt n lt 32 default n 5 Maximizing the lock level is based on mean values to suppress noise effects Has no effect if USE_FIDAREA was set LOCKPHASE s i The autoshim module is capable of optimizing the lock phase or shim gradient The shim optimization commands are GRADIENT and SIMPLEX see below while LOCKPHASE adjusts the lock phase s maximum step width i maximum number of iterations MAXLOCK m Limits the maximum value of the lock level to the specified value Avoids that the lock signal move out of the display during the shimming procedure Only required for testing ROTATION ON OFF Enables shimming with or without sample rotation GRADIENT si Example z1 1000 3 All gradients that should be optimized during auto shimming must be specified in this way s maximum step width i maximum number of iter ations Each time a GRADIENT is encountered this shim will be optimized This assumes that different gradients can be adjusted independently See the SIMPLEX command on how to adjust several s
93. The name may be of arbitrary length but only the first 7 characters are significant You can use the user specified lists like the regular fq lists in a pulse program to set frequencies but they will not be autoincremented after use There exist sepa rate commands to manipulate the list index Suffix operators inc dec res are available to increment decrement or reset the index respectively You can use a suffix operator carret in order to execute the list and increment the pointer at the same time This is similar to the behaviour known from phase programs Fur thermore you can address directly a list entry specifying its index in square bra ckets Take care when changing several frequencies within one duration d1 fqlist f1 fqlist f2 will set both channels to the same frequency as index manipula tion commands are evaluated only at the end of the duration Note The index runs from 0 and will be treated modulo the length of the list s th you can cycle through a list just by incrementing the index You can access and manipulate the index directly inside a relation adding the idx suffix to the list name The following example illustrates the use of the described features Example define list with offset relative to channel define list lt frequency gt fqlist 100 200 300 define list with absolute values 300 004 300 005 300 006 MHz define list lt frequency gt absfq O 300 4000 5000 6000 define list fro
94. U via RS232 It controls the different preamplifier modules and their signal routing The Acquire Menu P 74 Offset 01 8 Frequency SFO1 8 Square Power PLO 31 Reference Phase PHCORO 31 Receiver RG Fw Pulse PO 31 Delay D0 31 stop acquisition Figure 1 8 gs display Adjust parameter There are several possibilities to adjust a parameter Move the cursor onto the slider keep the left mouse button depressed and move the mouse along the scale The slider follows the cursor while changing the parameter value Move the cursor onto the scale and press the left mouse button The parameter value is incremented or decremented depending on the position of the cursor in relation to the slider position and the slider moves closer to the cursor Keeping the mouse button depressed results in a continuous parameter change In order to increase the stepsize of the increment decrement by a factor of 10 activate the sens 0 button The stepsize is decreased accordingly by a factor of 10 when the sens 0 button is activated Move the cursor onto the scale and press the middle mouse button The slider moves to the cursor and the parameter value changes accordingly 1 5 Setting up acquisition parameters P 75 e Enter the parameter via the keyboard If a parameter is entered that may not be varied within gs it is saved in its parameter file If it is an acquisition parame ter it will only become effect
95. Windows NT the default editor is Notepad 4 Execute the command config type it in or call it from the Acquire gt Spectrom eter setup menu config will display a menu of the required configuration steps Figure 1 1 By default all steps except for configuring a MAS or a BPSU unit are enabled If you click on the Start button the configuration commands will be executed in this sequence Whenever a step is complete you are invited to click on Continue to proceed or on Cancel to stop execution of the suite You may restart execution by clicking on Start Execution will begin with the first enabled command of the suite and skip all disabled commands Each step of the suite has a command name assigned given in brackets You may invoke a command directly from the key board Spectrometer configuration cf The purpose of cf is to make your spectrometer type and its hardware equipment known to XWIN NMR The program is capable of recognizing certain hardware components automatically others are asked for by cf The result of this configura tion process is saved in the file uxnmrpar located in the directory XWINNMRHOME conf instr lt name gt lt name gt is the instrument name defined during cf Acquisi tion commands will read the configuration parameters from these files It is there fore not necessary to invoke cf again if you terminate XWIN NMR and restart it However after installation of a new XWIN NMR version cf is mandatory If you
96. a factor given by the parame The Acquire Menu P 54 ter DDR digital digitizer resolution The total digitizer resolution which is the sum of the hardware resolution according to Table 1 18 and DDR is still character ized by DR DDR is related to DECIM according to DDR 2108 JDECIM 1 With DIGMOD digital or homodecoupling digital it is possible to use AQ_mod qsim or DQD digital quadrature detection but not AQ_mod qseq sequential data acquisition DR digitizer resolution Acquisition commands will normally set the digitzer to its maximum resolution the default of DR If you set DR to a smaller value acquisition will start with the modified setting DDR digital digitizer resolution For spectrometers equipped with digital filters Avance only For details see DIG MOD parameter DE pre scan delay in microseconds A waiting period between the last pulse and the begin of data acquisition digitizer start to avoid pulse feed through You may change DE by entering a new value DE includes the sections DE1 DE2 DEPA DERX and DEADC After DE1 the receiver gate is opened For AMX ARX type spectrometers the program calculates DE according to DE 1 4288 DW or half this value if AQ_mod qf DE1 and DE2 are constants For Avance type spectrometers you may change DE1 DE2 DEPA DERX and DEADC using the command edscon See edscon for details PHP preamplifier module selection AMX ARX type instruments only
97. ace Sie R EERS A 135 3 1 THtrOdUCHONS basa Nise mt Mi EEEE ES EAEE lel tea E te ie ti J A 135 3 2 Generate a new shape 0 2 eect teens A 136 3 3 Manipulate existing Shape 2 0 0 eee eee eee A 148 3 4 Analyze existing Shape 0 0 0 0 cece ccc cence A 154 3 5 The Interactive Display Command stdisp 0 002000 A 160 3 6 Examples cS eh eb ONG OS Lda Se tanec 8 E E Sided oe A 175 3 7 APPENDIX 333 255 as ae ike od Gags Oecd eae or ea Nee ead A 179 Chapter 4 Writing Pulse Programs cece cee cece cece reece ence A 181 4 1 Introduction eke eee Pere aad ition Vee gettin o Seen g A 181 4 2 Pulse program library 0 0 ee eens A 182 4 3 Pulse program display 0 0 0 e cee cece ete eee ae A 182 44 Basic syntax Tules ic raie este et auee oes Sap eee Root e ETRE dss A 182 4 5 Pulse generation commands 0 e cee eee tenet es A 186 4 6 Delay generation commands 0 e cee eee eee eee A 210 4 7 Simultaneous pulses and delays 0 00 e eee eee eee ee A 217 4 8 Decoupling a 5k Roose troce T a e Se tanh aE a e Shale Ra A 220 4 9 Composite pulse decoupling cpd 0 0 00 eee eee eee eee A 222 4 10 Loopcommands 00 cee cee eee ee A 228 4 11 Conditional pulse program execution 0 00 c eee eee eee A 230 _ 4 12 4 13 4 14 4 15 4 16 4 17 4 18 4 19 4 20 4 21 4 22 4 23 Commands to suspend the pulse program execution
98. ally using the edscon preset parameters They can also be generated manually which is useful if the command preset off has been used The gatepulse command will generate the transmitter blanking pulses the preamplifier blanking pulses and the ASU blanking pulses The syntax is delay gatepulse 1 I 2 Examples 3u gatepulse 1 generate blanking pulse for f1 p1 f1 d1 2u gatepulse 112 generate blanking pulses for f1 and f2 p1 f1 p2 f2 Printing messages The command print Hello World prints the message Hello World during runtime of an experiment The timing of the printout is not necessarily correlated to the execution of the pulse program because the TCU interprets the pulse program in advance of its execution However for debugging complex pulse programs it could be helpful
99. ameters similar to eda While the parameters appearing in the eda window are defined by the corresponding format file ased calls the pulse program compiler for the current pulse program PUL PROG and lets it determine which acquisition parameters are required Only those are displayed A description of the parameters is contained at the end of the pulse program deliv ered with XWIN NMR in the following way p1 f1 channel 90 degree pulse Such a description is taken over into the text field of the editor ased to facilitate the parameter editing For this purpose the description must follow the above conven tion The following parameters can be described in this way AVANCE Series e P0 31 DO 31 PLO 31 INO 31 INPO 31 LO 31 SPO 15 PCPD1 8 CNSTO 31 GPX0 31 GPY0 31 GPZ0 31 NBL AMX ARX ASX e P0 31 DO 31 INO 31 INPO 31 LO 31 HL1 4 S0 7 FSO 7 TPO 7 DPO 7 DBP0 7 TLO 15 SPO 15 NBL CNSTO 31 as works similarly but the parameters required by the pulse program are requested 1 5 Setting up acquisition parameters P 67 1 5 4 1 5 4 1 1 5 4 2 in form of a dialog Tuning the probehead wobb Introduction During the acquisition electric energy in form of pulses is transferred from the transmitter source to the probe drain As these pulses are in the radio frequency range it is vital that the output impedance of the transmitter is equal to the input impedance of the probe If the impedances do
100. ams if a cpd experiment is to be carried out i e if the pulse program contains commands such as cpdl cpd8 and cpds1 cpds8 They execute the cpd program given by the parameters CPDPRG1 CPDPRG8 the cpds commands differ from the cpd commands in that they will execute the cpd program synchronously with the pulse program The channel where a cpd com mand is to execute its associated cpd program must be specified behind the cpd command For example cpds5 f2 executes CPDPRGS5 on channel f2 in synchro nous mode If you click on the down arrow button right of the CPDPRG parameters a list of available cpd programs is displayed from which you may select one The list is created according to the contents of the directory XWINNMRHOME exp stan nmr lists cpd 1 5 Setting up acquisition parameters P 57 Initially after configuration of XWIN NMR is complete it contains Bruker s cpd programs You may add own ones with the command edcpd CPDPRG CPDPRGT CPDPRGB CPDPRG4 cpd programs AMX ARX type instruments with 3 channel interface MCD only These parame ters must contain the names of composite pulse decoupling cpd programs if a cpd experiment is to be carried out i e if the pulse program contains cpd type com mands The pulse program commands cpd and cpds execute the program CPDPRG cpds synchronously with the pulse program on the decoupler cpdt and cpdts exe cute CPDPRGT on the transmitter cpdb and cpdbs execute CPDPRGB on the s
101. an experiment with a single scan or slice This can be done setting the values of the parameters td 1 td 2 to 1 XWinNmr will recognize this and reduce the dimension of the generated dataset by 1 or 2 so that it can be processed as a 2D or 1D dataset without changing the PARMODE 4 18 Enhancements for the mc command For some 2D or 3D programs the simple loop wrapping the wr command is not sufficient To overcome this problem further loops can be nested in the F1 or F2 loop This is done specifying a number of inner loops in a FII F2I clause with its commands and loop counters E g in our little example from above d1 mc 0 to 1 FIQF id0 F1I ip3 2 id7 10 will expand to 133 td1 2 10 ze d1 0 333 d1 0 333 d1 0 333 pl d0 go 1 d1 0 333 wr 0 if 0 zd ip3 lo to 2 times 2 d1 0 333 id7 lo to 3 times 10 d1 0 333 idO lo to 4 times 13 AUNE Several loops can be defined in the form above Note that fractions of the delay of the mc command will be specified as delays The loop counter in the F1 loop will be calculated accordingly It is in the responsibility of the user however to make the loop counters divisors of td1 For the F2 loop F2I can be used in analogy To ease loop implementations a further loop FO can be inserted within the writing Writing Pulse Programs P 256 of the buffer Commands to be executed are specified in a FO clause In our exam ple from above d1 mc 0 to 1 FOGd9 F1QF id0 will
102. and FOQ F1PHO clauses need not be written on the same line but no other com mands must occur between them The order in which FO F1PH clauses occur is not important in 3D mode aqseq 312 will interchange the order of the F1 and F2 loop The pulse program must contain a ze command after the parameter definitions The symbol amp is expanded to a delay The table below shows which expansions will be done for different FAMODEs delay loop split incre delay inc into 2 mentdiv phase phaseinc in inner FnMODE loops by 2 reset inserted loop QF y QSEQ y y y y y TPPI v y y States Ni y V States y V TPPI EA y y Table 4 25 Results of use of different FnMODEs Writing Pulse Programs P 258 For those who need to go into details here some more explication The mc command is in fact some sort of macro in that sense that the text contain ing the mc command will at some step be expanded into a regular pulse program This pulse program can be visited in the pulseprogram file of the expno once the experiment has been started There are some things to consider when investigating the expanded pulseprogram MCWRK is the fraction of the delay with which the mc command is specified and which is calculated automatically MCREST is the difference between the delay of the label and the delay of the mc command recalculations of id0 id31 parameters are done after ze i e
103. and shaped pulses To account for the devia tion from a rectangular pulse a power correction value must be specified for shaped pulses The program expects this number in db in the correspond ing SP entry of the shaped pulse parameter table This example sp1 would fetch the correction value from entry 1 you could also enter the com mand sp1 on the keyboard to set the value Example 6 pulse auto pl2 p2 f2 ph4 Generate a pulse using a width defined by the acquisition parameter P2 and a power defined by PL2 This command is equivalent to p2 f2 ph4 except that the power PL2 is set and the flip angle can be inspected by the command ased 4 6 Delay generation commands 4 6 1 Table 4 4 shows the available types of commands for the generation of delays The duration of a delay is selected according to the name of the delay command d0 d31 The command do would execute a delay of width DO where DO is an acquisition parameter It is set from eda or by typing dO on the keyboard Likewise the command 4 6 Delay generation commands P 211 d0 dl 431 Generate a delay whose duration is taken from the oe acquisition parameter DO D31 respectively Generate a delay whose duration is taken from the acquisition parameter DO D31 and which is do r d31 r randomly varied according to the percentage specified in the acquisition parameter V9 A Sudom Oits G
104. anger operation with bar code reader This AU program moves the sample carousel to the next sample and reads the sample information from the bar code label The information is entered into the set up file the sample is inserted and the experiment executed A bar code con sists of the following components Experiment 2 digits Solvent 2 UserID 3 LabelID 5 Checksum 1 Example in decimal form 0 017 002 00001 9 Experiment Solvent UserID LabelID also appear in readable for on the label Experiment Code for the experiment to be performed 0 99 The code assigned to a par ticular experiment may be viewed with edexp This command displays a table of experiments allowed for bar code operation It may be adapted to The Acquire Menu P 100 d your requirements In order to restore the original table provided by Bruker type edexp new edexp displays its information from the file XWINNMRHOME conf instr barcode exp Solvent The solvent UserID Defines the USER parameter of the data set Remember that a the data set path is DU data USER nmr NAME EXPNO pdata PROCNO NAME is constructed from the first 5 characters of the name of the set up file fol lowed by the LabelID EXPNO is set to 10 for the first experiment with a sample 11 for the next experiment etc if any PROCNO ist set to 1 DU is defined in barcode_sx and may be changed there if required LabelID A label identification number created automatically w
105. annel Fx Filenames for a prosol parameter set are for example 1H F1 A2 1H F2 A2 13C F2 Al 13C F3 A5 The directory where the prosol parameter files are located depends on the selected solvents and the selected probe For all solvents the prosol parameter files are saved in lt XwinNmrHome gt conf instr spect prosol lt probe Id gt For individual solvents the prosol parameter files are saved in lt XwinNmrHome gt conf instr spect prosol lt probe Id gt lt solvent gt The button Copy to probe lets you choose one or more probes from a list The buttons Save to selected Solvents or Save to all solvents copy the defined prosol parameter sets to these selected probe heads as described above The button Print screen prints out the prosol parameter values standard hard standard soft also the user defined hard and user defined soft pulse and power lev els for the currently selected nucleus probe head and logical channel The getprosol Comand Any acquisition parameter P 0 P 31 PL O PL 31 D O D 31 SPNAMO SPNAM 16 can be set to the value of a prosol parameter using the getprosol com mand The relations file contains the assignment for the acquisition parameters and the prosol parameters Each line of the relations file has to end with a Each line assigns acquisition parameter to the prosol parameter of channel F x Here is a sample relations P 0 P9
106. ans that FCU no 1 is connected to amplifier no 2 1H 100 W standard RSEL O is unused If there are more than 3 FCUs a second router must be installed and the output 1 of the second router must be connected to input 3 of the first one Router 2 is used for FCUs no 3 5 If there are more than 5 FCUs a third router must be installed and output 1 of the third router must be con nected to input 3 of the second In this case RSEL 5 1 means that input 1 of the third router goes to output 1 of the first router via output 1 of 3 input 3 of 2 out put 1 of 2 and input 3 of 1 The graphical interface in edsp and edasp shows these connections in a simplified manner SWIBOX channel switching Avance only Some of the amplifiers contain fast switches which direct the output to the 1H module or to the X BB module or to the 19F module of the preamplifier These switches can be set by software with the parameter SWIBOX 1 15 If no such switch is installed SWIBOX n n XWIN NMR cannot guarantee however the correct connections between these outputs and the preamplifier modules PRECHAN preamplifier channel Avance only The connection to the preamplifier modules is described by PRE CHAN 1 15 If there is no preamplifier involved PRECHAN n 5 The order of the preamplifier modules is determined by their soft addresses 0 2H 1 X BB 2 1H 3 UserBox QNP 4 19F OBSCHAN observation channel 1 5 Setting up acquisition param
107. ard or be used in an AU program See also Euro therm unit command edte NBL number of buffers Used by pulse programs acquiring NBL fids in the memory of the acquisition processor before writing them to disk NBL is evaluated by the pulse program commands lo to x times nbl which performs this many loops ze zd wr if df st and st0 Normally NBL is 1 If you set NBL to a bigger value you may acquire up to NBL fids in memory limited by the equipment of the acquisition processor A buffer of the required size is reserved NBL TD ze and zd will clear the buffer stO will set the memory pointer where the next fid should be placed during acquisi tion to buffer start st will increment the pointer by TD wr will copy NBL fids from acquisition memory to disk in a ser file starting at buffer begin if and df will increment the file pointer in the ser file by NBL TD If TD is not a multiple of 256 1 5 Setting up acquisition parameters P 59 corresponding to 1024 bytes the buffer space for an fid is extended to become a multiple of 1024 bytes The pulse program commands decribed above will all work with the corrected buffer size The effect is that an fid always begins at a 1K byte block in acquisition memory as well as on disk PAPS phase cycling mode Only for AMX ARX type spectrometers The values cp ap and qp are legal They define in which way consecutive scans of an fid are handled cp adds them ap adds two scans and
108. are being used before the first pulse hits the probe For those of you still fond of the Led System acbdisp also configures the top part of the BSMS keyboard display where the cho sen amplifiers forward and reflected power values pulse type observed channel and mismatch leds may still be found The set of leds on the BSMS keyboard may also be configured using the acbbsms command which updates the display silently without starting up the acb display Amplifier Sampling The amplifiers are sampled at regular intervals between five and fifteen times per second user selectable from the Controls window This ensures that the worksta tion need only handle that amount of sampling necessary to achieve an accurate picture of the current experiment Should a fault condition develop the user is notified by means of the status display line showing the first major fault plus a list of all faulting amplifiers The XWIN NMR status line also gives notice of the fault In paused mode the amplifiers are still scanned once a second to check the respec tive amplifier status bits for a possible fault condition If everything is functioning correctly the Status line shows a standby status and may occasionly show blank meaning that specified transmitter is currently blanked The blank status is not a failure condition Controls The Controls pulldown menu provides access to acbdisp program itself as well as the ACB directly The scan rate push buttons control the
109. are or software 5 A semicolon indicates the beginning of a comment You can put it anywhere in a line Following its occurrence the rest of the line will be treated as a com 4 4 Basic syntax rules P 183 3zgcw30 savance version 1D sequence with CW decoupling susing 30 degree flip angle include lt Avance incl gt 1 ze d11 pl14 f2 d11 cw f2 2 d1 p1 0 33 ph1 go 2 ph31 wr 0 d11 do f2 exit phl 02201331 ph31 02201331 pl1 f1 channel power level for pulse default p114 f2 channel power level for cw hd decoupling p1 f1 channel 90 degree high power pulse d1 relaxation delay 1 5 T1 d11 delay for disk I O 30 msec 6 Table 4 1 Pulse program example ment include lt filename gt or include filename This command allows you to use pulse program text which is stored in another file in your pulse program It helps you to keep your pulse program reasonably sized and to re use the same code in other pulse programs By convention if the filename is given in angle brackets lt gt the file must be stored in the working directory XWINNMRHOME exp stan nmr lists pp Alternatively double quotes are normally used to specify the entire path name of the file to be included lze Any pulse program line may be preceded by a label 1 in this case You need Writing Pulse Programs P 184 to label only those lines which must be reached by loop or
110. ated by a space In Read Phase Slice modes the trim indices 0 1 2 as well as direct scale values of gradient points are displayed so that Read corresponds to the X direction Phase to the Y direction and Slice to the Z direction In general the program tries to display all numeric values centered inside their area If it is absolutely impossible to print them at least partly inside their area without overlap they are not printed at all The program does not support incre mentable delays pulses and loop counters variable lists hl1 hl4 fll fl4 sO s7 commands or multi oblique gradient experiments only the first slice of any multi oblique scan is displayed All drawings are made in the free scale Some ppgDisplay features may be available only in one of the XWIN NMR or ParaVision modes 2 7 BSMS panel bsmsdisp P 121 2 7 2 7 1 2 7 2 2 7 2 1 BSMS panel bsmsdisp Introduction Prerequisite Skills This description to the BSMS display tool version 1 0 is intended for users which are already familiar with the operation of the Bruker Smart Magnet Control Sys tem BSMS accessed by either the BSMS keyboard version HR 20 BOSS 1 or version BOSS 2 For any questions to the general operation of the BSMS please refer to the BSMS User Manual About the BSMS Display Tool The BSMS display tool is a user interface to the BSMS hardware Functions con trolled by the BSMS can be accessed and manipulated from
111. ation 1 dl Starting delay pl pulsing do waiting go 1 acquiring fid and loop for adding dl wr 0 write to buffer A 2D experiment results when some parameter per convention often dO is varied To make this a working 2D experiment quite a number of things must be done e increment the file pointer after each write e initialize the buffer after each write Writing Pulse Programs P 250 e increment the parameter d0 in each loop e adda loop outside the wr 0 command to a second label size is usually td1 e for phase sensitive acquisition add a phase increment When the second dimension is acquired not phase sensitive the resulting pulse program has the form ze dl pl d0 go 1 d1 wr 0 if 0 zd idO lo to 2 times td1 Ne A new command mc has been introduced to facilitate the tasks listed previously The mc command replaces the wr 0 command and has additional parameters for the delay increment and phase increment In the 1D sequence above only the line d1 wr 0 has to be replaced by dl mc 0 to 1 FIQF id0 When this sequence is executed with parmode 2D then the above 2D sequence is executed The way how to vary the delay is specified as argument to a FIQF clause The reason for this difficult syntax is that the main application for the mc command is simplifying phase sensitive acquisition The cosy sequence e g exists in different forms for phase sensitive acquisition cosytp cosyst cosysh Al
112. ave decoupling hd homodecoupling composite pulse decoupling with cpd sequence 1 8 cpds1 cpds8 synchronous mode composite pulse decoupling with cpd sequence 1 8 epdl cpd8 asynchronous mode do terminate decoupling Table 4 5 Decoupling commands Each pulse program line may contain one and only one decoupling command For example the line d1 cw fl would turn on cw decoupling on channel f1 at the same time that d1 starts The line go 2 cpds1 f2 would turn on composite pulse decoupling on channel f2 at the same time that fid 4 8 Decoupling p 221 4 8 2 4 8 3 detection starts Decoupling commands are legal in pulse program lines containing delay com mands or go but not in lines with pulses adc rcyc lo if and goto commands or expressions Decoupling will remain active until explicitly turned off with do e g 0 1u do f1 turn decoupling off on channel f1 Decoupling frequency The decoupling frequency is selected by specifying the spectrometer channel behind the decoupling command Omitting the channel is illegal For example dl cw f2 would turn on cw decoupling on channel f2 i e with the frequency SFO2 This syntax is the same as used for selecting pulse frequencies cf the section Pulse fre quency in this chapter The next example 0 1u cpds1 f3 would turn on the composite decoupling sequence 1 on channel f3 i e with the frequency SFO3 The final exam
113. be shown on the title bar earlier than in that time However if a dangerous increase of the temperature appears the preemphasis unit hardware should automatically switch the gradients off Entering the value of zero disables temperature measure ment The temperature measuring feature is unavailable for GREAT Rate to check error status enter how often in seconds the setpre module should check whether some error has occured in the preemphasis hardware It cannot be guaranteed that any error message from the preemphasis unit be shown in the error message field earlier than that time It follows that if several error messages come very rapidly after each other some of them may be lost while at least one of them namely the latter one is guaranteed to be displayed Entering the value of zero for this parameter disables the error checking feature Clear all preemphasis values set all preemphasis parameters for all channels to The Acquire Menu P 96 1 6 9 7 1 6 9 8 zero This could be used at the very start of the adjustment procedure to put the preemphasis unit in a well defined state The offset loop and impedance parame ters of the GREAT units are not cleared by this command The Channel pulldown The Channel pulldown is used to switch the setpre module to adjust another preemphasis channel All preemphasis parameters of the preceding channel are frosen before switching and cannot be recalled from memory or undone except f
114. because DE2 PHASPR FCUCHAN 1 is larger than DE DERX after this time the receiver RX22 RXC or SE451 is opened default is 2 0 us DEADC after this time the digitizer is unblanked default is 3 0 us For optimum spectrometer performance the following conditions should hold DEPA lt DE1 lt DERX lt DEADC DERX DE1 gt 1 2 us 1 3 The configuration suite config P 31 lg DE r gt DEPA preamplifier blanking DE2 receiver phase eer oe a DERX receiver blanking la DEADC digitizer blanking Figure 1 6 The DE delay 1 3 14 Avance frequency routing edsp edasp edasp is usually called from the NUCLEI button of the eda window but may also be invoked as a keyboard command In addition to nuclei setup the edasp window also shows the connections between the hardware parts of the spectrometer namely FCUs amplifiers routers high power modules and preamplifier modules This feature is only available for Avance type spectrometers Table 1 10 shows the available command buttons The Avance edasp edsp display is logically divided into several vertical parts Some elements may be connected with the elements of the next part by clicking on the corresponding two buttons The rules to be obeyed are described below Frequency The basic frequencies BF1 BF8 cannot be modified they correspond to the selected nucleus For spectrum referencing the para
115. ble XWIN NMR Offers the following possibilities of editing the nucleus table Changing the frequency Move the cursor onto a frequency value and depress the left mouse button A new number may be entered now The Acquire Menu P 8 1 3 1 3 Deleting a nucleus Move the cursor onto the name of a nucleus and depress the left mouse button ADD insert nucleus Move the cursor onto this command field and depress the left mouse button The file nuclei all appears on the screen and a nucleus can be selected It is inserted according to its mass number RESTORE Activate this command field if something failed during the edit session The nucleus table is restored entirely from the file nuclei all SAVE All changes are saved and the nuclei table disappears QUIT All changes are discarded and the nuclei table disappears The result ist stored in the file XWINNMRHOME conf instr lt instrument name gt nuclei and is required by the commands edasp edsp where the table is displayed to select a nucleus At the end a window appears presenting an overview of the spectrometer configu ration This overview is stored in the text file XWINNMRHOME conjf instr lt instru ment name gt uxnmr info and may be viewed or printed like any text file Related Files The text file XWINNMRHOME conjf instr curinst contains the instrument name as entered in cf All files used and created by cf reside in the directory XWIN NMRHOME conj instr lt in
116. ble 4 2 Pulse generation commands e power amplitude and shape e flip angle The following paragraphs will describe these items Pulse duration The pulse duration is selected according to the name of the pulse command p0 p31 The command pO would execute a pulse of width PO where PO is an acquisition parameter It is set from eda or by typing pO on the keyboard Likewise the command pl would execute a pulse of width P1 Writing Pulse Programs P 188 4 5 1 2 4 5 1 3 Fixed length pulses The command 10mp would execute a pulse of width 10 milliseconds called a fixed pulse because its duration cannot be further manipulated cf below The duration must be followed by up mp or sp These units indicate microseconds milliseconds and seconds respectively If you omit the terminating p a delay is executed rather than a pulse User defined pulses The command p30d1H would execute a pulse whose name is defined by the user and whose duration is determined by an arithmetic expression For example the line define pulse p30d1H would define p30d1H to be a pulse command and the line p30d1H p1 0 33 which must be quoted using double quote characters would constitute the expression for its duration The define line must be placed somewhere at the beginning of the pulse program before the beginning of the actual pulse sequence Note The defining expression of a user defined puls
117. buffers to the file ser of the current data set For ser files Start writing into the file at the current position of the disk file pointer which initially is at the beginning of the file wr 1 wr 2 wr 3 Transferring is performed to the file fid or ser belonging to the data set with the number 1 2 3 contained in the data set list given by the acquisition parameter DSLIST wr Transferring is performed to the file fid or ser of the data set which is pointed to by the data set list pointer Its initial position is one item before the beginning of the data set list DSLIST where the current data set is made available The list pointer can be incremented by 1 decremented by 1 or reset to list begin using the commands ifp dfp and rfp respectively if 0 if 1 if 2 Advance the disk file pointer for ser files by TD NBL remember that TD is rounded to the next multiple of 256 data points if it is not a multiple of 256 df 0 df 1 df 2 Decrement the file pointer inverse of if rf 0 rf 1 rf 2 Reset the file pointer to the beginning of the ser file rf 0 m rf 1 m rf 2 m Set the file pointer to position m TD NBL of the ser file where m is an integer number Table 4 24 Writing acquisition buffers to disk Writing Pulse Programs P 248 disk files The name of the output file is fid or ser An fid file contains a single
118. calcsuspend stop precalculation and stop execution on command calcautosuspend stop precalculation and stop execution always Table 4 15 Commands to suspend pulse program execution Commands to start data acquisition XWIN NMR provides 5 basic pulse program commands to start data acquisition go label gonp label gosc goscnp adc The most commonly used command is go abel It is a macro command i e it includes a number of different actions required for successful data acquisition adc allows you to control any fine detail of the acquisition process All three acquisi tion commands place the digitized signal into a memory buffer but do not store it on disk The wr command described in a later section is provided to write the buffer contents to disk The commands go label gonp label gosc goscnp The left column of Table 4 18 shows a simple example of how to use go label in a pulse program All go type commands perform the following actions A parallel sequence of 5 different pre scan delays are executed cf the description of DE1 DE2 DERX DEPA DEADC in the chapter The Acquire Menu Note that all delays start simultaneously The sequence in which the actions are performed depends upon the length of the individual delays 1 At the end of DEPA preamplifier blanking delay the preamplifier is switched to observe mode 2 At the end of DERX delay for receiver blanking the receiver gate is opened 3 At the end of DEI
119. can in the Stop entry field Please note that if any FCU channel is enabled in the Observe setup table the contents of the Start entry will be ignored and simula tion will always start at time zero equivalent to the first scan number You may use negative numbers for the scan number This will cause the simulation of dummy scans if specified in the acquisition parameter set If you want to simulate just the first scan of an experiment enter 0 for Start and 1 for Stop You are now ready to click on the Run simulation button Note that if you change acquisition parameters or the pulse program you have to quit the pulse program display and restart it Just running the simulation again is not sufficient Simulation time depends on the selected time or scan interval usually a few seconds for a small number of scans If you are doing FCU simulation and if you are using a pulse program that changes the phase very frequently e g a pulse program with a CPD sequence the simulation time can be very long and it is also possible that the memory limit is exceeded or the graphic gets too large and will be truncated an error message will appear if this happens After running the simulation the actual pulse program display window Figure 2 4 is opened containing all the channels selected in the Observe setup You may disa ble or re enable selected channels from the Setup display button without modify ing the Observe setup The Zoom in button allows you
120. ce to which the sample changer is connected Device for BACS unit tty08 The RS232 device configuration is stored in the file XWINNMRHOME conf instr lt instrument name gt rs232_device bacs If the spectrometer is equipped with a sample changer then cfbacs asks whether the sample changer or the BSMS should control the LIFT function Should the Sample Changer control the lift no Finally the delay between the change sample command sx and the next command frequently ro turn sample rotation on must be specified to allow for the sample to settle in its position Delay between SX and next command sec 10 Typical values are 5 to 30 seconds depending on the magnet cfbacs then connects to the sample changer to get the number of sample holders This number is stored in the file XWINNMRHOME conf instr lt instrument name gt bacs_params 1 3 4 Setting up the solvent table edsolv Use this command to set up a table of the solvents you intend to use for your NMR experiments It is a configuration command which should only be executed by the administrator edsolv opens a dialog window where you may add change or delete lines by clicking on the corresponding button New entries must get assigned an The Acquire Menu P 14 1 3 5 arbitrary but unique reference number A typical entry in the table looks like the following Acetic Acetic Acid D4 02 The reference number must be specified in brackets It is used for i
121. ci fied in two adjacent lines are executed sequentially Actions specified within the same line are started simultaneously and execute in parallel 10 2 dl Execute a delay whose duration is given by the acquisition parameter D1 This line is preceded by the label 2 which is where the command go 2 loops back to 11 p1 0 33 ph1 Execute a pulse on frequency channel f1 whose duration is given by the acqui sition parameter P1 multiplied by 0 33 For convenience P1 is often used to hold the pulse width for a 90 degree flip angle The command p1 0 33 would 4 4 Basic syntax rules P 185 then execute a 30 degree pulse In general you may specify the operator behind not before a pulse or delay command followed by a floating point number Please note that the channel f1 does not occur explicitly If no channel is given fl is assumed and the command p1 0 33 is identical to p1 0 33 f1 The pulse is executed with a power amplitude defined by the acquisition parameter PL1 PL1 is the default power level for channel f1 but you may also use a different parameter For example the command pl7 f1 would set the chan nel f1 power from the parameter PL7 You would not specify however this command in the same line as p1 0 33 but previously along with a delay in order to give the transmitter time to settle before the pulse is executed The phase of this pulse is selected according to ph1 with ph1 being the name of a phase program or
122. d after NS scans are complete Using the command tr transfer you may force the soft ware to write the accumulated data on disk for processing or plotting before acqui sition terminates And this is the difference between zg and go If your current data set already con tains acquisition data a file fid or ser from a previous acquisition zg will over write them and they are lost This is done silently if the system variable ZGsafety is set to no Otherwise a warning is printed and you may prevent acquisition start Enter the command setres or call User interface from the Display gt Options sub menu to set this variable accordingly In contrast to zg the command go will add the acquired data to an already existing fid or ser file It is dangerous however to continue an experiment with go interrupted with stop or halt which terminate acquisition immediately or after the current scan respectively This could occur in the middle of a phase cycle or a nD delay increment loop In order to interrupt acquisition at a well defined position of a pulse program the pulse program com mand suspend see Chapter Writing Pulse Programs is provided The keyboard command suspend will halt the pulse program as soon as it encounters the pulse program suspend statement and resume acquisition there when the command resume is typed in The command run Run starts a series of experiments You may enter run as soon as you have defined at least 1 expe
123. d on the button itself there s no space left on the button but in two value fields in the lower part of the control panel The two display fields show the current and old function value With additional control elements this value can be changed refer to chapter 2 7 3 7 for changing function values Toggle and value functions cannot be distinguished on the panel directly there s no visual difference between these two classes of buttons This knowledge must come out of your experience Function Buttons Toggle Functions Value Functions Figure 2 12 Toggle and Value Functions Figure 2 12 shows the Sample panel with its five function buttons LIFT ON OFF SPIN ON OFF and SPIN CALIB are toggle functions whereas the first and third currently is turned off and the second SPIN ON OFF turned on indi cated by a highlighted button SPIN RATE and SPIN MEAS in turn are value functions SPIN RATE currently is highlighted as its value is displayed in the two value fields 1 Depending on the current color setup The Windows Menu P 126 2 7 3 4 Toggle On Off Functions 2 7 3 5 A toggle function is a function with two states turned on and turned off The state of a toggle function is indicated on the corresponding button itself a but ton with a bright color represents a function turned on whereas a dark colored button a function that is
124. dentifying the solvent on a barcode label when a barcode controlled experiment is performed e g using an automatic sample changer equipped with a barcode reader In order for such experiments to be executed properly we recommend not to change the num bers any more once assigned to a particular solvent Initially edsolv displays a solvent table suggested by Bruker from the text file XWINNMRHOME exp stan nmr lists solvents all If you apply modifications to the table and then exit via the SAVE button the mod ified table is stored in the file XWINNMRHOME exp stan nmr lists solvents Now the file solvents has been created and future invocations of edsolv will dis play this file containing your personal settings In order to define a solvent for an experiment type eda eda is described further below in this chapter and in the up coming dialog window click on the down arrow button right of the SOLVENT parameter The solvents file is displayed and you may select a solvent from the table SOLVENT is evaluated by the commands prosol lock acqu sref and lopo and during quicknmr and run For the latter two applications the acquisition parameters are obtained in the following way They are initialized with the parameters of the specified experiment The probe head and solvent dependent parameters see command prosol are then inserted according to the setting of SOLVENT and the current probe head see next section Finally any param
125. der changes i e reset back the values which were just after switch ing to this preemphasis channel or after startup of setpre if no channel was switched yet Clear set all three Gain sliders to zero to begin adjusting the channel from a well defined state Important notes 1 Neither Recall nor Exchange is possible if nothing has been Stored after switch ing to this channel or after startup 2 Undo is possible only after something has been changed for this channel 3 Important One has to distinguish between the Store and Recall actions which operate only on the current preemphasis channel and in the computer memory The Acquire Menu P 94 1 6 9 5 NOT on the disk and the File gt Write and File gt Read which influence all the preemphasis parameters for all the channels and operate on the disk files also clearing the Store Recall and Undo states 4 Very important Note that these five buttons only influence the current preem phasis channel and are immediately forgotten after switching to another one The File gt Cancel and Edit gt Clear commands influence all preemphasis values and channels and are always in effect The File pulldown Read default read preemphasis parameters from the default file and load them into the preemphasis unit The default file is exp stan nmr parx preemp lt CUR HEAD gt default where lt CURHEAD gt is current probehead number defined by the edhead command If no probehead
126. domain size Defines the number of data points of the fid For data set dimensions bigger than 1 TD for F1 and F2 usually specifies the number of increments It may be used in pulse programs e g by the pulse program commands lo to x times td1 or lo to x times td2 Enlarging TD will give a better resolution of the fid see parameter FID The Acquire Menu P 48 RES and hence the spectrum at the expense of a longer scan time AQ PARMODE dimension of acquisition data ID 2D or 3D Specifies the type of data to be acquired If you change PARMODE to a smaller dimension unnecessary parameter files are deleted If you switch to a higher dimension the required additional parameter files are fetched from the directories XWINNMRHOME exp stan nmr par standard2D or XWINNMRHOME exp stan nmr par standard3D Existing acquisition data are deleted after approval by the user NS number of scans Defines the number of accumulation loops the pulse program commands go n and rcyc n should perform DS number of dummy scans Defines the number of loops the pulse program command go n should perform without digitizing and accumulating data before continuing with NS true scans Used to get steady state conditions D0 D31 delay parameters in seconds 32 duration parameters to be specified in seconds They are executed as delays without any further actions by the pulse program commands d0 d31 In Bruker pulse programs D1 is most often us
127. done according to BLKTR RSEL FCUCHAN channel TGPPA 1 5 Preamplifier blanking pulses They are generated on the TCU word 3 Bits 8 12 together with the transmitter gating pulses TGPCH 1 8 prolonged at the beginning by the times BLKPA 1 5 Routing is done according to BLKPA PRECHAN SWIBOX RSEL FCUCHAN channel The routing according to PRECHAN is done by selecting the preamplifier module HPPR via RS232 at the beginning of the experiment and cannot be changed afterwards The routing according to SWIBOX is done with the switches SELH H F NMR2 Bit 2 and SELX X F NMR2 Bit3 This can be changed at runtime BLKPA L1 5 The blanking of the 5 preamplifier modules may be switched on a time t2 before the pulse PHASPR 1 8 phase presetting The switching of the phase programs may be done a time t3 before the pulse in order to ensure a stable phase when the pulse begins SHAPPR 1 8 shaped pulse presetting The propagation time of the phase versus the amplitude may be taken into account by setting SHAPPR t4 This value should be equal or larger than 1 4 usec Other wise the shaped pulse itself will be delayed by this time Please note At the end of each shaped pulse the power is reset to its default value e g for channel 1 pl1 and as consequence of this power setting the phase correc tion corresponding to this power is set as well If the shaped pulse is terminated before this setting has taken place because
128. dow appears promting for the number of off resonance frequencies encoded in the shape If the answer is 0 the A AT factor is determined automatically otherwise a value should be entered in the second field To save the shape in new JCAMP DX format use the command Save As For writing gradient files the commands Save Gradient and Save Gradient As are available For reading gradient files change the path to shape directory in the Options menu to XWINNMRHOM E exp stan nmr lists gp then use the Open command to open a file selection box and specify a file name The Shape Tool P 162 In order to save a fraction of a shape use the commands Save Fraction and Save Fraction As Figure 3 2 File Selection Box 3 5 2 The Split Menu The Shape Tool allows to split the display window in several subwindows The active window s is are surrounded by a blue frame You can activate one sub window by clicking on it with the left mouse button To activate all subwindows use the menu entry Select all To split a window hori zontally or vertically use the corresponding menu entries Split horizontally and Split vertically To return to single window display use the menu entry Remove The splitting of the display window may also be done interactively by dragging the blue frame with the left mouse button depressed to any position within the window 3 5 The Interactive Display Command stdisp P 163 3 5 3 The Sha
129. dth for Refocusing My fbandw2ry Special Bandwidth Calculations Calculate gammaB imax fealebimo Calculate gammaB imax for Adiabatic Shapes feaicbhtadia Calculate average Power Level fcalcpav integrate Shape fintegr3 integrate Adiabatic Shape fintegradia Simulate l Figure 3 5 The Analyze Menu 3 5 4 1 Bandwidth Calculations Bandwidth calculations for excitation bandw2 inversion bandw2i and refocus ing bandw2r shapes are available The resulting Bandwidth Factor Aw AT is dimensionless and can be used to calculate the bandwidth A of a pulse or the pulse length AT for the corresponding excitation region The Bandwidth Factor for a 90 degree Gaussian shape Figure 3 6 is 2 122 For a pulse length of 10000 usec results a width of excitation A of 212 2 Hz A little calculator is implemented in the Results Window Enter A and AT is calculated or vice versa The Update Parameters button will store the length of the shaped pulse The Shape Tool P 166 3 5 4 2 bandw2 DeltaOmega Deltal factor using transverse magn Calculator DeltaOmega in Hz DeltaT in usec Figure 3 6 Results from Bandwith Calculation The bandwidth is measured at the 3 dB point i e the point where the amount of magnetization has dropped to 70 8 In the case of excitation transverse magnetization V Mx Mx My My is evalu ated Separate routines are available for inversion and refocussing pulses looking at M
130. e analog filters on the HRD16 external box during measurements with the FADC For this kind of application the RXC must not be defined in the hardware list file and the acquisition parameter SEOUT must be set to BB Layout of serial device connectors All serial devices on the spectrometer are located at the ccu e The RS232 device tty00 is located on the CCU frontpanel and may be used by a console terminal During the boot procedure all messages are printed to this device It is therefore not allowed to connect any spectrometer unit to this device e There is a connector panel above the CCU equipped with 9 RS232 and 2 RS485 devices The 9 RS232 devices correspond to tty01 tty09 the RS485 devices correspond to tty10 and tty20 Note 1 On all CCU s prior to ECL20 tty08 and tty 0 and respectively tty09 and tty20 may only be used alternatively as these devices are connected to the same port On CCU s with ECL20 or higher this restriction does not apply Note 2 If the spectrometer is equipped with an AQS rack then the RS485 1 Communication Control Unit 1 3 The configuration suite config P 11 devices are not connected to the connector panel Instead tty 0 is connected to the connector HPPR at the ACB S or PSD and tty20 is connected to the con nector SBS BUS CH2 at the ACB S or ACB X If more devices are needed it is possible to add up to 4 SIB s Each SIB is equipped with 6 RS232 devices CH1 CH6 which correspond to
131. e aware that you should use ICON NMR for routine spectroscopy based on standard experiments and for automation using a sample changer ICON NMR is described in its own manual set run and quicknmr serve the same purpose but are historically older They are just maintained for compatibility reasons e quicknmr Easy routine execution of experiments e Displaying the lock and fid window The Acquire Menu P 98 1 7 1 1 7 2 The commands zg go tr halt stop suspend and resume Both the zg and the go command compile the current pulse program PULPROG and the acquisition parameters set up with eda or ased as gs The compiled out put is loaded into the acquisition processor and the pulse program is started The acquired data are written to disk according to the wr statements in the pulse pro gram The most frequently used wr statement is wr 0 Each time it is encountered in the pulse program the acquisition data are stored on disk in the file fid or ser depending on the type of pulse program of the data set from where zg or go was started Acquisition runs in background and you may switch to another data set and process or plot it while the experiment is in progress Alternatively you may enable the Observe fid window and look at the fid or for 1D experiments at the transformed fid in real time Acquisition may also be started from the Observe fid window In 1D pulse programs the wr 0 statement is often placed at the en
132. e cag_par the rotation and scaling is done as specified in this file Example 0 5 Scaling of 1st or read dimension 0 5 Scaling of 2nd or phase dimension 0 8 Scaling of 3rd or slice dimension 4 23 Miscellaneous commands P 267 1 0 0 0 0 0 Scaling of 1st read or x dimension 0 0 1 0 0 0 Scaling of 2nd or y dimension 0 0 0 0 1 0 Scaling of 3rd or z dimension 1 0 0 0 0 0 lst rotation matrix 0 0 1 0 0 0 0 0 0 0 1 0 0 707 0 707 0 0 2nd rotation matrix 707 0 707 0 0 the 1st and 2nd dimensions are rotated by 0 0 0 0 1 0 45 degrees Table 4 26 example of a cag_par file In this case you can acquire 2 slices with different orientation Like function indi ces you can manipulate slice indices with the commands zslice islice dslice sslice rslice 4 23 Miscellaneous commands 4 23 1 Switching on off of Presetting of Blanking Pulses preset The presetting of blanking pulses can be switched off by the command preset off at the beginning of the pulse program The generation of blanking pulses before the pulse itself is then switched off i e the program will behave as if all preset param eters command edscon would have been set to 0 The preset off command must be written at the beginning of the pulse sequence and cannot be changed after wards Writing Pulse Programs P 268 4 23 2 Generation of Blanking Pulses gatepulse 4 23 3 Blanking pulses are usually generated automatic
133. e in dB power relativ to a square pulse of 100 3 4 8 command integr3 integrate shape and calculate power level compared to hard pulse Syntax st analyze Gauss integr3 lt pulDurShape gt lt pulDurHard gt lt totRot gt double lt pulDurShape gt length of shaped pulse in us double lt pulDurHard gt length of reference hard pulse in us double lt totRot gt total rotation in degree Example st analyze Gauss integr3 10000 6 6 180 Result integral ratio compared to a square pulse of 100 Flip angle not evaluated corresponding difference in dB Flip angle not evluated change of power level compared to level of hard pulse in dB 3 4 9 command integradia integrate adiabatic shapes Syntax st analyze lt adiabatic shape gt integradia_ lt pulDurShape gt lt pulDurHard gt double lt pulDurShape gt length of shaped pulse in us The Shape Tool P 158 double lt pulDurHard gt length of reference hard pulse in us Example st analyze SmoothedChirp integradia 10000 8 Result sweep rate on resonance in Hz sec B1 max 2n V Q 3 4 10 commands no longer listed in pulldown menu of stdisp 3 4 10 1 command integr Integrate shape and compare to square integr needs no additional parameters Example st analyze Gauss integr Result integral ratio compared to asquare pulse of 100 corresponding difference in dB 3 4 10 2 command integr2 Calcula
134. e must occur before the actual start of the pulse sequence It is evaluated at compile time of the pulse program not at run time Legal names for user defined pulses consist of alphanumeric char acters where the first character must be an alphabetic character The maximum length of the name is 11 characters Of course it must not be identical to any of the reserved words like adc go pulse etc 4 5 Pulse generation commands P 189 4 5 1 4 4 5 1 5 Variable list pulses The command vp executes a pulse whose duration is given by the current value of a pulse list A pulse list is a text file containing one pulse duration per line Pulse lists are set up with the command edlist described in the chapter The File Menu The command vp uses the list file given by the acquisition parameter VPLIST When the pulse program begins the first duration in the list is valid The pulse program command ivp can be used to advance the list pointer to the next duration If the end of the list is encountered the pointer is reset to the beginning The command ivp must be specified behind a delay for internal reasons Examples dl ivp 0 1u ivp The delay length is not important any small or large duration is legal It is also possible to calculate the list position by means of an equation Example vpidx 5 vp The command vp will execute a pulse whose duration is selected from position 5 of the pulse list At the right of the e
135. e problems because the slider changes RG linearly although RG has an exponential effect With small RG values espe cially the slider is too sensitive Use any of the other methods mentioned above to change RG by a small value The Acquire Menu P 76 1 5 5 2 gs on AMX ARX ASX spectrometers As soon as gs has been activated the information window displays the parameter O1 its current value along with its range of values the mouse sensitivity and the fid integral Adjust parameter Move the cursor onto the modify button keep a mouse button depressed and move the mouse up or down Fine ajustment may be achieved via the left mouse button coarse adjustment via the righthand button The middle button has an intervening sensitivity Alternatively all parameters which may be varied within gs as displayed in the select window can be entered via the keyboard If a parameter is entered that may not be varied within gs it is saved in its parameter file If it is an acquisition parameter it will only become effective after gs has been stopped and restarted All changed parameters except RG will become active at the earliest with the next scan while RG itself will become active immediately Select new parameter to modify Activate the select button A dialog window is opened containing all parameters that may be varied within gs Use the mouse cursor to select the desired one Cer tain parameters pulses delays require an index e g 5
136. e to be modi fied accordingly The desired shapes may be defined by typing the shape type in the input field By clicking on the Arrow Button right oft the shape field a selection box with all allowed shapes is opened Figure 3 12 3 5 The Interactive Display Command stdisp P 173 Figure 3 12 Selection Box for Shape Type Clicking on the desired shape will fill the input field automatically Fig 3 11 Click the OK button to start the calculation of the shape If you want to update parameters in an XWIN NMR experiment click the Update Parameter button Then the length and the power level of the shaped pulse as well as the name of the shape are stored in the parameter set of the current experiment The relation between Shape Tool parameters and XWIN NMR parameters are defined using the Options Menu 3 5 5 3 Further Manipulation commands e Single Sine Modulation sinm2 Calculates an amplitude modulation such that the pulse excites at two symmet ric sidebands offset with opposite phase The Shape Tool P 174 Single Cosine Modulation cosm2 Calculates an amplitude modulation such that the pulse excites at two symmet ric sidbands offset with same phase Linear Sweep sweep Calculates a phase modulation according to a linear frequency sweep Const Adiabaticity Sweep caSweep Calculates a phase modulation according to a constant adiabaticity sweep Power of Amplitude power Calculates power of amplitude
137. e valid in pulse programs 1 Pulses and delays specified on subsequent lines are executed sequentially 2 Pulses and delays which are specified on the same line and which are enclosed in the same set of parentheses are executed sequentially 3 Pulses and delays which are specified on the same line and which are enclosed in different sets of parentheses are executed simultaneously The first item within a set of parentheses is started at the same time as the first item in the other parentheses You may specify an arbitrary number of sets of parentheses on a line Writing Pulse Programs P 218 4 7 2 4 7 2 1 4 7 2 2 4 7 2 3 Examples Rule 1 The pulse program section p1 ph1 f1 100u p2 ph2 f2 would execute a pulse on channel f1 followed by a delay followed by a pulse on channel f2 Figure 4 1 fl p1 _100u f2 p2 Figure 4 1 Rules 1 and 2 An example Rule 2 The pulse program section p1 ph1 100u f1 p2 ph2 f2 would as shown in the example above execute a pulse on channel f1 followed by a delay followed by a pulse on channel f2 Figure 4 1 Rule 3 The pulse program section p1 ph1 f1 100u p2 ph2 f2 would execute a pulse on channel f1 At the same time the 100u delay would 4 7 Simultaneous pulses and delays P 219 begin since it is enclosed in a separate set of parentheses The pulse on channel f2 would not be executed before either p1 or 100u are finis
138. ec ond decoupler cpd4 executes CPDPRG4 on the fourth channel requires a special hardware equipment If you click on the down arrow button right of the CPDPRG parameters a list of available cpd programs is displayed from which you may select one The list is created according to the contents of the directory XWINNMRHOME exp stan nmr lists cpd Initially after configuration of XWIN NMR is complete it contains Bruker s cpd programs You may add own ones with the command edcpd GRDPROG gradient program Requires Avance or AMX ARX type instruments with 3 channel interface MCI This is the name of a gradient program which must be located in the directory XWINNMRHOME exp stan nmr lists gp It is executed by the pulse program command ngrad See also edgp command For Avance type spectrometers we recommend to use the pulse program commands gron groff for gradient control and the gp pulse option for shaped gradients which are more convenient LOCNUC lock nucleus Must be set to the desired lock nucleus before invoking the edlock command which sets up the lock parameters for this nucleus SOLVENT solvent Must be set to the solvent used in the current sample SOLVENT is evaluated by the commands prosol lock acqu sref and lopo and during quicknmr and run For the latter two applications the acquisition parameters are obtained in the following way They are initialized with the parameters of the specified experiment The
139. ecification after the command is not nec essary in CPD programs Frequency Setting from Lists The first method is to use a frequency list The commands fql fq8 corresponding to the frequency list parameters FQILIST FQ8LIST set the frequency from the next list item thereby advancing the list pointer to the next item In contrast to the pulse program the list assignment is done at compile time not at run time In the following example the frequency setting at the first fq1 statement uses the first item of the frequency list the next command the second item If the program loops back to label 1 and the frequency list contains more than 2 items nevertheless dur ing the next execution of the loop the frequency will be set from the first 2 list items Like in pulse programs the frequency offset can be specified in two ways either the offset is at the to of the list in MHz or no offset is specified in the list In this latter case the measure frequency of the appropriate channel SFO1 for F1 SFO2 Writing Pulse Programs P 228 for F2 etc is used as list offset 4 9 4 2 Frequency setting using the parameters CNSTO0 31 The command fq cnst25 will set the frequency SFO1 CNST25 Hz The param eter CNST25 can also be modified during gs If used on channel F2 the basic fre quency SFO2 instead of SFO1 will be used etc 4 9 4 3 Direct Specification of Frequencies The command fq 3000 will set the frequency SFO1 2 3 3000 Hz 4 1
140. ecute the following sequence of commands to prepare XWIN NMR for data acquisition Some of the commands will request the NMR superuser pass word XWIN NMR uses the concept of an NMR superuser This is a normal system user who was defined to be the NMR superuser by the system administrator If an NMR superuser is defined commands such as cf will prompt for the pass word of the NMR superuser otherwise for the root password An NMR superuser may be set up or changed using the NMR user manager of ICON NMR Please check the ICON NMR manual In addition the NMR superuser may also be entered at installation time of XWIN NMR The command cfpp requires the root password since it modifies the system file 1 3 The configuration suite config P 3 1 3 1 etc inittab 1 Create a user id on your computer for anyone who should be allowed to start up XWIN NMR Invoke the respective operating system user manager tool for this purpose 2 Define a data set You may either select an existing data set using the command search the commands of the File gt Open menu or create a new one with the File gt New command 3 Some of the configuration commands display a text file requiring changes Exe cute the command setres and set the system variable Editor to the name of your preferred text editor e On Unix systems the default editor is xedit provided by the X Windows system On SGI computers the editor jot is preferred by many users e On
141. ed as a relaxation delay and DO and D10 as incrementable delays for 2D and 3D experiments although any delay may be incremented or decremented using the pulse program commands id0 id31 or dd0 dd31 respectively The changes are given by the parameters INO IN31 The pulse program commands rd0 rd31 reset a respective delay to its original value On Avance systems delays may also be changed by means of arithmetic expressions during pulse program execution P0 P31 pulse length parameters in microseconds 32 duration parameters to be specified in microseconds They are executed by the pulse program commands p0 p31 which execute a pulse on the specified channel during the respective duration parameter In Bruker pulse programs P1 is most often used as a 90 degree pulse Pulses may be incremented or decremented by the pulse program commands ipu0 ipu31 or dpuO0 dpu31 respectively The changes are given by the parameters INPO INP31 The pulse program commands rpu0 rpu31 reset a respective pulse length to its original value On Avance systems 1 5 Setting up acquisition parameters P 49 pulses may also be changed by means of arithmetic expressions during pulse pro gram execution NDO ND10 number of delays DO or D10 Number of d0 and d10 commands in the increment loops of a pulse program for 2D or 3D experiments Used to calculate the sweep width for the F1 and F2 dimen sions according to SW F1 1 SFO1 NDO INO SW F2 1 SFO1 ND10
142. edhead window without storing changes DELETE Table 1 5 Command buttons in edhead dialog window 1 3 6 Solvent probe depend paramters edprosol getprosol These parameters are required to run a series of experiments using ICON NMR Routine Spectroscopy and Automation or by the PROSOL function of the command eda If the values are not known at this time you may skip the command for now and invoke it at a later time ICON NMR Routine Spectroscopy and Automation are designed to run experiments based on standard parameter sets provided by Bruker or set up by your system administrator If one of these commands is active the acquisition parameters for the experiment are obtained using the following sequence 1 They are initialized with the standard parameters of the selected experiment 2 Parameters depending on the probe head and solvent are inserted according to the current probe head and to the setting of the SOLVENT 3 Finally any parameter changes the user requested are applied The purpose of edprosol and getprosol is to set up the parameters used in step 2 1 3 The configuration suite config P 17 1 3 6 1 The Prosol Parameter Set The prosol parameter set contains the parameters for the standard hard pulses standard soft pulses for the user defined hard and for the user defined soft pulses and the global pulses
143. el Layout When the tool is started the first time after a new display tool installation the panels pop up at default positions on the screen which can be customized individ ually If you wish the display tool to place the panels at your customized positions on the screen on start up use the Save Layout command from the Options pulldown menu of the main panel Calling this command saves the current panel positions so the panels must be placed correctly before the command is issued Save Function Sensitivities Using the button to change the current function value needs the step size a value which is added subtracted when this button is pushed the same is true for the slider We saw earlier that the step size can be compared to a kind of sensitiv ity by which the function value is changed The button held down with a larger step size changes the function value faster in bigger steps Step Size Slider Button 2 2 Button Figure 2 15 Step Size 2 7 BSMS panel bsmsdisp P 133 2 7 4 5 2 7 4 6 To save all function sensitivities use the Save Function Sensitivity entry from the Options pulldown menu in the main panel When restarting the display tool you should find again your saved sensitivity values Setup Colors 5 different colors are used by the display tool which can be set up individually A color for 1 the background of all panels 2 t
144. enerate a delay of fixed length u a microsecond delay m millisec s sec Generate a delay whose name is defined by means compensationTime of a define delay statement and whose duration is defined by an expression vd Generate a delay whose duration is looked up in a delay list del de2 de depa derx Generate a delay of length DE1 DE2 DE DEPA deadc DERX DEADC respectively dw dwov Generate a delay of length DW DWOV aq Generate a delay of length AQ Table 4 4 Delay generation commands dl would execute a delay of width D1 4 6 2 Random delays The command do r would execute a delay of width DO which is varied randomly within a percentage as specified in the acquisition parameter V9 It is set from eda or by typing v9 on the keyboard Please note that during gs the randomization is disabled Writing Pulse Programs P 212 4 6 3 Fixed length delays The command 10m would execute a delay of 10 milliseconds called a fixed delay because its duration cannot be further manipulated cf below The duration must be followed by u m or s These units indicate microseconds milliseconds and seconds respectively 4 6 4 User defined delays 4 6 5 For example the line define delay compTime would define compTime to be a delay command and the line compTime d1 0 33 which must be quoted using double quote characters would constitute the expression for its duration
145. enerated int lt size gt shape size in number of points double lt cycles gt number of cycles to calculate double lt window size gt window size in e Example st generate CosSinc 1000 4 50 e Literature G J Galloway W M Brooks J M Bulsing I M Brereton J Field M Irving H Baddeley amp D M Doddrell J Magn Reson 73 360 368 1987 3 2 Generate a new shape P 147 3 2 5 2 Sine Sinc Shape Syntax st generate SineSinc lt size gt _ lt cycnum gt int lt size gt shape size in number of points int lt cycnum gt number of cycles to calculate Example st generate SineSinc 256 8 If only amplitude data are needed The call is st generate SineSinc 256 false 8 Literature D M Doddrell J M Bulsing G J Galloway W M Brooks J Field M Irving amp H Baddeley J Magn Reson 70 319 326 1986 3 2 6 Special Shapes for Decoupling 3 2 6 1 Swirl Shapes Syntax st generate lt shape type gt _ lt size gt int lt size gt shape size in number of points The following Swirl lt shape types gt are implemented Swirlll Swirll2 Swirll7 Example st generate Swirll1 256 If only amplitude data are needed The call is st generate Swirll7 256 false Literature H Geen amp J M Boehlen J Magn Reson 125 376 382 1997 The Shape Tool P 148 3 3 Manipulate existing Shape 3 3 1 Syntax st manipulate lt shape type gt lt command gt lt further param
146. er See also DIGMOD parameter DECIM decimation rate of digital filter For spectrometers equipped with digital filters Avance only For details see DWOV and DIGMOD parameters DSPFIRM firmware used for digital filtering For spectrometers equipped with digital filters Avance only For details see DIG MOD parameter DIGTYP digitizer type XWIN NMR supports the digitizer types of Table 1 18 The SADC is not prepared for sequential acquisition i e AQ mod must not be set to gseg DIGTYP must be set to a type installed in your spectrometer more than one may be present When executing the expinstall command you may enter a desired type In this case the DIGTYP parameter of all standard parameters sets are updated accordingly DIGMOD digitization mode For spectrometers equipped with digital filters Avance only The following three modes are available analog digital homodecoupling digital Analog disables dig ital filtering and uses the analog filters in the conventional way Digital turns on digital filtering Homodecoupling digital also enables digital filtering but limits the sampling rate so that homodecoupling is still possible 1 5 Setting up acquisition parameters P 53 DIGTYP dynamic range minimum DW slow 12 bits 3 microsec 16bit 16 bits 4 microsec fast 9 bits 0 1 0 05 microsec BC132 12 12 bits 0 1 microsec BC132 16 16 bits 2 microsec FADC BC133 12 bits 0 05 microsec
147. er data set parameters for which a data set already exists it will be display as soon as you click on the OK button of the dialog box This is the same as if you had selected the data set using one of the dir commands or the search command see The File Menu Any acquisition com mand issued now would overwrite existing acquisition data with the new fid or ser file XWIN NMR will output a warning prior to acquisition start only if the system variable ZGsafety is set to yes Use the command setres to set ZGsafety which is equivalent to invoking User interface from the Display gt Options menu If no data set exists corresponding to the specified parameters a new one is cre ated and is initialized with the same set of acquisition processing and plot param The Acquire Menu P 42 1 5 1 5 1 eters valid for the currently displayed data The program display switches to the new data set i e makes it the current data set but the data area of the XWIN NMR window remains blank since no data are present yet Defining the data set for an experiment to be executed from quicknmr Use the sample name entry field in the quicknmr dialog window Defining the data sets for a series of experiment to be executed by run Use the name entry field in the set dialog window Setting up acquisition parameters This section will discuss the following set up commands for data acquisition e edinfo edit sample information e eda rpar general acquisit
148. ers such as shim values influencing the lock signal may be adjusted from the SCM or BSMS keyboards or from the BSMS panel window see below The lock signal enters an RS232 channel on the acquisition rack of the spectrometer and is transferred to the workstation over a network connection The RS232 channel number must be specified when executing the configuration com mand cf The lock display window provides a number of commands which may be activated 2 4 Amplifier control acbdisp P 105 2 4 2 4 1 2 4 2 by clicking on the bottom row command buttons grid This is a toggle command displaying a grid a vertical bar a horizontal bar or nothing in addition to the lock signal The vertical bar divides the window in a left and a right part of equal size The horizontal bar divides the window in an upper and a lower part at 85 of the window s height mode This command toggles between two color modes In the first mode both forward and back sweeps of the lock are displayed in the same color In the second mode the color of the back sweep is different store This command allows you to save the current grid and mode settings the size and the position of the lock window in a file When lockdisp is executed and no such file exists the lock window will come up with default settings pro grammed in XWIN NMR If several save files exist and one of the files is called default the lock window will appear according the settings sto
149. ers for the n th RCU are taken from data set n of the data set list DSLIST The following parameters are relevant AQ_mod DECIM DIGMOD DIGTYP DR DSPFIRM DSPFVS FILPGN NBL OVERFLW SEOUT SFO1 SW SW_h TD 4 21 Real time outputs The TCU provides a number of real time outputs which are used to control the var ious spectrometer components such as gating and blanking the transmitters Please refer to your hardware documentation for information on which output is con nected to a particular device The pulse program compiler will select the correct output automatically e g for a command like p1 f2 Writing Pulse Programs P 260 4 21 1 The file XWINNMRHOME exp stan nmr lists pp Avance incl contains a number of macro definitions based on the outputs which can be used in pulse programs The hardware documentation will also inform you which of the outputs are still free for special purposes e g for controlling a laser from a pulse program Type 1 outputs RCPs These are 35 outputs which can be set with an accuracy of 12 5 nanoseconds and a minimum of 50 nsec also called RCPO RCP34 Two syntactically different ways are provided to enable or disable the outputs 1 The commands pl cO Su c25 vp c15 would generate pulses of duration P1 5 microseconds and according to the current pulse list pointer on the output channels 0 25 and 15 respectively 2 The command lu setnmr0 15 would activate
150. erx define delay rdeadc rde 1l de del rde2 de de2 rdepa de depa rderx de derx rdeadc de deadc define DE1 del rdel adc ph31 syrec define DE2 de2 rde2 ph30 f1 define DEPA depa rdepa RGP_PA_ON define DERX derx rderx RGP_RX_ON define DEADC deadc rdeade RGP_ADC_ON Table 4 21 The explicitly programmed pre scan delay displays an example of how this can be achieved It performs identically to the middle pulse program in Table 4 18 but now the dwell pulses are externally gener ated in the pulse program i e by the TCU using the x pulse option A corre sponding cable connection between TCU and RCU is required In this pulse program the waiting time aq has been replaced by a loop generating as many dwellpulses as required to measure TD data points 4 14 Working with acquisition memory buffers P 245 define delay dx define pulse px dx dwov 2 px dwov 2 ze 2d1 p1 phl f1 DE1 DE2 DE3 DEPA DERX DEADC 3 dx px x external dwell pulse lo to 3 times tdov Table 4 22 Acquisition based on external dwell pulses Please refer to the Bruker pulse program libraries for high resolution solids and imaging experiments for more examples using the x option 4 14 Working with acquisition memory buffers The acquisition commands go label gonp label and adc place the acquired data points into a memory buffer where they reside until new data points are added or until they are re
151. es and displays the gp with the read phase and slice gradients scaled according to the appropriate values for read phase and slice This means that gradient amplitudes now depend upon the field of view and slice thickness but not upon patient position and slice orientation All intensities are expressed in percentages Trim numbers are still available The gradient axes are labeled READ PHASE SLICE and Read Phase Slice G cm compiles the gp in the same manner as in the previ ous case but expresses all gradient amplitudes in Gauss per centimeter However amplitudes of multiplicative gradient pulse functions are expressed as values between 0 and 1 without units The axes are labeled READ PHASE SLICE and G cm The Windows Menu P 114 X Y Z compiles and displays the gp with the x y and z gradients scaled according to the appropriate values for read phase and slice as well as to the gra dient matrix This means that read phase and slice gradients are now intermixed with each other and mapped to x y and z depending upon patient position and slice orientation The trim numbers are expressed in percentages The axes are labeled X Y Z and X Y Z and G cm compiles the gp in the same manner as in the previous case but expresses all amplitudes in Gauss per centimeter The axes are labeled gt cae sy SA and G c
152. ess 1 5 7 Acquisition parameter setup with extset The command extset was designed to set up experiments to be executed with the command run like the command set described in the previous section While set provides a dialog box to be filled in by the user extset looks for ASCII type text files containing the required information and converts the contents of such files to a form suitable for run Laboratories often employ a centralized sample management which requires that the experiments are not defined locally on the NMR spectrometer with set but rather on PCs or a central laboratory computer from where they must be trans ferred into the spectrometer via the network or via magnetic storage media XWIN NMR Offers the following means for accomplishing such tasks e The experiments for each sample may be defined in a text file in ASCII format e g on a remote computer The structure of such a file is described below The file name must be of the form Name NNN NNN is a sequence of 3 digits e g 001 and with Name may consist of up to 8 characters e Ifrun should execute such an experiment the file must be copied into the direc tory XWINNMRHOME prog tmp of the spectrometer computer e g using rcp or ftp in an Ethernet network e Start extset run may also be active but it does not have to be The command extset will remain active in the background as long as XWIN NMR is running or until it is called again which will termina
153. eter changes the user possibly requested are applied Table 1 4 describes the available command buttons Setting up the probe head table edhead Use this command to set up a table of the probe heads you intend to use for your NMR experiments and to define the current probehead installed in the magnet It is a configuration command which should only be executed by the administrator edhead opens a dialog window where you may add change or delete lines by 1 3 The configuration suite config P 15 Store modifications in the file SAVE XWINNMRHOME exp stan nmr lists solvents and quit ADD CHANGE Opens a new entry field at the end of the table After enabling this button clicking on a DELETE probehead entry will delete it CTRL K key undo last change ABORT close edsolv window without storing changes Table 1 4 Command buttons in edsolv dialog window clicking on the corresponding button New entries must get assigned an arbitrary but unique reference number A typical entry in the table looks like the following 5mm Dual 13C 1H 03 The reference number must be specified in brackets It is used for identifying the probe head on a barcode label when a barcode controlled experiment is performed e g using an automatic sample changer equipped with a barcode reader In order for such experiments to be executed properly we recommend not to change the numbers any more once assi
154. eter gt The shape type is loaded from XWINNMRHOME exp stan nmr lists wave The following manipulating commands are implemented offs phase modulation according to offset frequencies sinm2 single sine modulation offset cosm2 single cosine modulation offset sweep modulation according to linear frequency sweep caSweep modulation according to constant adiabticity frequency sweep power calculate power of amplitude scale scale the amplitude of a shape addphase add constant phase trev time reverse a shape add add two shapes command offs phase modulation according to offset frequencies The manipulate command offs has following subcommands b phase modulation beginning at phase 0 m phase modulation with phase of 0 at middle of shape e phase modulation ending at phase 0 Syntax st_manipulate_ lt shape type gt offs b lt pulDur gt lt n gt lt f1 gt lt f2 gt double lt pulDur gt pulDur length of shaped pulse in us double lt n gt number of offset frequencies double lt f1 gt offset frequency 1 in Hz 3 3 Manipulate existing Shape P 149 double lt f2 gt offset frequency 2 in Hz double lt fn gt offset frequency n in Hz Example st manipulate Gauss offs b 100 2 2000 3000 Calculates phase modulation beginning at phase 0 Optional commands are f frequencies taken from frequency list p Syntax st manipulate lt shape type
155. eters P 65 Avance only The parameter array OBSCHAN is used to define the channels which are used for observation By default always channel 1 is used as the default obser vation channel OBSCHAN I1 1 With the HPPR it is possible to switch between up to 3 channels for observation during the experiment To define the sec ond and third channel which can be used for interleaved acquisition set OBSCHANJ n to 2 or 3 if the n th channel should be used as the 2nd or 3rd observe channel in an interleaved acquisition experiment The value of OBSCHAN 1 is ignored by the program and the program behaves always as if OBSCHAN 1 1 With pulses from NMR control word 2 bit 7 the HPPR can be switched from one module to the next in the sequence defined by OBSCHAN The pulses must be 1 usec to switch to the next module and 4 usec to reset to the first one Example NBL 2 OBSCHAN 1 1 OBSCHAN 2 2 go 2 acquisition on first nucleus lusetnmr2I7 switch to the next HPPR module lu setnmr2 7 st switch to the next block in memory 3 dl pl go 3 second acquisition 4u setnmr2 7 switch back to the first HPPR module lu setnmr2 7 stO switch back to the first memory block The modules which are chosen on the HPPR are defined by the complete routing in the edasp or edsp window OVERFLW overflow handling Avance type systems only In certain applications small signals must be detected in the presence of very strong ones and many accumulati
156. execution of dummy scans by go gonp gosc goscnp and by adc combined with reyc or eosc even if DS gt 0 The commands ze and zd should be written behind a delay command with a delay gt 10 microseconds depending on the number of phase programs in the sequence Then they are executed during the delay If they are placed on a separate line their execution will require 3 milliseconds The cosy pulse program of the Bruker library Table 4 17 illustrates the use of ze and zd The command adc The command adc starts the digitizer and at the same time opens the receiver Please refer to the description of the parameters DW DWOV DIGMOD on how the sampling rate is calculated The result of adc will be a digitized fid signal of TD data points where the time domain size TD must be defined by the user The fid will be placed in the current memory buffer cf the section Working with acqui 4 13 Commands to start data acquisition P 241 1 ze enable dummy scans 2d1 3 pl phl do pO ph2 go 2 ph31 d1 wr 0 if 0 idO zd the next fid requires no dummy scans lo to 3 times td1 exit phl 0000111122223333 ph2 0 123 ph31 0202313120201313 Table 4 17 Cosy pulse program how to use ze and zd sition memory buffers It is the responsibility of the user of adc to account for the various switching delays provided automatically by the go commands cf description of go abel It is also the responsibility of the user to
157. false In the second case only amplitude data are generated int lt size gt shape size in number of points 3 2 Generate a new shape P 139 string lt shape type gt one of EBurp1 EBurp2 IBurp1 Burp 2 ReBurp UBurp1 Example st generate Burp1 256 Literature H Geen amp R Freeman J Magn Reson 93 93 141 1991 3 2 2 2 Gauss Shapes Syntax st generate Gauss _ lt size gt lt trunclevel gt or st generate Gauss _ lt size gt false lt trunclevel gt In the second case only amplitude data are generated int lt size gt shape size in number of points double lt trunclevel gt truncation level in Example st generate Gauss 256 10 Literature C Bauer R Freeman T Frenkiel J Keeler amp A J Shaka J Magn Reson 58 442 457 1984 L Emsley amp G Bodenhausen J Magn Reson 82 211 221 1989 3 2 2 3 GaussCascade Shapes Syntax st generate lt shape type gt _ lt size gt or st generate lt shape type gt lt size gt false In the second case only amplitude data are generated string lt shape type gt one of GaussCascadeG3 GaussCascadeG4 GaussCascadeQ3 GaussCascadeQ5 int lt size gt shape size in number of points Example st generate GaussCascadeG4 256 The Shape Tool P 140 e Literature GaussCascadeG3 GaussCascadeG4 L Emsley amp G Bodenhausen Chem Phys Lett 165 469 1990 GaussCascadeQ3 GaussCascadeQ3 L Emsley
158. fid whereas a ser file contains a sequence of fids The appropriate name is chosen by the pulse program compiler If a pulse program contains one of the increment dec rement or reset file pointer commands or st st0 a ser file will result Tranferring data to disk means adding the data to the data contained in an existing fid or ser file or replacing this data if no such file exists one will be created Addition will take place if the pulse program is started with the command go replacement will take place if started with zg However data replacement only occurs the first time a memory buffer is tranferred to disk Any further invocation of wr will cause the buffered data to be added to the data in the file The command zg will create the ser file before acquisition starts and fill it with zeroes if no ser file with the correct file size exists Otherwise the existing ser file is retained and the wr command in the pulse program initially will overwrite the ser file section defined by the current file pointer TD and NBL The contents of the other parts of the file will remain unchanged The wr commands and all other commands in Table 4 24 can be specified behind a delay cf the example in Table 4 23 The delay must not be shorter than 10 microseconds The delay is required to initiate the command not to execute it The only timing requirement for wr is that the disk transfer be complete before wr is called again otherwise a run ti
159. from the sw sfo button in the 1D utilities menu It ajusts SW so that it has the same value as the expanded region and also adjusts SFO1 so that the carrier frequency lies in the center of the expanded region For 2D and 3D experiments SW as described above corresponds to the width in the acquisition dimension while the widths of the other dimensions are calculated from the parameters INO IN10 NDO and ND10 FIDRES fid resolution in Hertz A temporary parameter calculated according to FIDRES SW SFO1 TD If you modify FIDRES to get a desired resolution the time domain size is recalculated according to TD nextpower of 2 of SW SFO1 FIDRES FW filter width in Hertz The analog filters are set according to this value when acquisition is started or with the ii command If you change the sweep width FW is recalculated according to FW 1 25 SWH or FW 0 3125 DWOV The latter equation is valid for Avance systems if digital filtering is enabled DIGMOD digital or homodecoupling dig ital DWOV is the oversampling dwell time see also parameter DIGMOD AQ acquisition time in seconds The time to record one scan Doubles if you increase TD or decrease SW by a fac tor of two If you change AQ TD is recalculated accordingly It will not be rounded to the next power of two but be set to an even number giving the closest match to the entered AQ value Then AQ is recalculated from TD and SW RG receiver gain The receiver gain controls
160. g in the PostScript format so that the current window contents be fit on the single page as for Export window contents and the rest of the drawing outside the window be distributed to other pages so that it should be possible to combine them later into a single longer ppg banner The resulting multipage file can be printed on a PostScript printer or viewed with a previewer however it cannot be used with XWIN PLOT because it does not yet support The Windows Menu P 118 multipage imports Multipage from start produces multipage PostScript export similar to the preceding command however the current window contents determines only the scaling of the picture but not its distribution on the paper pages The drawing begins from the left most corner of the very first page If the ppg drawing was not expanded then all the four export commands behave identically Select PostScript media opens the media selection dialog with the combo box for various standard Post Script paper formats and with the two radio buttons controlling the foreground color of the drawing either black or the same as on the screen the background color being always white Generate enhanced metafile exports the contents of the window in the Microsoft Windows Enhanced Metafile format under Microsoft Windows NT only The name for the export file is requested via the usual file selection dialog The produced enhanced metafile can be imported into
161. g to Table 1 12 expinstall copies them into the working directory XWINNMRHOME exp stan nmr lists gp where they are searched for by commands such as edgp and by the acquisition commands The Acquire Menu P 38 XWINNMRHOME exp stan nmr lists gp exam AMX high resolution XWINNMRHOME exp stan nmr lists gp dexam AVANCE XWINNMRHOME exp stan nmr lists gp solids AMX ASX solids XWINNMRHOME exp stan nmr lists gp imag micro imaging XWINNMRHOME exp stan nmr lists gp tomo tomography Table 1 14 Sample gradient file directories 1 3 15 6 Install library shape files On the release media shape file for a number of NMR experiments are delivered for various types of instruments in own directories according to Table 1 12 expin XWINNMRHOME exp stan nmr lists wave exam AMX high resolution XWINNMRHOME exp stan nmr lists wave solids AMX ASX solids XWINNMRHOME exp stan nmr lists wave imag micro imaging XWINNMRHOME exp stan nmr lists wave tomo tomography Table 1 15 Sample shape files directories stall copies them into the working directory XWINNMRHOME exp stan nmr lists wave where they are searched for by the acquisition commands 1 3 15 7 Convert standard parameters sets After installation of XWIN NMR from the release media the directory XWINNMRHOME exp stan nmr par 300 contains a collection of so called standard experiments An experiment is a direc tory wit
162. gned to a particular solvent Initially edhead displays a probe head table suggested by Bruker from the text file XWINNMRHOME exp stan nmr lists probeheads all If you apply modifications to the table and then exit via the SAVE button the mod ified table is stored in the file XWINNMRHOME exp stan nmr lists probeheads Now the file probeheads has been created and future invocations of edhead will display this file containing your personal settings In order to inform XWIN NMR which probe head of the table is currently installed in the magnet click on the Define current button and then on the desired table entry It will be stored in the file XWINNMRHOME conf instr probehead The current probe head is evaluated by the commands prosol edlock lock acqu and lopo and during guicknmr and run For the latter two applications the acquisition parameters are obtained as described in the previous section edsolv The Acquire Menu P 16 The XWIN NMR acquisition commands zg go store the current probe head in the acquisition parameter PROBHD of the acquired data set for future reference Table 1 5 describes the available command buttons Store modifications in the file SAVE XWINNMRHOME exp stan nmr ists probeheads and quit ADD CHANGE Opens a new entry field at the end of the table After enabling this button clicking on a probehead entry will delete it CTRL K key undo last change ABORT close
163. grams On the release media pulse programs for many NMR experiments are delivered for various types of instruments in own directories according to Table 1 12 expin XWINNMRHOME exp stan nmr lists pp exam AMX high resolution XWINNMRHOME exp stan nmr lists pp rexam ARX high resolution XWINNMRHOME exp stan nmr lists pp dexam AVANCE XWINNMRHOME exp stan nmr lists pp solids AMX ASX solids XWINNMRHOME exp stan nmr lists pp imag micro imaging XWINNMRHOME exp stan nmr lists pp tomo tomography Table 1 12 Sample pulse program directories stall copies them into the working directory XWINNMRHOME exp stan nmr lists pp where they are searched for by pulse program manipulation commands such as edpul and by the acquisition commands If the item Enable Define Statements in Pulse Programs is higlighted expinstall opens each pulse program prior to instal lation and removes all double semicolons occurring at the beginning of a pulse program line Definitions of pulse program parameters such as d11 30m or d12 20u are now enabled as suggested by Bruker for certain experiments Composite pulse decoupling programs expinstall copies them from the directories of Table 1 12 to the directory XWINNMRHOME exp stan nmr lists cpd rexam AMX ARX ASX XWINNMRHOME exp stan nmr lists cpd dexam AVANCE Table 1 13 Sample cpd program directories 1 3 The configuration suite config P 37
164. gt offs b f lt pulDur gt lt freqlist gt string lt freqlist gt file with frequency list Example st manipulate Gauss offs b f 100 freqlist additional phase setting Syntax st manipulate lt shape type gt offs m p lt pulDur gt lt n gt lt f1 gt lt p1 gt lt f2 gt lt p2 gt double lt pulDur gt pulDur length of shaped pulse in us int lt n gt number of offset frequencies double lt f1 gt offset frequency 1 in Hz double lt p1 gt initial phase 1 in degree double lt f2 gt offset frequency 2 in Hz double lt p2 gt initial phase 2 in degree double lt fn gt offset frequency n in Hz double lt pn gt initial phase n in degree Example st manipulate Gauss offs m p 100 2 2000 90 3000 3000 s with additional scaling Syntax st manipulate lt shape type gt offs e s lt pulDur gt lt n gt lt f1 gt lt s1 gt gt lt f2 gt lt s2 gt double lt pulDur gt pulDur length of shaped pulse in us int lt n gt number of offset frequencies double lt f1 gt offset frequency 1 in Hz The Shape Tool P 150 3 3 2 double lt s1 gt scaling factor 1 in double lt f2 gt offset frequency 2 in Hz double lt s2 gt scaling factor 2 in double lt fn gt offset frequency n in Hz double lt sn gt scaling factor n in e Example st manipulate Gauss offs e s 100 2 2000 50 3000 75 The options f p and s respectively may be
165. h a complete set of acquisition processing and plot parameters prepared e g for a proton measurement a 13C decoupling measurement a COSY experi ment etc These parameter sets were compiled and tested on a 300 MHz spectrom eter in the Bruker application laboratory Before you can make use of them they must be adapted to your local requirements Afterwards they are stored in the directory 1 3 The configuration suite config P 39 1 3 15 8 XWINNMRHOME exp stan nmr par where they may be accessed by commands such as rpar and dirpar The conversion utility first requests the logical name of your printer and plotter e g hplh4p See command cfpp on printer plotter installation These names are inserted in the CURPRIN and CURPLOT parameters defining the output devices At any later time you may overwrite these default settings if required using the command edo The next question is about the paper format of your plotter The plot parameters of the standard parameter sets are adjusted for A3 size You may leave A3 or change it to A A4 or B A3 and B will take over the default settings A4 and A will change parameters according to the contents of the text file XWINNMRHOME exp stan nmr lists plotconvpar If you want to produce your own default values you may edit this file according to the description in its header and run expinstall again enabling only the Convert standard parameter sets function The next question asks for
166. hases of ph4 by 360 5 degrees The next time that ph4 is encountered in the pulse program its phase cycle will be changed to 5 1 2 3 4 The commands dp0 dp31 are inverse to ip0 ip31 and decrement all phases of the associated phase program The commands rp0 rp31 reset all phases of a phase pro gram to their original values i e to the values they had before applying ip0 ip31 or dp0 dp31 the first time The commands 6u ip3 2 7 5u dp4 2 would increment ph3 by 2 90 180 degrees and decrement ph4 by 2 360 5 144 degrees An increment decrement phase program command must always be specified Writing Pulse Programs P 202 4 5 3 8 4 5 3 9 behind a delay which must be long enough for the increment decrement to be computed The required time depends on the number of phases in the phase pro gram and amounts to 1 5 microseconds per phase and channel Phase presetting A pulse program command such as p1 ph8 f2 suggests that phase switching to the current phase of the specified phase program is executed at the same time as the pulse begins Depending on the hardware how ever the phase may take a certain amount of time to become stable For this rea son XWIN NMR allows you to instruct the pulse program to set the new phase somewhat earlier Eight parameters PHASPR1 PHASPRS8 are provided to be set from the edscon parameter editing command one for each spectrometer channel Their default value is 3 microseconds Therefo
167. hat ipp8 is specified on the same line as p1 and therefore does not introduce an extra delay between p1 and p2 In general the increment commands ippO ipp31 are provided for the phase programs phO ph31 These com mands can also be specified with a delay For example dl ipp7 would advance the pointer to the next phase in ph7 Adding a constant to a phase program You may change all phases in a phase program by a constant amount without hav ing to modify the phase program itself Each phase program ph0 ph31 has a con stant assigned PHCORO PHCOR31 accessable from eda or from the keyboard The phases of the pulse p1 ph8 r f2 4 5 Pulse generation commands P 201 4 5 3 7 would be 2 92 182 272 degrees if ph8 0 1 2 3 and PHCOR8 2 degrees With out the r option the phase cycle of p1 would be 0 90 180 270 The r option can be combined with the sign e g p1 ph8 r f2 Phase program arithmetic Each of the phase programs ph0 ph31 has 3 associated commands ip0 ip31 dp0 dp31 rp0 rp31 They can also be used with an integer multiplier n ip0 n ip31 n dpO n dp31 n Assume we had two phase programs ph3 0 2 2 0 and ph4 5 0 1 2 3 The pulse program command 20u ip3 would increment all phases of ph3 by 90 degrees The next time that ph3 is encountered in the pulse program its phase cycle will be changed to 1 3 3 1 Likewise the pulse program command 20u ip4 would increment all p
168. he description of the run command for details The command set must be used to set up the experiments to be executed by run All experiments you define in the set dialog window are stored in a file from where they are retrieved by run for execution set requests the name of the file upon start up as does run This feature that you may specify the name of the file yourself allows you to set up and maintain several such experiment files and run the experiments at a desired time An experiment file is stored in the directory XWINNMRHOME prog curdir changer The file name extension 0 will be appended for internal reasons set comes up with a dialog window containing up to 120 entries for experiments If a sample changer is to be used the number of entries is 60 or 120 depending on its capacity number of holder positions Otherwise you my configure the number of entries using the cfbacs command The experiment entry fields Each entry consists of the following fields STAT HOLDER NAME EXPNO SOLVENT EXPERIMENT Priority STAT Sample status U unused This entry is available for a new experiment R ready for acquisition Parameter set up is complete for this holder You may still apply changes as long as acquisition is not yet in progess Click on this field to The Acquire Menu P 78 cancel R mode and to return to U mode Everything set up for this holder will be lost nR ready for multiple experiments Like R but indicates
169. he following rules apply e Only one F1 F8 logical channel must be connected to each FCU e Several FCU s may be connected to a single amplifier e Router restrictions Router input 1 may be connected only to router output 1 2 or 3 router input 2 only to 1 2 3 and 4 Router inputs of the second or third router may be connected to the output of the first router only if no other input channel of this router goes to a different output channel of the first router e In the switch box each input button may be connected to any output button but this connection must be one to one Double connections from the same input button are not allowed e Each preamplifier may only be connected to one amplifier either through the switch box or directly Note however that the displayed connection to a pream plifier is of no physical influence as far as the connections between the amplifi ers and the preamplifier modules are concerned It is up to the operator to ensure that the wiring is correct The same is true for the correct connection to the probehead At the time the program creates the default routing the amplifier is chosen such that the nucleus type is considered For H or F nuclei an amplifier of type H is selected for other nuclei an X type amplifier Install standard parameter sets expinstall Execute the command expinstall also available in the Acquire gt Spectrometer setup menu XWIN NMR is delivered with sets of acquisitio
170. he font used for the buttons and labels of all panels exclusive the font of the function buttons 3 the function but tons in the control panel in the turned off state 4 the function buttons in the control panel in the turned on state and 5 the function button font To change the colors of the application use the Color command in the Options pulldown menu of the main panel Issuing the color command pops up a color dia log Select the type of color to change from the left box in the color dialog e g Panel background to set a new panel background color Select now one of the colors from the color palette on the right by clicking on the corresponding color button e g click on the red color on the color palette the panel background will change to red The panels will show the new color immediately Display Tool Calibration The panel can be calibrated with the Calibrate Display command in the Dis play pulldown menu When value functions are changed with the control panels the valid function range is displayed above the slider function minimum and function maximum in Figure 2 11 A value can be set only within this range other values are not accepted by the BSMS device The BSMS display tool does not know however these function ranges in advance they depend on the currently installed BSMS hardware and must be queried from the BSMS device by the display tool This is done wi
171. he lower button in NUC1 NUC8 in the logical channel group allows you to select the nucleus The displayed table is taken from the file XWINNMRHOME conjf instr lt instrument name gt nuclei which is set up during the configuration command cf 1 3 The configuration suite config P 33 The parameters NUC1 NUC8 and the frequency offsets OFSxx are global param eters in XWIN NMR They are not only stored in the acqu file of the current data set as acquisition parameters but also in the file XWINNMRHOME conf instr lt instrument name gt specpar at the time the SAVE command is executed in edsp or edasp They may be imported from there into any dataset with the command edsp this is actually the difference between edasp and edsp Usage of edsp and edasp Invoke edasp if the parameters of the current data set should be used as default edsp should be used if the frequencies and nuclei of another experiment previ ously defined with edasp or edsp but in a different dataset should be transferred to the current data set A typical example is the setup of a H experiment and a 3C experiment with H decoupling For the first experiment a dataset 1 is created Within this dataset the nucleus H and the frequency SFO1 are chosen with the command edasp Then within a second data set the nucleus C for F1 and H for F2 are chosen using the command edsp Automatically the frequency SFO1 from experiment 1 is transferred to SFO2 of experiment 2
172. hed whichever is longer Figure 4 1 Figure 4 2 Rule 3 example 1 The following example is a typical section of a DEPT pulse program p4 ph2 f2 p1 ph4 d2 f1 pO ph3 f2 p2 ph5 f1 The pulses p4 and p1 begin at the same time p4 on channel f2 and p1 on channel f1 The pulses pO and p2 start again simultaneously but not before the sequence with the longest duration of the previous line has terminated Figure 4 3 fl pl d2 p2 p4 po f2 Figure 4 3 Rule 3 DEPT example The following 2 lines were extracted from the COLOC Bruker pulse program d6 dO p4 ph2 f2 dO p2 ph4 f1 p3 ph3 f2 p1 ph5 f1 We have three sets of parentheses in this case The first items in each parenthesis start at the same time namely d6 and dO After d0 p4 on channel f2 and p2 on Writing Pulse Programs P 220 channel f1 start simultaneously Assuming that d6 is larger than d0 p4 and d0 p2 the second line would be executed after d6 has terminated A final example for rule 3 is a line from the HNCO3D Bruker pulse program p14 sp3 ph1 f2 p22 ph1 f3 The shaped pulse p14 is started simultaneously with the rectangular pulse p22 4 8 Decoupling 4 8 1 Decoupling commands Table 4 4 shows the available types of decoupling commands Composite pulse decoupling is discussed in more detail in the next section of this chapter in more detail cw continuous w
173. hen printing labels with the command prlabel described in the chapter The 1D Output Menu Checksum Provided to be able to detect read errors While run based on barcode_sx is active you may invoke set at any time and view which sample is in progress and what has been measured so far You may even insert a sample without bar code label in an empty holder of the sample changer and define an experiment in set also with priority An own AU program which must be stored in the directory XWINNMRHOME exp stan nmr au modsrc e g to realize centralized sample management An example AU program remote_sx is part of the XWIN NMR release It fetches the experiment file via Ethernet ftp from a remote computer Please note that such solutions depend on the particular laboratory environment 3 First holder position O continue run will start with the specified holder position It remembers the last one and allows you to continue there if a run was aborted 4 Enter name of list file While run proceeds it builds up a list of data sets successfully acquired and stores it in the specified file At any a later time you may process or re process the acquisition data using the command run proc It will ask you to enter the list file name the whole path or only the file name if located in your home direc tory and the command to apply to all or to the selected data sets of the list You may specify any XWIN NMR command such as efp or xau_ lt pr
174. hims simultaneously DELAY n In order to give the lock enough time to settle when new shim values are loaded the program will wait n seconds before it starts reading the lock level TIMES n END The Acquire Menu P 88 1 6 2 3 1 6 3 1 6 4 This is a loop construct Everything between TIMES n and END will be executed n times Nested looping up to a depth of 5 is possible RSH RSH lt filename gt The command rsh is executed If no name is specified the program will assume the current solvent name as defined by the acquisition parameter SOLVENT AUTOSHIM ON OFF lt gradient list gt When the tune command has terminated the shim unit itself will continuously auto shim the gradients specified by this command Example for BSMS AUTOSHIM ON Z1 2 Z2 Example for BSN18 AUTOSHIM ON Z1 Z2 For the BSMS a step width may be set for each shim individually For the BSN18 the maximum number of shims is 4 AUTOSHIM OFF will disable auto shimming by the shim unit The AUTOSHIM command may be written anywhere in a tune file It will not become effective before tune has terminated SIMPLEX lt list of gradients gt SET lt gradient gt w c The commands SET and SIMPLEX provide a simplex based optimization proce dure for several shims SET sets the maximum step width w and the convergence limit c for a gradient e g SET Z1 20 3 SIMPLEX starts the simplex optimization for the specified gradients e g SIMPLEX Z1 Z2 Gradient sh
175. hl r ph2 The option r indicates that the phase program ph1 controls the reference phase The value PHCORI is added to all phases of this phase program see below PHCORO PHCO31 PH_ref is not used in this case The phase program ph2 refers to the digitizer phase It may only contain phases corresponding to 0 90 180 or 270 degrees Such phases are realized in such a way that the fids A and B of the 2 quadrature channels are added to or subtracted from the previous scans as fol lows 0 A B 90 B A 180 A B 270 B A The total receiver phase is the sum of the phases of the two phase programs speci fied If the acquisition is started with the adc command and ends with rcyc or eosc the receiver phase program is specified after rcyc or eosc for AMX ARX systems and 1 5 Setting up acquisition parameters P 61 after the adc command for AVANCE systems For both systems the reference phase must be set explicitly see chapter pulse programming PHCORO0 PHCOR31 correction angles for phase programs in degrees In pulse programs any phase program may have appended the option r e g pl ph2 r The value PHCOR2 is added to any phase of phase program ph2 before execution See PH_ref for the special case of receiver phases ROUTWD1 ROUTWD2 router control words For AMX type spectrometers only Do not modify these parameters unless you have a detailed hardware knowledge of your spectrometer The control words are set automat
176. ibr Avance only hardware_list text file in a special format containing a list of hardware components text file created by cf containing information about the mas_param P MAS unit text file containing the table of nuclei selected either in nuclei cf or by ednuc eon parameter file containing spectrometer parameters is created by edscon text file created by cf containing useful information uxnmrinfo about the spectrometer hardware It is displayed when cf is finished standard parameter file created by cf containing the uxnmr par answers of the operator to the cf questions Table 1 2 Configuration files P 9 The Acquire Menu P 10 1 3 1 4 Is created by cf and contains text files for the device configuration of several units e g HPPR BSMS RX22 cortab Is created by the automatic spectrometer adjustment rs232_device prosol Is created by prosol users Is created by eduser Table 1 3 Configuration subdirectories must not be modified A safe copy should always be available on magnetic tape and in form of a paper printout If a spectrometer is equipped with a 4 phase modulator but not with a HPCU it is possible to define this hardware equipment in the hardware list file cf is required afterwards The unit may be connected to tty10 or tty20 on the CCU DMX spectrometers which are equipped with HRD16 and FADC digitizers can use th
177. ically at the time you define the nuclei NUCLEI button in eda or with edsp SP07 shaped pulse parameter table For Avance type spectrometers only The pulse program command pl sp2 f1 would execute a shaped pulse of length P1 on channel f1 The shaped pulse param eters are taken from entry 2 of this table indicated by the sp2 option The table has totally 16 entries with index 0 15 so that the options sp0 sp 5 may be used with a pulse command Each table entry has 3 parameters assigned a power level a frequency offset and a file name A file with the specified name must exist in the directory XWINNMRHOME exp stan nmr lists wave It must contain the shape of the pulse generated for example with Bruker s shape or xshape programs Shaped pulse parameters may also be set from the keyboard Example The commands spnam2 spoffs2 and sp2 allow you to set the file name frequency offset and power level for entry 2 of the table TP07 DP07 DBP07 shaped pulse parameter tables For AMX ARX type spectrometers only Each table has 8 entries The spx fy type pulse options for Avance systems see SP07 parameter table above must be replaced by the options tp0 tp7 to execute a shaped pulse on the transmitter dp0 dp7 to execute a shaped pulse on the decoupler and dbp0 dbp7 to execute a shaped pulse on decoupler B GP031 gradient parameter table For Avance type spectrometers only The pulse prog
178. ig ure 3 1 Zoe apli nata 1 to Ht l m kok i E S S Lae pairce Figure 3 1 Main Window of Shape Tool 3 5 The Interactive Display Command stdisp P 161 Buttons for vertical scaling 2 2 8 8 and vertical reset are available on the but ton panel 3 5 1 The File Menu All file related functions of the Shape Tool can be found in the File menu For reading a shape file from disk use the Open command The Save command writes the actually displayed shape using its type name as file name to disk The com mand Save As allows you to specify your own file name All file related commands read or write their files by default from to the direc tory XWINNMRHOMEYLexp stan nmr lists wave The default directory can be changed using the Set Path to Shape Directory com mand in the Options menu cf Chapter 3 5 6 The command Open opens a file selection box to specify a file name Figure 3 2 The default shape directory can also be changed within the file selection box by editing the Filter entry After changing the Filter click the Filter button to change to the entered directory To read Shapes in ASCII format use the command Open ASCII Shape This com mand reads files in old xShape ASCII format Shape Tool needs some more infor mation than stored in the ASCII shape format First the type of shape is defined using a selection box After selecting the type a dialog win
179. iles libary Table 1 11 Libraries to be installed with expinstall expinstall is to install all desired items in their working directories for your type of instrument and to update certain parameters accordingly Since this is a critical configuration procedure it should only be excuted by the system administrator expinstall starts up with a table of spectrometers Select the correct one the instru ment specified during cf configuration is enabled by default and click on the Pro ceed button A new table comes up showing the possible actions that may be performed The highlighted buttons define the minimum required for data acquisi tion with Bruker pulse programs and automated measurements based on Bruker standard parameter sets You may click on a highlighted button to disable installa tion and on other buttons to enable installation As soon as you click on the Pro ceed button of the dialog box all highlighted features will be installed expinstall may be executed again at any later time to install items not selected earlier Please do not enter other commands while expinstall is in progress It will print a message when complete Without compilation of AU programs expinstall termi nates within a few minutes Compilation may take a few hours depending on the The Acquire Menu P 36 1 3 15 1 1 3 15 2 number of AU programs and computer speed The following sections describe the features that may be installed Pulse pro
180. imming FOCUS gradshim Gradient shimming is described in its own manual Please open the Help gt Other topics gt Gradient shimming menu item to view or print it BSMS unit Please refer to the description of the command edlock HPCU High power control unit The HPCU handling inlcuding commands such as edhpcu is described in a sepa rate manual which can be viewed by selecting the 1 6 Interface control commands P 89 Help gt Other topics gt Solids manual menu item 1 6 5 MAS Magic angle spinning unit The MAS handling including commands such as mas is described in a separate manual which can be viewed by selecting the Help gt Other topics gt SB MAS manual menu item 1 6 6 Amplifier protection limits The command edacb opens a dialog windows where you can define the amplifier hardware protection limits for pulse power pulse width and duty cycle 1 6 7 RDCU Radiation Damping Control Unit The command rdcu reads the current setting of the RDCU and then pops up a win dow which contains e atoggle button to switch the damping control on or off and e alist of four different filter settings The popup window displays the current setting Each time a value is changed it is set immediately on the RDCU Exiting the rdcu command is done by closing the popup window 1 6 8 Sample rotation insertion and injection The command ro allows one to turn sample rotation on or off and to enter the spin
181. in this directory 1 4 Defining the acquisition data set new edc P 41 1 4 Defining the acquisition data set new edc Before you can set up the parameters for a data acquisition you must define a data set where the acquired data fid and later on the spectrum are to be stored In XWIN NMR a data set is characterized by the 5 parameters DU USER NAME EXPNO PROCNO From these parameters two directories are derived DU data USER nmr NAME EXPNO DU data USER nmr NAME EXPNO pdata PROCNO Examples u data guest nmr sucrose 1 u data guest nmr sucrose l pdata 1 In the first directory acquisition data are stored by the acquisition commands in the files fid or ser A ser file contains multiple fids and is the result of a two three or higher dimensional experiment Defining a data set for a single experiment acquisition with zg In order to define a new data set call the command New from the File menu or enter new or edc on the keyboard A dialog box is displayed where you may enter the data set parameters DU is the disk partition where the data are to be located and USER is the user s own or another legal login name NAME is an arbitrary name assigned to the data set EXPNO is a number allowing you to run experi ments under the same NAME and differentiating them by the EXPNO Similarly PROCNO is a number and may be used to store several processed data sets derived from the same acquisition data If you ent
182. ing fid two successive data points originate from different detectors but were sampled at the same time The acquisition time difference of two pairs of data points is two times the dwell time parameter DW e DQD digital quadrature detection only available on suitably equpipped Avance type spectrometers Requires the acquisition parameter DIGMOD to be set to digital or homodecoupling digital Digital quadrature detection has the advantage over the previously described analog modes that the two receiver channels are generated mathematically by the digital filters of such instruments and for this reason are not offset against each other leading to a cleaner fid sig nal FnMODE acquisition mode in 2D and 3D experiments When the mc command is used in the pulse program the type of experiment and phase type of acquisition in F1 in 2D experiments and for F1 and F2 in 3D experi 1 5 Setting up acquisition parameters P 47 ments can be set with the FnMODE parameter Processing will then use the FnMODE parameter instead of the MC2 parameter to determine the correct type of transformation When the mc command is not used the parameter must be set to the value undefined In this case the MC2 processing parameter must be set to the correct value Possible values are e undefined mc command not used in pulse program MC2 processing parame ter must be set to the correct value for processing e QF subsequent fids are acquired with incre
183. ion parameter set up for the commands zg go gs e ased as acquisition parameter set up for the commands zg go gs restricted to parameters referred to in the current pulse program e wobb probehead tuning e gs interactive adjustment of acquisition parameters e set parameter set up for a series of experiments started with run e extset external parameter set up for run using ASCII files Setting up the sample information file edinfo This command is not required for data acquisition to perform properly However it allows you to store sample or company specific information of your choice such as sample id order number etc to be entered and stored along with acquisition data You may also append this information to the spectrum plot Please refer to the description of edinfo in the chapter The File Menu 1 5 2 Acquisition parameter setup with eda eda is the most general parameter setup for a data acquisition to be started with zg With eda you get the settings for the current data set displayed and you may mod ify them eda may also be called from the set dialog window which is the parame ter set up for experiments executed by the run command Likewise eda may be called from the quicknmr dialog window Before you call eda you may use rpar 1 5 Setting up acquisition parameters P 43 1 5 2 1 see chapter The File Menu to initialize the current acquisition parameters with a standard parameter set from the d
184. iour d20 pl9 f1 set power to value of pl9 pl spO currentpower f1 execute shaped pulse with 100 amplitude p19 dl after execution of the shaped pulse the power is reset to p11 p2 fl so this rectangular pulse is executed with power setting pl1 Note The use of a shaped pulse with power levels very different from the one specified at definition may currently result in deformations of the pulse shape Making use of this feature you must be aware of this possibility and check very carefully experimental results You can access the table entries not only from eda but also from the keyboard For example the command spnam5 would display the file name corresponding to table entry 5 spoffs2 the frequency offset of entry 2 and sp15 the power value of entry 15 Using shapes with variable pulse length Shaped pulses can be used with some restrictions in connection with variable length durations The duration can be varied only in steps which are multiples of the number of defining points with the timer resolution on the FCU 12 5nsec The limit for a variable shape duration is about three times the minimal duration of the shape When you use a shape outside its specification an error message will be printed and the shape will be used with the previous settings Example A shape consists of 1000 points Its minimal execution length is 1000 50ns 50us Then it can ve varied only in a range from 3 50us up to some seconds in steps of 100
185. irectory XWINNMRHOME exp stan nmr patr Please note Certain buttons in the eda dialog window such as PULPROG will open a box with a list of items e g pulse program names In order to select an item you must click on it If you happen to click outside the box the box will be disabled If you move the cursor back into the box no mouse clicks will be accepted until you re enable it by hitting the ESC key Invoking eda from the keyboard or from the Acquire menu The acquisition parameters displayed in this case are a copy of those of the data set where the new command was given You may overwrite them with an arbitrary predefined parameter set using the command rpar rpar displays the table of param eter sets available in the directory XWINNMRHOME exp stan nmr par It contains the Bruker standard experiments see expinstall as well as others you or your sys tem administrator copied there with the wpar command rpar allows you to selec tively overwrite either your current acquisition plotting or processing parameters or all of them After rpar you may change individual parameters with eda The command eda displays all acquisition parameters of the current data set at once in a table and allows you to apply modifications The parameters are loaded from the parameter file a text file DU data USER nmr NAME EXPNO acqu Upon exit from eda via the SAVE button of the eda dialog window all changes are written into this file Any para
186. is a text file whose lines are frequency values cf command edlist on the exact list format and how to set up a list For example the command d1 fq2 f3 or d1 fq fq2 f3 4 5 Pulse generation commands P 195 4 5 2 3 uses the frequency list whose file name is given by the acquisition parameter FQ2LIST fq1 would use FQILIST etc You may set FQILIST etc from the eda command and you can modify a selected list with edlist The example would set the frequency of channel 3 f3 by taking the current value from the list defined by FQ2LIST The current value is the first value in the list when you start the pulse program and fq2 is executed the first time Next time fg2 is ecountered e g because it occurs several times in the pulse program or because it is contained in a loop the current value will be the next one in the list etc At the end of the list the current value will be reset to the first list value In general fq1 fg8 not only set a frequency but also increment the list pointer to the next frequency in the list The fql fq8 commands must be written behind a delay The frequency change occurs at the beginning of this delay which must not be shorter than 2 microseconds The list can optionally contain a frequency offset in MHz If this is the case the frequency list values in Hz are added to this offset If not the list values are added to the channel frequency SFO1 for F1 SFO2 for F2 etc The frequency can also be
187. is parameters However one can switch to another channel and start or stop autoadjustment of its offset Therefore it is possible to make simultaneous offset adjustments for different channels If autoadjustment on some channel takes place is displayed on the setpre window title bar For older GREAT units which do not have auto offset adjust feature the auto tog gle button is disabled For the GREAT 3 60 unit there exist also an option menu to select the Amplifier gain out of six stages from 10 A to the maximum of 60 A The amplifier matching parameters on the GREAT such as control loop resistors capacitors and impedance may also be adjusted by qualified personnel if enabled The Acquire Menu P 92 1 6 9 3 via special commands in the setpre menu There are five pushbuttons under the slider box Store Recall Exchange Undo Clear with the functions similar to a pocket calculator to store currently displayed slider values in memory recall them back exchange memory and display undo all changes and clear the gain preemphasis values At the bottom of the setpre window is the scrollable error message field On startup the currently set values contained within the preemphasis unit are read by the program and displayed accordingly The sliders are then on line and changes in their values are written directly and instantly to the preemphasis unit Also the type of the preemphasis hardware is automatically detected and the fea
188. it is possible to calculate the power level required for the shaped pulse To do this use the command Integrate Shape integr3 An editor for this command Figure 3 7 is started and asks for the length of soft pulse for the flip angle and for the length of the hard pulse Soft pulse and hard pulse are entered from the parameters of the actual XWIN NMR data set if not available default values are used Click OK to start calculation The results for a Gaussian shape with 1000 points and 1 truncation are shown in Figure 3 7 The integral ratio and the corresponding difference in dB are calcu lated simply on the basis of the amplitude and phase of shape Including the three parameters entered in the Editor window gives the change of power level informa tion For adiabatic pulses the change of power level can be calculated from the length of the corresponding 90 degree pulse length and the length of the hard pulse The Update Parameters button will save the length of the shaped pulse as well as the required power level taken from the power level of the hard pulse and the cal culated difference in the actual XWIN NMR dataset The Shape Tool P 168 Figure 3 7 Results of Integrate Shape integr3 The relation between Shape Tool parameters and XWIN NMR parameters are defined using the Options Menu 3 5 4 5 Simulate The analyze command Simulate starts the program NMR SIM also distributed with NMR Suite on the actual displayed
189. ite the data on disk in regu lar intervals for example every 1000 scans To accomplish this you would set NS 1000 and add the line lo to 1 times 30 before the exit command The pulse program would then accumulate 30 000 scans totally but store the result every 1000 scans Please note that the loop must branch to the ze command The rea son for this is that wr 0 adds the last acquired data to the data already present in the file The real time fid display will only show the data currently present in the acquisition processor s memory 14 exit Signals the end of the pulse program 4 5 Pulse generation commands Table 4 2 shows the available types of commands for the generation of high fre quency pulses A high frequency pulse is described by its duration pulse width frequency phase 4 5 Pulse generation commands P 187 4 5 1 4 5 1 1 p0 pl p31 Generate a pulse whose duration is taken from the acquisition parameter PO P31 respectively 3 5up 10mp 0 1sp Generate a pulse of fixed length up a microsecond pulse mp millisec sp sec Generate a pulse the name of which is defined by means of a define pulse statement and whose duration is defined by an expression Generate a pulse whose duration is looked up in a pulse list pulse flipangle auto duration pulse flipangle power auto Generate a pulse causing the specfied flip angle Ta
190. ivd 0 lu ivd The delay length is not important any small or large duration is legal It is also possible to calculate the list position by means of an equation Example vdidx 5 vd vd will execute a delay whose duration is selected from position 5 of the delay list At the right of the equal sign any dimensionless expression is allowed which may contain parameters from Table 4 3 4 6 6 User defined delay lists In a similar way to user defined delays entire lists of delays can be specified in a define statement in the following way define list lt delay gt Dlist 0 1 0 2 0 3 This would define a delay list Dlist with values 0 1sec 0 2sec and 0 3sec As you see from the example above user defined delay lists have to be initialized at defi nition time Apart from assigning values directly in brackets there are two ways to do this from a file The name of a file in the vd directory can either be specified directly in angled brackets lt gt or indirectly via the VDLIST parameter by including VDLIST in lt gt Example define list lt delay gt D2list lt mydelaylist gt read data from EXPDIR lists vd mydelay list define list lt delay gt D3list lt VDLIST gt __ read data from file addressed in VDLIST parameter Writing Pulse Programs P 214 In the further context of the program the command D1list would execute a delay of 0 1seconds the first time it is invoked In order to access different list e
191. ive after gs has been stopped and restarted All changed parameters except RG will become active at the earliest with the next scan while RG itself will become active immediately Select new parameter group to modify In the left part of the gsdisp window all selectable parameter groups are listed so simply select one of these groups by klicking onto it Klicking on Stop acquisition will stop the acquisition Note it is not necessary to click exactly on the button klicking onto the name of the parameter group works just as well Save adjusted parameter In order to save the last touched parameter for a later data accumulation with go or zg activate the save button in the gsdisp window A status message gives informa tion about the parameter and its saved value Save all adjusted parameters In order to save all touched parameters for a later data accumulation with go or zg activate the save all button in the gsdisp window A status message gives infor mation about which parameters have been saved Reset adjusted parameter In order to reset the last touched parameter to its last saved value activate the reset button A status message gives information about the parameter and its value Reset all parameters In order to reset all parameters to their last saved value activate the reset all but ton A status message gives information about which parameters have been reset Caveats e Changing RG with the slider may caus
192. l is st generate Vega 256 false e Literature D Abramovich amp S Vega J Magn Reson A 105 30 48 1993 3 2 3 Adiabatic Shapes 3 2 3 1 Hyperbolic Secant Shape e Syntax st generate HypSec_ lt size gt lt SW gt lt trunclevel gt lt full half gt lt sweepDir gt int lt size gt shape size in number of points double lt S W gt sweep width based on Isec pulse 3 2 Generate a new shape P 143 double lt trunclevel gt truncation level in bolean lt full half gt full or half passage true false int lt sweepDir gt Direction of sweep 1 high to low 1 low to high field Example st generate HypSec 256 6 75 1 0 true 1 If only amplitude data are needed The call is _st generate HypSec 256 false 6 75 1 0 true 1 Literature M S Silver R I Joseph amp D I Hoult J Magn Reson 59 347 1984 3 2 3 2 SinCos Shape Syntax st generate SinCos lt size gt lt trunclevel gt lt full half gt lt sweepDir gt or st generate SinCos lt size gt lt trunclevel gt false lt sweepDir gt int lt size gt shape size in number of points double lt factor gt phase amplitude factor 0 0 lt p lt 16 0 bolean lt full half gt full or half passage true false int lt sweepDir gt Direction of sweep 1 high to low 1 low to high field Example st generate SinCos 256 8 true 1 If only amplitude data are needed The call is st generate SinCos 256 false 8
193. l three variants can be achieved with a single pulse program cosyph that makes use of the mc macro cosyph 2D homonuclear shift correlation sphase sensitive d0 3u 4 16 A shortcut for acquisition in higher dimensions using the mc command P 251 1 ze dl 3 pl phl do pO ph2 go 2 ph31 d1 mc 0 to 2 F1PH ip1 id0 exit ph1 0 2201331 ph2 0 2021313 ph31 0 2201331 Here a slightly different form of the mc command is used introducing the Fl1PH clause The meaning of this is the following A parameter FnMODE for F1 and or F2 is introduced in 2D and 3D which contains the phase sensitivity mode in F1 or F2 Depending on the setting of this parameter the pulse program will be executed in different ways The FIQF FIPH or even FIEA clauses of the mc command determine which values are legal for the FAMODE 1 FIQF goes with QF FIEA with Echo Antiecho and FIPH with the remaining modes QSEQ States TPPI States TPPI This makes sense as the phase sensitive modes combined in the FIPH case usually can be generated with the same phase lists By the way the processing parameter MC2 will be set properly for the processing status In the case of the cosyph sequence the pulse program will virtually be expanded to the following forms for different settings of FaMODE we leave out the header and the definition of the phase programs as they will be the same in all the exam ples FnMODE QSEQ cosy in QSEQ mode 13 td1 2
194. l where the pulse is executed the default phase is zero when a pulse program is started and no phase was defined The four examples above can also be written in the following form 10mp ph3 f1 p2 0 33 ph4 f2 p30d1H 3 33 ph5 3 Writing Pulse Programs P 198 4 5 3 2 vp ph6 f4 This form expresses more clearly that a phase is a property of a spectrometer chan nel Phase programs Syntax A phase program may be specified according to the following examples 1 phl 00112233 2 phl 5 03241 3 phl 0 4 2 4 4 phl 0 2 1 5 ph1 0 2 414243 6 phl 1 3 4142 2 T phi 0 2 2 4142 8 phi O 2 42 341 42 9 ph1 5 1 2 241 10 phi ph2 2 ph3 A phase program may contain an arbitrary number of phases The list of phases in a phase program can be split over several lines In 1 the phases contained in the program are given in units of 90 degrees The actual phase values would therefore be 0 0 90 90 180 180 270 270 In 2 the phases are given in units of 360 5 degrees corresponding to the actual phase values 0 72 3 72 2 72 4 72 1 72 0 216 144 288 72 degrees The divisor to be specified in parentheses in front of the phase list may be as large as 65536 corresponding to 16 bits resulting in a digital phase resolution of 360 65536 which is better than 0 006 degrees In 3 9 the operators and 4 are introduced which allow you
195. lease note If the spectrometer requires a hardware_list file to be described later in this section it is necessary to create the configuration directory manually and put the hardware_list file there On Unix systems open a unix shell retrieve the hardware_list from the backup device and proceed as follows su cd XWINNMRHOME conf instr mkdir lt instrument name gt cp lt any dir gt hardware_list lt instrument name gt exit Now start XWIN NMR and configure the spectrometer Enter the name of the instru ment usually spect Enter new instrument name spect If you chose a name different from spect be sure to have this name set as alias in the hosts file see Troubleshooting page 11 Otherwise later cf is not able to con tact the spectrometer when it wants to check the spectrometer hardware cf offers a selection of spectrometer types Which type of spectrometer Avance AMX ARX ASX Datastation Apex_l Apex_2 Avance Please wait for some seconds for cf to check the spectrometer hardware On Avance spectrometers it will examine the FCU s the RCU and all its connected digitizers while on AMX ARX ASX systems it will detect the Aspect 3001 con The Acquire Menu P 6 figuration and the digitizers If the spectrometer is an Avance then cf might ask for the specific type of Avance What type of Avance DMX DRX DPX DSX DMX cf then asks for the 1H frequency of the magnet Basic 1H frequency with offset o1 0 in MHz 500 13
196. lock else if as in C is not allowed Example See Table 4 13 on page 234 The if block is executed if the condition is true at compile time in the above example if 15 is greater than 2 p1 is executed with phase program ph1 if not with phase program ph2 If 15 changes during the experiment and the condition becomes false the execution mode doesn t change 4 11 3 Conditions evaluated at run time XWIN NMR supports branching and evaluation of conditions within a pulse pro gram while the pulse program execution is in progress Table 4 14 lists the availa ble commands These commands do not introduce a delay in the pulse program At Writing Pulse Programs P 234 if IS gt 2 pl phl else pl ph2 Table 4 13 a condition evaluated at compile time goto label Unconditional jump to label if expression goto label Branch to label if the expression evaluates to true Branch to label if the trigger condition is true not yet available in XWIN NMR 1 0 and 1 1 Positive level trigger specifiers if trigger goto label trigpl1 trigpl2 trigpl3 trigpl4 Negative level trigger specifiers trignl1 trignl2 trignl3 trignl4 The same trigger specifiers as above are legal The next pulse program command will not be executed until the trigger condition becomes true Example lu trigpl1 aDelay trigger oe ae Positive edge trigger specifiers trigpel trigpe2 trig
197. lt further parameters gt The result is stored as XWINNMRHOME exp stan umr lists wave lt shape type gt If the generated shape should have another filename than lt shape type gt a new filename may by specified using the option lt filename newname gt The option lt nobwcalc gt will prevent an automatic calculation of the bandwidth factor SHAPE_BWFAC 0 0 e Example st generate Gauss 1000 1 filename Gauss new nobwcalc This example will generate a Gaussian Shape with 1000 points and a truncation level of 1 The shape is stored in XWINNMRHOME exp stan nmt lists wave directory as Gauss new No automatic calculation of the bandwidth factor is done 3 2 Generate a new shape P 137 3 2 1 Basic Shapes 3 2 1 1 Rectangle Shape Syntax st generate Rectangle lt size gt lt amplitude gt int lt size gt shape size in number of points double lt amplitude gt amplitude in Example st generate Rectangle 256 100 If no phase data are needed The call is _st generate Rectangle 256 false 100 3 2 1 2 Ramp Shape Syntax st generate Ramp lt size gt lt start gt lt end gt int lt size gt shape size in number of points double lt start gt start amplitude in double lt end gt end amplitude in Example st generate Ramp 256 10 80 If only amplitude data are needed The call is st generate Ramp 256 false 10 80 3 2 1 3 Sinus Shape Syntax st generate Sinus lt size g
198. lt phase gt lt average gt lt mod gt int lt size gt shape size in number of points double lt cycnum gt number of cycles to calculate double lt phase gt initial phase angle 0 0 lt p lt 360 0 double lt average gt average amplitude double lt mod gt amplitude of modulation Example st generate Sines 256 2 0 0 0 80 0 10 0 If only amplitude data are needed The call is st generate Sines 256 false 2 0 0 0 80 0 10 0 The Shape Tool P 146 e Literature S Hediger B H Meier R H Ernst J Chem Phys 102 4000 4011 1995 3 2 4 2 TangAmplitudeMod Shape e Syntax st generate TangAmplitudeMod lt size gt lt modulation gt lt phase gt lt ampl gt int lt size gt shape size in number of points double lt modulation gt Amplitude of Modulation double lt phase gt Phase Value max 95 degree double lt ampl gt Average Amplitude e Example st generate TangAmplitudeMod 256 5000 0 26 56 50000 0 If only amplitude data are needed The call is _st generate TangAmplitudeMod 256 false 5000 0 26 56 50000 0 e Literature M Baldus D C Geurts S Hediger B H Meier J Magn Reson A 118 140 144 1996 3 2 5 Special Shapes for Imaging Applications 3 2 5 1 CosSinc Shapes e Syntax st generate CosSinc lt size gt lt cycles gt lt window size gt or st generate CosSinc lt size gt false lt cycles gt lt window size gt In the second case only amplitude data are g
199. m The pp in each of the five cases is presented identically 2 6 2 2 Display Adjust display parameters Default display parameters Select drawing area font fedraw program display Regenerate program display Figure 2 7 The Display pull down menu Display a pull down submenu containing the following items 2 6 2 2 1 Adjust display parameters This adjusts via sliders six parameters which influence the display of the ppg 2 6 Pulse and Gradient Program Display P 115 These are min interval mid intervall mid duration max interval min height max height MAAE SAN signal FID ECHO background normal inverted Figure 2 8 Adjust display parameters The influence of these parameters is more easily understood with a description of how the ppg display routine works The ppg display routine goes through the the following steps in constructing the time and intensity axes The Windows Menu P 116 Step 1 Calculates all delays and pulses of the pp in pixels proportional to their values in microseconds Step 2 Searches for durations which are shorter in pixels than the min interval If they exist they are made as long as the min interval Step 3 Searches for durations which are longer in microseconds than mid duration and at the same time shorter in pixels than the mid interval If they exist they are made as long as the mid interval Step 4 Searches for durations which are longer in pixels
200. m file freqlist define list lt frequency gt filefq lt freqlist gt define list from file specified in FQILIST define list lt frequency gt fllist lt FQILIST gt ze lpl 4 5 Pulse generation commands P 197 d1 fqlist f1 fqlist inc execute and increment afterwards pl fl use frequency SFO1 100Hz d1 fqlist f1 execute and increment with postfix notation p1 f1 fglist res reset the list index to 0 use frequency SFO1 200 d1 fqlist f1 set frequency fqlist 0 pl fl use frequency SFO1 100Hz d1 fqlist 2 f1 access directly the third list member pl fl use frequency SFO1 300Hz fqlist idx 1 set index to the second list entry d1 fqlist f1 and thus address fqlist 1 pl fl use frequency SFO1 200Hz d1 fqlist dec decrement list index by 1 go 1 exit 4 5 3 Pulse phase 4 5 3 1 Phase programs Definition Pulse phases are relative phases with respect to the reference phase for signal detection A phase must be specified behind a pulse in form of a phase program For example the commands 10mp f1 ph3 p2 0 33 f2 ph4 p30d1H 3 33 f3 ph5 vp f4 ph6 would execute pulses on the channels f1 f2 and f3 f4 repectively The channel frequencies would be SFO1 SFO2 SFO3 and SFO4 The channel phases would be set according to the current value of the phase programs ph3 ph4 ph5 and pho respectively If a phase program is omitted from a pulse command the pulse will have the last phase assigned to the channe
201. may also be accessed from the keyboard Enter the command pl0 to set PLO etc PLO PL31 may also be accessed from CPD programs to control the power of hard and shaped pulses For example the CPD program command p31 sp1 180 pl pll uses PL1 for the shaped pulse spl CNST array of constants 32 floating point constants For free use in pulse programs usually in arithmentic expressions Example p2 p1 cnst1 This statement would use the array element CNSTT 1 NUCLEI set up nuclei NUC1 BF1 SFO1 O1 The edit NUCLEI button is used to assign nuclei to the frequency channels of the spectrometer The program will set the basic frequeny of a channel according to the selected nucleus For channel 1 this frequency is designated as BF1 for chan nel 2 BF2 etc The corresponding actual irradiation frequencies are SFO1 SFO2 etc They are calculated from the basic frequencies by adding a frequency offset which may also be specfied during nucleus setup Nucleus basic frequency irradi ation frequency and frequency offset are displayed in the eda window using the parameter names NUC1 BF1 SFO1 O1 O1P NUC2 BF2 SFO2 O2 O2P etc O1P corresponds to O1 but is displayed in ppm rather than Hertz channels 5 8 for Avance systems are located at the end of the eda table Only the offsets may be changed in the eda window the other parameters are there just to inform you about The Acquire Menu P 56 their current setting For Avance systems
202. me error message is printed The actual execution time of a disk write depends on the computer hardware the operating system and the system load according to simultaneously active processes and users This situa tion may become particularly critical if the destination disk is not physically con nected to the computer but is accessible only via a network Networked disks do not guarantee a defined response time It is legal to specifiy the commands if zd one of id0 31 one of ip0 31 and decou pling commands behind the same delay used for wr It is important to use either a zd or ze command after each wr before the next scan Otherwise the data will be added to some previously acquired data When a pulse program writing to a ser file is started using the command zg XWIN NMR will at first simulate the program to determine the required file size A ser file of this size is then created i e the ser file is not required to grow during the exper iment This method avoids the danger of running out of disk space while acquisi tion is in progress File size calculation takes into account the time domain size TD of the acquisition dimension NBL and loop commands in the pulse program The 4 16 A shortcut for acquisition in higher dimensions using the mc command _ P 249 simulation result should be equal to TD TD F1 for an nD experiment executed from a 2D type data set or to TD TD F1 TD F2 for an nD experiment executed from a 3D type data
203. menting time interval but without changing the receiver phase e QSEQ subsequent fids will be acquired with incrementing time interval and receiver phases 0 and 90 degrees e TPPI subsequent fids will be acquired with incrementing time interval and receiver phases 0 90 180 and 270 degrees e States subsequent fids will be acquired incrementing the time interval after each second fid and receiver phases 0 and 90 degrees e States TPPI subsequent fids will be acquired incrementing the time interval after each second fid and receiver phases 0 90 180 and 270 degrees e Echo Antiecho special phase handling for gradient controlled experiments AQSEQ acquisition sequence The parameter AQSEQ takes on one of the values 312 or 321 It is evaluated by the 3D Fourier transform and describes the sequence of fids acquired in a ser file dur ing a 3D experiment 3 the acquisition dimension 1 and 2 the orthogonal dimensions The processing parameter AQORDER is not evaluated if AQSEQ is set On Avance type systems 3D pulse programs will set AQSEQ automatically if td and td1 are used consistently within the pulse program However you may explic itly define AQSEQ in the pulse program For this purpose insert one of the follow ing statements in the pulse program header aqseq 321 or aqseq 312 On both AMX ARX and Avance type systems you can set or modify AQSEQ using the command 3s AQSEO before starting the transform TD time
204. ments for this sample If you use the same NAME parameter for the data sets the program will automatically assign EXPNO data set parameters e g 10 11 12 Defining a new composite experiment If the experiment you have selected for a holder number has the name COMPOS ITE corresponding to the last entry of the experiment table the n EXPERI MENTS button is used to create a new composite experiment This requires a permission to be granted with eduser A composite experiment is a sequence of up to 9 standard experiments i e non composite experiments which once defined will appear under the name it was given in the experiment table After clicking on the n EXPERIMENTS button a table is show where you can define the sequence of experiments that should constitute the composite experiment With the define EXP button you start a dialog which allows you to enter the name of the composite experiment a comment to appear in the experiment table together with the experi ment name and a list of users that should get the permission to execute the com posite experiment separate the list of users by a space character Before you define the new experiment in this way you may modify selected parameters of the component experiments via the EditPar button see below In order to delete a composite experiment click on a holder number Select the desired composite The Acquire Menu P 80 experiment Click on n EXPERIMENTS Click on define EXP
205. meter SR is derived from SF and BF1 The Acquire Menu P 32 The aquisition parameters will be SAVE saved on the disk Exchanges the F1 nucleus with the SWITCH F1 F2 F2 nucleus Exchanges the F1 nucleus with the F3 nucleus With the SWITCH buttons you may easily swap between observed and decoupled nuclei without having to reenter any frequencies SWITCH F1 F3 sets the default routing for the DEPAUEL selected set of nuclei CANCEL Exit without saving the parameters Shows the aquisition parameters as PARAM they would be stored by SAVE Table 1 10 Command buttons of edasp edsp window SR SF BF1 SR is specified in Hertz Note that for spectrometers equipped with a BSMS unit this number should be set to a value near 0 since the basic frequency of the nucleus is chosen such that the frequency reference standard e g TMS will have the frequency BF1 if the lock frequency has been set properly by the BSMS Logical channels There are two buttons for each logical channel The buttons F1 F8 are used to show and to alter the assignment of the physical FCU to the logical channel e g if F1 is connected to FCU2 this means that FCU number 2 will be used for the logi cal channel F1 If the nucleus for channel i is selected not set to off the button F with the number i must be connected to one of FCU1 FCU8 The selected FCU button must be connected to one of the amplifier buttons T
206. meter may also be entered from the keyboard Type in the parameter name followed by Return This will print the current value and waits for change or confirmation As a second possibility enter the parameter name followed by a space character then type in the new value followed by Return If the current data set is a 2D or 3D data set eda shows two or three columns labelled F2 and F1 or F3 F2 and F1 respectively The leftmost column F2 for 2D F3 for 3D defines the acquisition dimension whose parameters are stored in the file acqu Table 1 16 shows which parameter files correspond to the different dimensions You may access the parameters of any dimension also from the key board Table 1 16 also shows the keyboard commands to access the time domain size parameter TD which exists for all dimensions of a 2D or 3D data set Please The Acquire Menu P 44 F3 F2 F1 Data Param Comm Param Comm Param Comm set type Files and Files and Files and 1D acqu td 2D acqu td acqu2 2td 3D acqu td acqu2 2 td acqu3 ltd Table 1 16 eda columns corresponding parameter files and command example note that typing the parameter name in lower case characters always accesses the acquisition dimension if not preceded by a dimension number Acquisition commands such as gs zg go wobb or rga read in the acquisition parameters from the files acqu acqu2 acqu3 compile them in
207. mission file normal experiment experiment depending on 1 preparation experiment experiment depending on 2 preparation experiments Hinje o variable temperature experiment Table 1 8 Experiment types in a user permission file sponding number of measurements are performed with this sample Permissions The section Permissions contains 4 flags urgent editPAR composite and exit qnmr used to enable or disable certain features for this user Legal values of the flags are no or yes to be specified in the next line in the correct sequence e urgent flag yes This user may classify a sample as urgent during the set procedure In a sample changer run it will get priority 1 3 The configuration suite config P 23 e editPAR flag yes This user is allowed to change acquisition or processing parameters during set e composite flag yes This user may define composite experiments during set A composite experi ment is a sequence of up to 9 standard experiments After a new composite experiment was defined it will be added to the experiment table of the set dia log window e exit qnmr flag yes This user gets the permission to terminate the quicknmr command 1 3 8 Setting up the lock parameter table edlock The purpose of edlock is to define the lock parameters for the solvents to be used for a particular lock nucleus and store them on disk Before you call edlock enter the command locn
208. mple the com mand line d1 cpds1 ph2 f3 cpds2 ph4 f2 would start cpd sequence 1 on channel f3 and simultaneously cpd sequence 2 on channel f2 while at the same time d1 begins Sequence 1 is obtained from a text file whose name is given by the acquisition parameter CPDPRG1 Likewise sequence 2 is obtained from a text file whose name is given by the acquisition parameter CPDPRG2 etc The text file contains the user defined cpd sequence or a standard sequence provided by Bruker e g WALTZ16 GARP BB Cpd sequences cpd programs are set up with the command edcpd described in the 4 9 Composite pulse decoupling cpd P 223 4 9 2 chapter The File Menu Table 4 6 shows the commands available to start a cpd Start decoupling using the cpd program cpds1 cpds8 CPDPRGI CPDPRG8 The decoupling sequence will start at line 1 Like cpds1 cpds8 however the decoupling cpdl cpd8 sequence will continue from the line where it was stopped using do Channel selector To be appended to the cpd commands Like the cpd commands above however the transmitter gate for the specified channel will not be opened Gating is controlled by the main pulse program and can be tailored by the user cpdngsl cpdngs8 cpdngl cpdng8 Table 4 6 Available cpd commands decoupling sequence and Table 4 7 shows the commands available to build a cpd sequence Syntax of cpd sequences
209. n t match a part of or in worst case all the energy is reflected back to the transmitter The results are e a bad performance like long 90 degree pulses and bad signal to noise and e a high risk of destroying the transmitter by reflecting too much power into its output stage All probes used in spectrometers behave like a resonance circuit consisting of the coil and one or more capacitors The impedance of this circuit is frequency dependent and the nominal impedance is given for the resonance frequency only Therefore it is necessary e to tune the probe with the tune knob to set the resonance frequency of the cur cuit to the same value as the frequency of the transmitter pulses and e to match the probe with the match knob to set the impedance of the probe to the same value as the output impedance of the transmitter which is generally 50 Q Additionally only special cables with 50 Q impedance as provided with the spec trometer may be used for all radio frequency cables How to tune and match a probe The wobb command allows you to tune and match a probe in an easy way even when the coil is heavily mistuned and mismatched Firstly we should set the parameters which define the wobble curve 1 The acbdisp command on Avance or the router display on AMX ASX allow you to watch the reflected power as well as the forward power the part of the energy which really is trans ferred to the probe The Acquire Menu P 68 e
210. n processing and plot parameters for many types of NMR experiments They were compiled and tested on various instruments in Bruker laboratories expinstall lets you select your instrument type and stores the corresponding parameter sets pulse programs etc in their working directories XWINNMRHOME exp stan nmr par XWINNMRHOME exp stan nmr lists pp etc respectively During this process it adapts certain acquisi tion parameters such as the observe frequency to the basic frequency of your spec trometer cf must therefore have been executed before Since expinstall may overwrite existing files it should only be invoked by the 1 3 The configuration suite config P 35 administrator In order to exclude such conflicts we recommend not to modify parameter sets pulse programs etc provided by Bruker Instead before applying changes create a copy with a different name expinstall needs only be executed once after installation of a new XWIN NMR version or if at a later time additonal items are to be installed omitted initially On XWIN NMR release media in addition to the software modules Bruker provides pulse program libraries parameter sets etc as listed in Table 1 11 The purpose of Pulse program library Composite pulse decoupling library AU program library Gradient file library Shape file library Standard experiments library Standard composite experiments library Scaling region f
211. n P 97 1 6 9 9 1 7 Important notes 1 Preemphasis bypass and Amplifier modules can be enabled or disabled only for all channels at once for the BGU II and Acustar preemphasis units while they are enabled or disabled for the current channel if you are using the GREAT preempha sis unit 2 Important while it is possible to enable or disable some preemphasis feature explicitly there is no way to detect in which state it currently is Check the LEDs on the preemphasis panel 3 Very important it is not possible to load anything into the hardware while the Preemphasis bypass is enabled The setpre module memorizes all changes on the sliders if any and tries to actualize them in hardware After disabling bypass the changed values will be written into the unit The Disable pulldown All the commands of the Enable pulldown have their counterparts in the Disable pulldown menu Exceptions the Reset protection command is simply duplicated here to simplify reaching it and knowing NMR superuser password is unnecessary to disable Impedance amp loop editing See also the notes for the Enable pulldown Starting and stopping data acquisition This section covers the following commands e zg go Start 1 experiment based on parameter set up with eda ased as 4 run Start a series of experiments based on parameter set up with set extset or by means of bar code labels Must be used for automatic sample changer opera tion Please b
212. n X in the wobble curve causes LED X to be lit How does wobble work Since the output impedance of the transmitter and the impedance of the cables is 50 Q the probe should if possible also have this impedance in order to eliminate reflections The wobb routine therefore compares the probe impedance with a 50 Q reference resistor which is built into each preamplifier module The preamplifier offers the possibility of internally switching between this 50 Q resistor and the probe The heart of the wobble software is an endless loop which steps through the fre quencies in the wobble window The command wobb is very similar to the com mand gs go setup and is therefore used similarly in many cases After startup the preparations needed for the acquisition such as reading and defining acquisition parameters setting up a frequency list compiling a pulse program etc are made Now the 50 reference is measured first The receiver gain is adjusted so that the highest point of the aquired data falls within the range of 18 to 45 of the digi tizer resolution If a complete measurement with the reference resistor has been acquired the preamplifier switches to the probe After that measurement of the impedance of the probe is continuously repeated After a completed scan the com plex magnitude of the difference between probe impedance and 50 Q reference is calculated scaled for the optimal display region and then displayed The LED dis
213. n Zijl amp M Garwood J Magn Reson 125 250 1997 3 2 3 5 Wurst Shape Syntax st generate Wurst_ lt size gt lt total SW gt lt length gt lt power index gt lt sweepDir gt int lt size gt shape size in number of points double lt total SW gt Total Sweep Width double lt lenght gt Length of Pulse in usec double lt power index gt Amplitude Power Index int lt sweepDir gt Direction of sweep 1 high to low 1 low to high field Example st generate Wurst 256 40000 0 1500 0 20 0 1 If only amplitude data are needed The call is st generate Wurst 256 false 40000 0 1500 0 20 0 1 3 2 Generate a new shape P 145 Literature E Kupce amp R Freeman J Magn Reson A 115 273 276 1995 3 2 3 6 Constant Adiabaticity Shapes The following constant adiabaticity shapes are implemented caPowHsec constant adiabaticity hyperbolic secant shape caWurst constant adiabaticity wurst shape caGauss constant adiabaticity gauss shape caLorentz constant adiabaticity lorentz shape Syntax st generate lt shape type gt _ lt size gt lt additional parameters gt For the additional parameters see the corresponding shapes Example st generate caWurst 1000 40000 0 1500 0 2 0 Literature A Tannus amp M Garwood J Magn Reson A 120 133 137 1996 3 2 4 Special Shapes for Solids Applications 3 2 4 1 Sines Shape Syntax st generate Sines lt size gt lt cycnum gt
214. n first scan d1 pwl 2 f3 set power to 30dB always pwl idx pwl idx 3 d1 pwl f4 set power to 40dB in first scan and increment index p1 f1 p2 f2 p3 f3 p4 f4 go 1 exit Writing Pulse Programs P 206 4 5 4 3 Shaped pulses A shaped pulse changes its power and possibly phase in regular time intervals while it is executing The pulse shape is a sequence of numbers stored in a file see below describing the power and phase values which are active during each time interval The interval length is calculated by the program by dividing the pulse duration by the number of power values in the shape file Should it become less than 200 nsec an error message is displayed which tells you how much the pulse duration must be increased The next 3 examples would generate shaped pulses 10mp sp2 ph7 f1 pl sp1 ph8 f2 p30d1H 3 33 sp3 ph9 f3 vp sp4 ph10 f4 Illegal Shaped pulses with vp are not supported The pulse durations would be 10 milliseconds P1 and p30d1H 3 33 respectively The pulses would be executed on the frequency channels f1 f2 and f3 i e the pulse frequencies would be SFO1 SFO2 and SFO3 respectively The pulse shape characteristics would be described by the entries 2 1 and 3 corresponding to sp2 sp1 and sp3 of the shaped pulse parameter table This table is displayed when you click on the SP07 label within eda The table has 32 entries with index 0 15 You may use spO sp31 in a shaped p
215. n must have a time dimension You may therefore include acquisition parameters such as pulses fixed pulses delays fixed delays acquisition time AQ dwell time DW etc within the expression but also parame ters without a dimension such as the time domain size TD The complete list is shown in Table 4 3 An expression must be double quoted It can be placed anywhere in the pulse program but must occur before the line containing the cor responding delay command which would be d13 in our example Please note that the second expression in the example above assigns a new value to d13 each time the expression is encountered e g if contained in a pulse program loop 4 7 Simultaneous pulses and delays P 217 4 6 11 Manipulating the durations of user defined delays Users may define their own delay commands using a statement such as define delay compensationTime at the beginning of the pulse program The delay would be executed with the com mand compensationTime The delay length would be defined by a pulse program line such as compensationTime d1 0 33 For such an expression the same rules apply as for the manipulation of d0 d31 described in the previous section Note The defining expression of a user defined delay must occur before the actual start of the pulse sequence It is evaluated at compile time of the pulse program not at run time 4 7 Simultaneous pulses and delays 4 7 1 Rules The following rules ar
216. nal column R Shift The value in ppm entered here is added to the default calibration done by the sref command This allows chemical shift corrections where for whatever reason the reference shift is not calculated accurately enough The parameters described last are used by the command sref for automatic calibra tion referencing of a spectrum width in ppm defines the range that a reference signal is searched for by sref in order to determine the exact origin 1 3 9 Printer plotter configuration cfpp Execute the command cfpp to inform XWIN NMR of which types of plotters or printers are connected to your computer and to which devices During this proce dure you will also assign names to these devices They are used to define where a spectrum plot or text printout is to be sent All details of cfpp are explained in the chapter The 1D Output Menu 1 3 10 Configure MAS unit cfmas 1 3 11 Execute cfmas if your spectrometer is equipped with a MAS pneumatic unit You must specify the RS232 device to which the unit is connected You may also spec ify the pressure the air on time in seconds for sample insertion and ejection and the sample diameter normal or wide bore Configure BPSU unit for LC NMR cfbpsu Execute cfbpsu if your spectrometer is equipped with a BPSU accessory designed to run LC NMR experiments cfbpsu asks for the RS232 device of the spectrome ter where the BPSU is connected to e g tty 3 1 3 The config
217. name of a macro which was defined at the beginning of the pulse program by means of a define statement e g define oneThird 0 33 Writing Pulse Programs P 216 4 6 9 Manipulating delays Changing d0 d31 by a constant value Each delay command d0 d31 has assigned an acquisition parameter INO IN31 containing a duration in seconds The pulse program commands id0 id31 add INO IN31 to the current value of d0 d31 respectively Likewise ddO dd31 sub tract INO IN31 from the current value of d0 d31 The commands rdO rd31 reset d0 d31 to their original value i e to the values of the parameters DO D31 set up with eda For internal reasons the commands presented in this paragraph must be specified behind a delay whose length is of no importance Examples d1 id3 0 1u ddO dl rdO In Bruker pulse programs DO and D10 are used as incrementable delays for 2D and 3D experiments INO and IN10 are the respective increments which are used to calculate the sweep widths SW F1 and SW F2 respectively cf INO IN10 in the chapter The Acquire Menu for more details 4 6 10 Manipulating delays Redefining d0 d31 The duration of the d0 d31 commands is normally given by the parameters DO D31 However you may overwrite these values in the pulse program using an expression in C language sysntax The following examples show some of the pos sibilities d13 3s aq dw 10 d13 d13 p1 3 5 d2 5 7 td The result of such an expressio
218. ncy control units FCUs For each frequency channel one FCU is responsible The pulse program display simulates the behaviour of the TCU and the FCUs using a TCU simulator and a FCU simulator Figure 2 2 The TCU sim ulator uses the same source code that is used by the embedded controller on the TCU and the FCU simulator uses that same memory image that is also used by the FCU That means that everything that comes out of this two simulation programs reflect exactly what happens on the spectrometer hardware You may specify the duration of the simulation in terms of seconds or number of scans The pulse pro gram output is recorded during this time and visualized on the display You will find any fine detail of a timing sequence even of implicite delays certain pulse program macro commands such as go n apply The command pulsdisp uses the current pulse program defined by the parameter PULPROG In order to set or examine it type in pulprog or eda Figure 2 3 shows the main window of the pulse program display routine First click on the Observe setup button A table of possible channels will appear Enable the channels you want to observe by clicking on the checkbuttons CH etc denote the timing chan nels FCU etc the output of the frequency units and GCU X Y Z the outputs of the gradient unit FCU channels need only be enabled if phases or powers shapes are to be displayed Click on Apply or OK to make the current checkbutton settings effecti
219. nels Normally only one or two control panels are needed at one time Opening and Closing Control Panels Control panels can be opened only from within the main panel using the control buttons Level Lock Sample etc of the lower button row in the main panel A click on the Level button for example will open the Level panel itt Mie Additional menu entry Figure 2 10 Opening a Control Panel When a panel is opened an entry like Close Level Panel is appended to the Dis play pulldown menu to close the corresponding panel again Figure 2 10 A control panel currently not needed can be closed either by using the entry Close Panel from the Display pulldown menu refer to Figure 2 10 or by using the window managers Close or Quit entry When a control panel is closed the additional menu entry Close Panel in the Display pulldown menu of the main panel disappears again The Display pull down menu always contains the list of all currently opened control panels The Windows Menu P 124 2 7 3 2 Control Panel Design A closer look at the control panels reveals one design used throughout the display tool The upper area of the control panel contains a set of buttons the so called Function Buttons which refer to functions on the BSMS device They are used either to switch functions on the device on or off or are used t
220. nfo label at the bottom of the program window The other portion of the window is reserved for the display of the ppg The Windows Menu P 112 a Le mH Eal im Lal iridis Si eee T pe y ji a353 w le i dd Ee pl di dS a Iip AS da dd ag d a5 d di d d iu Abiu daau JA Slee Abuda le Blu 1 Siu di I Bisu Soa 10 Su 20 im gu ig ba azko times amp l bo li cetimey NSLICES I Le atii pia Wk i ptio siari Figure 2 5 Display of the current Pulse Program 2 6 2 Pull down menus The following menu items are available Compile Display Loops Export and Exit 2 6 Pulse and Gradient Program Display P 113 2 6 2 1 Compile GADPROG IXA AeadiPhasefStice X Read haserSlhce PGfcm XEYE fe ie ie ae Gemi Figure 2 6 The Compile pull down menu Compile a pull down submenu containing five compilation options for display ing the ppg in different modes These are GRDPROG gp compiles and displays the gp so that the read phase and slice gradient intensities are presented exactly as they are defined in the text of the gp All fixed gradient values trim values and intensities of gradient functions are expressed in percentages Trim numbers are available Gradient scaling due to field of view or slice thickness is not performed in this representation The gradient axes in the picture are labeled READ PHASE SLICE and gp Read Phase Slice compil
221. ng scans are required This can lead to an overflow of the 32 bit maximum dynamic range of an fid resulting in a distorted spectrum after Fourier transformation XWIN NMR does not normally check for such an event since such situations only occur in special experiments and there are possiblities to work around those However an acquisition parameter OVERFLW is available that allows for user control of overflow detection By default OVERFLW is set to ignore instructing the acquisition software not to care about overflows Alternatively you may set OVERFLW to check and the acquisi The Acquire Menu P 66 1 5 3 tion software will check before each scan whether an overflow would most proba bly occur during the next transient In this case the experiment is halted This allows you to specify a large NS whithout the inherent danger of overflowing When the experiment is done you can examine the actual number of scans per formed using the command dpa or 2s ns Please note Overflow checking is a time consuming procedure carried out by the RCU If ena bled the minimum recycle time between scans is noticeably enlarged which may cause certain experiments to fail DQDMODE Avance type systems only The acquisition parameter DQDMODE defines the fre quency shift applied in Digital Quadrature Detection mode as positive add or negative subtract Acquisition parameter setup with ased or as ased opens a dialog window of acquisition par
222. ning the GPX GPY GPZ parameter table Enter eda and select the GP031 button 4 22 2 Shaped gradients A shaped gradient changes its field in regular time intervals while it is applied The gradient shape is a sequence of real numbers between 1 0 and 1 0 and stored in a file see below namely the gradient strength values valid for each time interval The interval length is calculated by the program by dividing the desired gradient duration by the number of strength values in the shape file The gradient duration must formally be specified by means of a pulse command The gradients are reset to zero at the end of the shape if the shaped gradient is specified via the gp com mand and if no gradient command is immediately following The next 3 examples would generate shaped gradients 10mp gp2 pl gpl gradPulse 3 33 gp3 vp gp4 Illegal Shaped gradients with vp are not supported The gradients would be applied for a duration of 10 milliseconds P1 and grad Pulse 3 33 respectively The gradient shape characteristics would be described by the entries 2 1 and 3 corresponding to gp2 gpl and gp3 of the gradient parameter table This table is displayed when you click on the GP031 button 4 22 Gradients P 263 within eda The table has 32 entries with index 0 31 You may use gp0 gp31 in a shaped gradient command to refer to entry 0 31 Each entry of the shaped gradient parameter table has 4 assigned parameters GPX GPY
223. ntries the list index can be incremented by adding a inc suffix dec remented by adding dec or reset adding res Any index operations are done mod ulo the length of the list i e when the pointer reaches the last entry of a list the next increment will move it to the beginning Furthermore list entries can be spec ified directly in squared brackets counting from 0 i e the command D1list 1 would execute a delay of 0 2 seconds with the above definition Lists can be exe cuted and incremented at the same time using the caret postfix operator The com mand D1list is equivalent to D1list D1list inc Finally you can set the index directly in an arithmetic expression within double quote characters appending idx to the list name The following example summa rizes all list processing features list definitions define list lt delay gt locallist 0 1 0 2 0 3 0 4 define list lt delay gt fromfile lt mydelaylist gt define list lt delay gt fromvarfile lt VDLIST gt locallist locallist inc delay of 0 1sec change index from 0 to 1 locallist locallist res delay of 0 2 sec set index to 0 locallist 2 delay of 0 3 sec independent from index setting locallist locallist dec delay of 0 1 sec after index reset change index from 0 to 3 locallist delay of 0 4 sec locallist idx 3 set index to 3 locallist delay of 0 4 sec move index on to 0 locallist delay of 0 1sec 4 6 Delay generation commands P
224. nu how to set up variable pulse lists VTLIST variable temperature list file The AU program command rvtlist makes the specified list file available to the AU program The AU program command vt sets the Eurotherm temperature according to the current position in the list teready lt seconds gt lt accuracy gt waits for the temperature to settle The AU program continues if the temperature is reached with the specified accuracy 0 0 1 0 or the specified time has elapsed In order to pro ceed to the next list position the command ivtlist must be used dvtlist goes to the previous position If you replace rvtlist by gvtlist the temperature list file is not taken from the VTLIST parameter but the AU program will prompt for it See The Acquire Menu P 64 command edlist in The File Menu how to set up variable temperature lists The command edte is provided to control the Eurotherm parameter settings FCUCHAN FCU for channel fx Avance only This is an array describing the usage of the 8 possible FCUs for the 8 logical channels f1 f8 FCUCHAN 1 2 means that FCU no 2 is used for channel f1 FCUCHAN X 0 if the channel is not used FCUCHAN 0 is always unused This routing is done completely by software RSEL transmitter select Avance only This is an array describing the connections of the 8 possible FCUs to the amplifiers The routing is done by the digital routers RSEL x 0 means no connection RSEL 1 2 me
225. o an openable loop the loop signature is highlighted e Left button release if the cursor just pointed to an openable loop which would be highlighted the loop is opened The pp and the gp loops are opened inde pendently from each other e Middle button click toggle between displaying the pp loops or the gp loops e Right button click toggle between displaying the textual information and dis playing only the drawing lines without any textual information Some mousing features may be also less conveniently accessed via the Loops pull down menu items Short Description of the Information Displayed There are three types of lines displaying information in the ppg e duration lines e RF pulse lines and e gradient pulse lines The duration lines vertical ticks separate different durations and lines with arrow heads show loops for gp loops if the line has no arrow head it represents the begin end block For durations the symbolic name is displayed if any as well as its numeric value The default units for both delays and pulses are millisec onds If the value is expressed in microseconds the letter u is added while the let ter s is added to represent seconds For fixed pulses the letter p is added No numeric value is shown for durations such as vd vp and any incrementable delays The Windows Menu P 120 For pp loops the pulse program text describing the loop is printed as well as the value
226. o select a so called value function a function representing a value displayed in the lower area of the control panel which can be changed with buttons sliders or text display fields The following figure describes the general layout of a control panel Control Panel Name Function Buttons Right Display Field Current Function Diff Mode Button Left Display Field a Function Maximum Function Minimum Slider Step Size Slider Button Button 2 2 Button Figure 2 11 Layout of a Control Panel 2 7 3 3 Toggle and Value Functions Most of the function buttons in the control panels can be assigned to one of two function classes toggle or value functions The BSMS device has many functions that can be controlled by the display tool Some of them represent a simple state like being turned on or being turned off The LIFT ON OFF command is one example These functions are referred to as toggle functions A click on a function button representing a toggle function has an immediate effect on the BSMS device when the button is highlighted the func tion is currently turned on Clicking that button will turn off the corresponding 2 7 BSMS panel bsmsdisp P 125 function on the BSMS visualized by changing the button color to the background color These buttons show the state of the function on the BSMS unit directly The other class of functions represent a value which is not displaye
227. ocess gt 1 7 Starting and stopping data acquisition P 101 1 7 3 1 7 4 where lt process gt is a suitable AU program The data set list is created by the command mkcurdatlist in the AU program started by run 5 First sample already in magnet and locked Answer y or n to inform run in which way to start 6 Processing all samples Answer y or n y enables processing After a data set has been acquired its cor responding processing AU program will be started given by the processing parameter AUNMP of this data set The AU program usually contains Fourier transform and plot commands Processing is carried out in background i e the next sample will be measured while processing or plotting of the previous ones are in progress If you answer n processing will be omitted At any later time you may process the data with run proc see 4 Each time you start run a protocol file is created overwriting an existing one XWINNMRHOME prog curdir protocol The file contains the starting times of the experiments It is a text file you may view or print with the respective operating system utilities For error tracking or other purposes you may generate additional entries in the protocol file You must add the AU command PROTOCOL text at the desired place of the AU program text must be a char variable a text string according to the C language The command quicknmr quicknmr is an easy to use tool for routine spectroscopy
228. omponent displays the deviation in the direction matching the horizontal component displays the deviation in the direc tion tuning Matching represents a measure for the impedance value at the cur rently tuned frequency one lit matching LED meaning zero and all LEDs lit representing the curve maximum The tuning display corresponds to the deviation of the frequency of the curve minimum from the center frequency If the difference between the two frequencies is zero the two middle LEDs are lit if the difference is plus or minus half the wobble sweep width the entire left side or the entire right side of the LEDs is lit respectively The goal of the tuning process is therefore to keep the number of matching LEDs minimal optimal 1 and to bring the lit tuning LEDs into the middle optimal the middle two For accurate tuning the deviations are weighted with a square root function This means that the sensitivity of the LEDs around zero becomes greater However in order to get an idea for the direction of tuning for greatly mistuned impedances 1 5 Setting up acquisition parameters P 71 1 5 4 4 tendency LEDs have also been integrated into the operating panel If the matching tendency LED is lit upwards the deviation from the optimal matching setting is becoming greater and conversely If the tuning tendency LED is lit leftwards the curve minimum moves to the left towards smaller frequencies and vice versa A tendency of directio
229. on of dummy scans DS and NS should therefore be a multiple of the number of phases in the list The go abel command executes a delay the so called pre scan delay to avoid pulse feed through before it starts digitizing the NMR signal During this time Writing Pulse Programs P 186 the receiver gate is opened and for certain instruments the frequency is switched from transmit to receive You can read more about DE and its compo nents DEI DE2 DEPA DERX and DEADC in the chapter The Acquire Menu Normally you can accept the default DE value suggested by the program The total time the go abel command requires to execute a scan is DE AQ 3 milli seconds The last duration is required for internal reasons namely the prepara tion of the next scan The 3 msec are valid for Avance type instruments Older instruments require 6 milliseconds 13 wr 0 Writes the accumulated data as file fid into the EXPNO directory of the current data set Please note that the way the zgcw30 pulse program is built data are not stored on disk before all NS scans have been accumulated However while acquisition is in progress you can force the program at any time to store the data acquired so far by entering the command tr on the keyboard or by calling it from the Acquire menu You may process and plot this data while the acqui sition continues If you want to protect your data against power failures during long term experiments we recommend that you wr
230. ond title for the first exp of the comp TITLE This is a third title for the second exp of the comp NAME June16 EXPERIMENT PROTON TITLE This is a title nwith two lines 1 6 Interface control commands P 85 EXPERIMENT C13CPD TITLE This is a title nwith three lines nThird line HOLDER 9 NAME June17 SOLVENT CDCI13 EXPERIMENT PROTON TITLE This is a default title EXPERIMENT C13CPD TITLE This is a default title EXPERIMENT C13DEPT45 TITLE This is a default title Only one END statement per complete file END 1 6 Interface control commands 1 6 1 Initialize interface The command ii loads acquisition parameters such as frequencies power levels etc into the spectrometer hardware just as it would do it before a data acquisition but without starting the acquisition ii can for example be used to check whether the software has access to all spectrometer components 1 6 2 Shim control 1 6 2 1 Writing reading deleting viewing and setting shim values Shim values are stored in files located in the directory XWINNMRHOMEYexp stan nmr lists scm In case of an instrument with BSMS this must be XWINNMRHOME Texp stan nmr lists bsms wsh wsh lt filename gt Save the shim values which are read from the shim unit in the specified file The Acquire Menu P 86 rsh rsh lt filename gt Read the shim values from the specified file and loads them into the shim unit delsh delsh lt filename gt
231. ontinuously A vertical line is drawn at the center fre quency SFOx to provide optical information on the frequency which is to be tuned The horizontal axis of the coordinate system is scaled in MHz and labeled accordingly Useful information like nucleus tuning frequency frequency of the minimum of the wobble curve and wobble width is displayed in the information window Simultaneously the LED display on the preamplifier is set and refreshed accordingly See Preamplifier operating panel on page 70 The wobble curve shows a dip downwards which changes while you turn the tune or match knobs of the probe 1 High Performance PReamplifier with up to five preamplifier modules The wobb command is only available on spectrometers equipped with a HPPR preamplifier 1 5 Setting up acquisition parameters P 69 bad matching and tuning bad matching good tuning Eea tes gt good matching bad tuning good matching and tuning Figure 1 7 Examples of wobble curves with different matching and tuning 1 Turn the tune knob so that the dip moves towards the center of the screen Keep on turning until the dip is exactly in the center across the vertical line 2 Turn the match knob so that the dip becomes deeper Keep on turning until the base of the dip is at a minimum This occurs at the zero level line for most probes 3 On most probes the matching influences the tuning and vice versa so repeat ste
232. oportional to the duration Doubling the duration means cutting the offset half An error message will be printed when you change the duration of a shape with offset Shaped pulse presetting Please read the description of the parameters SHAPPR 1 8 in the chapter The Acquire Menu to ensure that shaped pulses are executed correctly Generating pulses causing a desired flip angle The pulse generation commands described so far do not allow one to specify a flip angle The flip angle is implicitly defined via pulse duration and power In fact flip 4 5 Pulse generation commands P 209 angle power and duration are not independent of each other Once two of them are known the third one can be calculated XWIN NMR provides the possibility of storing calibrated 90 degree pulses using the pulse widths and the corresponding power levels for different probe heads and solvents cf commands prosol and solvloop Based on these values the command pulse lipangle power duration generates a pulse of the desired flip angle provided the user specifies the flip angle and one of the two other arguments and sets the unknown argument to auto Note that this feature is not yet available in XWIN NMR 1 0 and 1 1 Example 1 pulse 90 deg 0 dB auto f1 ph1 Generate a 90 degree pulse using a power level of 0 dB The program calcu lates the required pulse width and executes the pulse on channel f1 using the phase program ph1 Please note that a
233. ouble lt rotation gt total rotation in degree Example st analyze Gauss bandw2ry 180 Result bandwidth factor Aw AT The Shape Tool P 156 3 4 4 Special Bandwidth Calculations bandw2e calculate bandwidth for excitation My bandw2r calculate bandwidth for refocusing My gt bandw2rx calculate bandwidth for refocusing My Sytanx and Result of these commands are identical to the other bandwidth calcula tion commands 3 4 5 command calcblmo calculate yB 1 max at offset Syntax st analyze Gauss calcblmo lt pulDurShape gt lt rotation gt lt offset gt double lt pulDurShape gt length of shaped pulse in us double lt rotation gt total rotation in degree double lt offset gt offset in Hz Example st analyze Gauss calcblmo 100 90 3000 Result maximum YB1 on resonance corresponding 90 degree square pulse 3 4 6 command calcbladia calculate yB1 max for adiabatic shapes Syntax st analyze Gauss calcbladia lt pulDurShape gt double lt pulDurShape gt length of shaped pulse in us Example st analyze Gauss calcbladia 10000 Result sweep rate on resonance in Hz sec maximum YB 1 2n V Q on resonance 3 4 Analyze existing Shape P 157 3 4 7 command calcpav calculate average power calcpav needs no additional parameters Example st analyze Gauss calcpav Result amplitude relativ to a square pulse of 100 corresponding differenc
234. output channel 15 using active low logic It will remain active until explicitly deactivated e g with the command lu setnmr0 15 sje The characters vertical bar and circumflex can be used to set and clear a bit in a register consisting of 35 bits For this reason several outputs can be disabled or enabled simultaneously For example the command lu setnmrO 14113 15 would enable the output channels 14 and 13 and disable channel 15 The command setnmr0 must be specified behind a delay in the previous exam 4 22 Gradients P 261 ples it is 1 microsecond The minimum delay is 200 nanoseconds Using the setnmr syntax a pulse on a desired channel could be realized accord ing to the following example a4 microsecond pulse on RCP7 4u setnmr0 7 lu setnmr0 7 4 21 2 Type 2 outputs NMR control words These are 128 outputs which can be set with an accuracy of 25 nanoseconds and a minimum of 50 nsec They are organized in 8 registers of 16 bit size called NMR control words The commands setnmr1 setnmr8 are provided to enable or dis able the channels 0 15 of each register The syntax is identical to setnmr0 described in the previous section For example the command lu setnmr3 10113 15 would enable the output channels 0 and 13 and disable channel 15 of register 3 4 22 Gradients A gradient in a particular spacial dimension x y z is added to the homogenous magnetic field in
235. pdated at a user defined interval Each gradient may be independently selected by means of the Channel pulldown menu It is possible to set some parameters important for microimaging such as Gradient calibration constant and scaling factor The slider box consists of six sliders controlling the time and gain values for the respective phase of the preemphasis action slow mid fast and three option menus controlling the time base for which the time sliders are responsible either 0 2 msec 2 msec 20 msec or 200 msec The slider values themselves are shown on the right hand side next to the slider Should you wish to enter new values directly from the keyboard simply click on the slider value to move text cursor into it and type the new value in The time values are shown in milliseconds the time slider ranges and sensitivity depend on the time base The gain values are shown on a scale from 100 to 100 The two arrow buttons with the numeric value to the right from the slider value are used to change mouse sensitivity for each slider For the GREAT units there exist one more slider to adjust Amplifier DC offset between 100 and 100 With the Auto toggle button one can start or stop autoadjustment of the DC offset of the current channel This toggle button is in selected state if offset autoadjust ment for the current channel is in progress otherwise it is shown unselected While autoadjustment it is not allowed to change any preemphas
236. pe3 trigpe4 Negative edge trigger specifiers trigne1 trigne2 trigne3 trigne4 Table 4 14 Conditional pulse program execution 4 11 Conditional pulse program execution P 235 run time pre evaluation is performed during the cycle time of the loops in which the commands are embedded If in a particular pulse program loops are executed too fast a run time message is printed Example 1 ze lab1 d1 pl do if d0 2 7m gt 500m goto lab2 dO d0 10m p2 lab2 go lab1 Assume that we will start with d0 10m The pulse p2 will no longer be exe cuted as soon as the expression d0 2 7m gt 500m becomes true Example 2 ze lab1 if trigpl2 goto lab3 lab2 d1 pl aq lo to lab2 times ds goto lab1 lab3 d1 pl go lab1 The TCU has 4 trigger input channels signals arriving at the TCU can be checked using the trig specifiers This example performs DS dummy scans to maintain steady state conditions as long as no positive level is detected on input channel 2 If such a level is detected NS data acquisition scans are executed then the pulse program again checks the external trigger signal Example 3 ze lab1 d1 trigpl2 Writing Pulse Programs P 236 pl go lab1 This example starts executing the pulse sequence as soon as a positive level is detected on input channel 2 After each scan the pulse program will wait until the next trigger signal is detected Example 4 ze lab1
237. pecial options no_scale Gradient is not scaled Writing Pulse Programs P 266 direct_scale or shim_scale Gradient is not scaled and not rotated e Hardware dependencies can be accounted for by specifying different values for XYZ Examples 10u grad 0 lr2d 100 0 Ramp in the 2nd or phase dimension 1m grad sin 50 200 1r3d 8919019 1 cos 50 200 20 I 21113 direct_scale The 1st or read dimension contains sin 50 200 that means a sine function with 50 amplitude The 2nd parameter indicates a gradient shape consisting of 200 values every value applied 1 200 ms 5 us Every sine value is multiplied with the current value of r3d 8919019 The ampli tude of r3d is different for xyz to account for hardware dependencies The 1st dimension also contains a 2nd gradient shape cos 50 200 You can com bine several gradient shapes in one statement but the same length should be used The 2nd or phase dimension contains 20 indicating a scalar gradient with 20 per cent amplitude The 3rd or slice dimension contains 21713 direct_scale indicating a scalar gra dient with 2 per cent amplitude in x direction 1 per cent in y and 3 per cent in z independent of rotation and scaling 4 22 6 Rotation and Scaling If the EXPNO directory of the current data set contains a text file cag_par the rotation and scaling is done as specified in this file Else if XWINNMRHOME exp stan nmr lists gp contains a text fil
238. pes Menu The commands described in the previous chapters may also be invoked from men ues To generate a new shape cf Chapter 3 2 Generate a new shape use the Shapes menu Figure 3 3 Figure 3 3 The Shapes Menu To generate a new gaussian shape click on Gauss in the Shapes menu Now an edi tor window Figure 3 4 opens which allows to define parameters for the selected The Shape Tool P 164 shape In the case of a gaussian shape two parameters are required size of the shape truncation level Click the OK button to generate a gaussian shape with 1000 points and truncation level of 1 The Apply button starts the calculation of a new shape but the editor window will stay open for further changes Size of Shape Truncation Level Figure 3 4 Editor for Shape Parameters The type and number of parameters required depends on the selected shape see Chapter 3 2 for more details Shape files can also be generated in AU programs or from the commnad line in XWIN NMR To create the above mentioned gaussian shape use the command st generate Gauss 1000 1 3 5 The Interactive Display Command stdisp P 165 3 5 4 The Analyze Menu To analyze a displayed shape cf Chapter 3 4 Analyze existing Shape use the Ana lyze menu Figure 3 5 The results of the analyze commands are displayed in a text window Calculate Bandwidth for Excitation fbandw2 Calculate Bandwidth for inversion fbhandw2i Calculate Bandwi
239. placed by new data replace mode is turned on by the commands ze and zd A memory buffer provides space for TD data points where TD must be set by the user All experiments having a single fid and as a result need just one memory buffer All digitized data are accumulated in this buffer by the acquisition commands and then stored on disk Applications such as multi dimensional experiments imaging experiments exper iments varying parameters such as the decoupling frequency or recovery time gen erate several fids The developer of a pulse program has the choice of utilizing a Writing Pulse Programs P 246 single or several memory buffers to carry out such experiments If a single buffer is used the buffer content must be transferred to disk before the next fid can be measured If several buffers are used several fids can be measured before a disk transfer is required The latter method is appropriate if the fids of the experiment succeed one another so quickly that no disk transfer is possible in between them The acquisition parameter NBL determines the number of memory buffers pro vided default NBL 1 Each buffer has a size TD The buffer size will be rounded to the next multiple of 256 data points if the TD is not a multiple of 256 The acquisition commands will put the fid into the current buffer The current buffer is buffer 1 by default The pulse program command st makes the next buffer the current buffer and the command
240. ple 3m do f3 would terminate decoupling on channel f3 with the beginning of the 3 millisecond delay Decoupling phase The relative phase of the decoupling frequency can be controlled using a phase program This is equivalent to controlling the phases of pulses cf the section Pulse phases in this chapter Examples d1 cpds1 ph2 f3 0 1u cw phl f2 Please note that phase cycling cf the section Phase cycling in this chapter is Writing Pulse Programs P 222 applied to phase programs specified after decoupling commands in the same way that phase programs are specified with pulses A simple example demonstrating this feature is the pulse program section 1m cw ph1 f2 d1 do f2 which is equivalent to the section 1mp ph1 f2 dl A 1 millisecond pulse is executed on channel f2 followed by a delay d1 Its phase is cycled according to phl 4 8 4 Decoupling power The power of the spectrometer channel specified with the decoupling command is valid The power setting commands are pl0 p131 cf the section Power and shape in this chapter for details For composite pulse decoupling additional power set ting features are provided see below 4 9 Composite pulse decoupling cpd 4 9 1 General Composite pulse decoupling as opposed to cw and hd decoupling offers a large degree of freedom for the users to set up their own decoupling pulse sequences Up to 8 different cpd sequences can be used in a pulse program For exa
241. ple scans this array and copies the single results to the double array retValue Now all results of the analyze command are available for further calculations 3 7 APPENDIX Format of a Gaussian Shape File TITLE u xwinnmr3 0 exp stan nmr lists wave Gauss JCAMP DX 5 00 Bruker JCAMP library DATA TYPE Shape Data ORIGIN Bruker Analytik GmbH OWNER lt wk gt DATE 00 03 23 TIME 08 19 08 SHAPE_PARAMETERS Type Gauss Truncation Level 1 MINX 1 000000e 00 HMAXX 9 999954e 01 MIN Y 0 000000e 00 MAX Y 0 000000e 00 SHAPE EXMODE Universal SHAPE_TOTROT 9 000000e 01 SHAPE_BWFAC 2 122000e 00 SHAPE_INTEGFAC 4 115776e 01 SHAPE_MODE 0 NPOINTS 1000 The Shape Tool P 180 XYPOINTS XY XY 1 000000e 00 0 000000e 00 1 018591e 00 0 000000e 00 1 037490e 00 0 000000e 00 1 056700e 00 0 000000e 00 1 076227e 00 0 000000e 00 1 096073e 00 0 000000e 00 1 116245e 00 0 000000e 00 1 136746e 00 0 000000e 00 1 157580e 00 0 000000e 00 1 178753e 00 0 000000e 00 1 200269e 00 0 000000e 00 1 200269e 00 0 000000e 00 1 178753e 00 0 000000e 00 1 157580e 00 0 000000e 00 1 136746e 00 0 000000e 00 1 116245e 00 0 000000e 00 1 096073e 00 0 000000e 00 1 076227e 00 0 000000e 00 1 056700e 00 0 000000e 00 1 037490e 00 0 000000e 00 1 018591e 00 0 000000e 00 1 000000e 00 0 000000e 00 END Chapter 4 Writing Pulse Programs 4 1 Introduction A pulse program is an ASC
242. pler respectively from the current position of the respective frequency list file The next time such a com mand is encountered the next frequency is taken from the list Example d1 o1 set transmitter frequency during a delay of length D1 from the list defined by FILIST See command edlist in The File Menu how to set up frequency lists FQILIST FQ8LIST frequency list files For Avance type spectrometers only The pulse program commands fql fq8 set the frequency of a spectrometer channel from the current position of the respective fre quency list file You must append one of the options f1 f8 to these commands to define the channel For example the command d1 fq2 f1 takes the frequency value from the current entry of FQ2LIST and loads it to channel f1 Execution is performed during the delay D1 The next time the command is encountered the next frequency is taken from the list See command edlist in The File Menu how to set up frequency lists DSLIST data set list file 1 5 Setting up acquisition parameters P 63 The pulse program command wr 0 stores acquisition data in the files fid or ser of the current data set In contrast the pulse program command wr 1 stores these files in the first data set specified in the list file wr 2 in the second data set etc You may also access the data set list via a pointer pointing to the first data set in the list when the pulse program is started The command wr stores the
243. program phases lu cpdngs2 f2 p1 phi d1 f1 1 p2 d2 f2 lo to 1 times 10 lo to 2 times 10 4 9 3 Phase setting in cpd programs addphase setphase In cpd programs addphase is the default mode i e addphase needs only be specified to switch back to default mode in the case where setphase mode was previously used Example 1 Commands in cpd program addphase pepd 180 Pulse program command to start the cpd sequence d1 cpds2 f2 ph2 Resulting phase of the pcpd pulse 180 plus the current phase in ph2 Example 2 Commands in cpd program addphase pcpd sp15 Pulse program command to start the cpd sequence d1 cpd2 f2 ph2 Resulting phase of the pcpd shaped pulse shaped pulse phase according to 4 9 Composite pulse decoupling cpd P 227 the phases in the shape file plus ph2 Example 3 Commands in cpd program setphase pepd sp15 180 Pulse program command to start the cpd sequence d1 cpd2 f2 Resulting phase of the pcpd shaped pulse shaped pulse phase according to the phases in the shape file plus 180 Please note that in this example a phase program must not be used with cpd2 since the FCU does not support the real time addition of more than two phases 4 9 4 Frequency Setting in CPD Programs 4 9 4 1 There are three ways to change the frequency of the channel where the CPD sequence is applied They are similar to the frequency setting commands in the pulse program except that the channel sp
244. program syntax for the 4 phase modulator phl x y x y This is equivalent to the following conventional phase program ph1 0 90 180 270 Whenever the special syntax is used in a phase program the phases will be selected from the 4 phase modulator rather than from the FCU s digital frequency generator The 4 phase modulator has a number of internal adjustment parameters which can be set with the command ed4ph If the spectrometer is not equipped with a HPCU the modulator must be defined in the file xWINNMRHOME conf instr lt intrumentName gt hardware_list cf is required afterwards The unit may be connected to tty 0 or tty20 on the CCU Power and shape Rectangular pulses A rectangular pulse has the same constant power while it is executing The power is like the pulse frequency set via the spectrometer channel number f1 f8 There are acquisition parameters PLO PL31 which hold power values in dB You set the amplitude for a particular channel from these parameters using the pulse program commands pl0 p131 For example d1 pl5 f2 would set the transmitter power for channel f2 to the value given by PL5 Any pulse executed on this channel would therefore get the frequency SFO2 and the Writing Pulse Programs P 204 4 5 4 2 power PLS The pl0 pl31 commands must be written behind a delay The power change occurs within this delay which must not be shorter than 2 microseconds The default power levels
245. ps 1 and 2 until the dip is exactly in the center of the screen and its base at minimum level Then the probe is tuned and matched Now you are finished with tuning and matching and may stop wobb by activating the stop button or by entering stop via the keyboard The Acquire Menu P 70 1 5 4 3 Change wobble sweep width and center frequency during wobb Activate the button wobb SW and confirm the question Change the nucleus with the ENTER key Then enter the desired center frequency and wobble sweep width here the minimum value for WBSW is also 0 001 MHz After that the wobble routine stops the acquisition and restarts with the new parameter setting Select another nucleus If more than one nucleus is defined which may be wobbled you can switch to another nucleus either e by pressing the CHANNEL SELECT button on top of the preamplifier or e by activating the button wobb SW and typing y to the question Change the nucleus Alternatively you can enter wbchan via the keyboard wobb then selects the nucleus with the next higher frequency and restarts the acquisition After a few seconds the wobble curve is displayed again Preamplifier operating panel Depending on the location of the magnet you may not be able to see the display screen when tuning the probe Therefore the operating panel of the preamplifier has been equipped with an LED display which in the case of wobbling shows the interpreted wobble curve The vertical c
246. pu0 rpu31 reset p0 p31 to their original value i e to the values of the parameters PO P31 set up with eda For internal reasons the commands presented in this paragraph must be specified behind a delay whose length is of no impor tance Examples d1 ipu3 0 1u dpud d1 rpu0 Manipulating pulse durations Redefining p0 p31 via an expression The duration of the pulses p0 p31 is normally given by the parameters P0 P31 However you may overwrite these values in the pulse program using an expres sion The following examples show some of the possibilities p13 3s aq dw 10 p13 p13 p1 3 5 d2 5 7 td The result of such an expression must have a time dimension You may therefore include acquisition parameters such as pulses fixed pulses delays fixed delays acquisition time AQ dwell time DW within the expression but also parameters without a dimension such as the time domain size TD The complete list is shown in Table 4 3 An expression must be quoted using double quote characters It can be placed anywhere in the pulse program but must occur before the line con taining the corresponding pulse command which would be p13 in our example Please note that the second expression in the example above assigns a new value to p13 each time the expression is encountered e g if contained in a pulse program loop Note that expressions in labelled lines are not supported Give the labelled line a small duration and p
247. qual sign any dimensionless expression is allowed which may contain parameters from Table 4 3 User defined pulse lists In a similar way to user defined pulses entire lists of pulses can be specified in a define statement in the following way define list lt pulse gt Plist 10 20 30 This would define a pulselist Plist with values 10microsec 20 microsec and 30microsec As you see from the example above user defined pulse lists have to be initialized at definition time Apart from assigning values directly in brack ets there are two ways to do this from a file The name of a file in the vp directory can either be specified directly in angled brackets lt gt or indirectly via the VPLIST parameter by including VPLIST in lt gt Writing Pulse Programs P 190 Example define list lt pulse gt P2list lt mypulselist gt read data from EXPDIR lists vp mypulselist define list lt pulse gt P3list lt VPLIST gt _ read data from file addressed in VPLIST parameter In the further context of the program the command Pllist would execute a delay of 10microseconds the first time it is invoked In order to access different list entries the list index can be incremented by adding a inc suffix decremented by adding dec or reset adding res Any index operations are done circular i e when the pointer reaches the last entry of a list the next increment will move it to the beginning Furthermore list entries can be specified
248. r hardware configuration did not change you may simply hit the Enter key to any The Acquire Menu P 4 E m E m a F aj m E m Figure 1 1 Configuration suite question posed during cf Correct execution of cf is a prerequisite for the acquisition commands to work and should only be performed by the administrator of the spectrometer We strongly recommend to save the files uxnmr par and hardware_list if existent on tape dis kette or elsewhere after a successful configuration You should also keep a print out of these files on paper If needed they may be restored into the XWINNMRHOME conf instr lt name gt directory cf executed thereafter will only require the Enter key to be hit for all questions 1 3 The configuration suite config P 5 1 3 1 1 1 3 1 2 Reconfiguration If at any earlier time cf was executed successfully configuration is an easy proce dure since the answers to all questions are stored in a file and are prompted as default As long as the spectrometer hardware has not changed the operator may simply hit the Enter key to all questions until cf is finished At the end a window will appear giving an overview of the spectrometer configuration You should now check whether the configuration is correct and repeat cf if required Configuration from scratch If there was no configuration directory on disk e g on a replaced disk drive cf will start a configuration from scratch P
249. r excitation bandw2i calculate bandwidth for inversion bandw2ry calculate bandwidth for refocusing My Special Bandwidth Calculations bandw2e calculate bandwidth for excitation My bandw2r calculate bandwidth for refocusing My gt bandw2rx calculate bandwidth for refocusing My calcb1mo calculate yB1 max at offset calcbladia calculate yB1 max for adiabatic shapes calcpav calculate average power level integr3 integrate shape and calculate power level compared to hard pulse integradia integrate adiabatic shapes The following commands are available for st_analyze command but no longer listed in pulldown menus of stdisp integr integrate shape and compare to square integr2 calculate power level compared to hard pulse calcb1m calculate yB1 max on resonance 3 4 Analyze existing Shape P 155 3 4 1 command bandw2 calculate bandwidth for excitation Syntax st analyze Gauss bandw2 lt rotation gt double lt rotation gt total rotation in degree Example st analyze Gauss bandw2 90 Result bandwidth factor Aw AT 3 4 2 command bandw2i calculate bandwidth for inversion Syntax st analyze Gauss _bandw2i lt rotation gt double lt rotation gt total rotation in degree Example st analyze Gauss bandw2i 180 Result bandwidth factor Aw AT 3 4 3 command bandw2ry calculate bandwidth for refocusing My Syntax st analyze Gauss bandw2ry lt rotation gt d
250. r frequency sweep Syntax st manipulate lt shape type gt sweep lt pulDur gt lt sw gt double lt pulDur gt length of shaped pulse in us double lt sw gt total sweep width in Hz Example st manipulate Gauss sweep 1000 5000 3 3 4 2 command caSweep Calculates a phase modulation according to a constant adiabaticity frequency sweep frequency t J amplitude t dt Syntax st_manipulate lt shape type gt _caS weep lt pulDur gt lt sw gt double lt pulDur gt length of shaped pulse in us double lt sw gt total sweep width in Hz Example st manipulate Gauss caSweep 1000 5000 The Shape Tool P 152 3 3 5 3 3 6 3 3 7 3 3 8 command power Calculate power of amplitude This is a tool to compare a theoretical shape to an observed shape on the scope e Syntax st manipulate lt shape type gt power lt exponent gt double lt exponent gt exponential factor e Example st manipulate Gauss power 2 command scale Scale the amplitude of a shape to a given percentage e Syntax st manipulate lt shape type gt scale lt scale gt double lt scale gt new scaling in e Example st manipulate Gauss scale 50 0 command addphase Add a constant phase to a shape e Syntax st manipulate lt shape type gt addphase lt phase gt double lt phase gt phase constant to be added in degree e Example st manipulate Gauss 90 0 command trev Time reverse
251. ram commands gron0 gron31 are used to switch on static gradients groff to turn them off Example to enable static gradients for the duration D1 D2 The Acquire Menu P 62 dl gron2 d2 d3 groff The gradient parameters for this example are taken from entry 2 of the gradient parameter table Other entries are accessed using the respective gron command The table has totally 32 entries with index 0 31 Each table entry has 4 parame ters assigned a gradient strength for each dimension in the range 100 100 and a file name The file name does not play a role for static gradients However you may also generate shaped gradient pulses by means of the pulse options gp0 gp31 For example the pulse program command p1 gp5 would generate a gra dient pulse of length P1 Gradient strenght and pulse shape would be taken from entry 5 of the gradient parameter table The specified file must be located in the directory XWINNMRHOME exp stan nmr lists gp It must contain the shape of the pulse generated for example with Bruker s shape or xshape programs Gradient parameters may also be set from the keyboard Example The commands gpx2 gpy2 gpz2 and gpnam2 allow you to set the gra dient strength in the 3 dimensions and the file name for entry 2 of the table FILIST F3LIST frequency list files For AMX ARX type spectrometers only The pulse program commands o1 03 set the frequency of the transmitter decoupler or second decou
252. rate at which the ACB is sampled for transmission information The push buttons may be activated by click ing on the appropriate button after having pulled down the window by clicking on the Controls part of the menu bar If you wish to pause the display at any time use the pause display feature ACB Reset resets the ACB and initializes all observed channels afresh This is necessary to free all amplifiers for action after the Trans mission Power Down Button has been activated on the BSMS Keyboard it takes 2 5 Pulse program pulsdisp P 107 about 10 seconds This also provides a useful way of testing all amplifiers cur rently connected to the system as the reset command searches for all amplifiers on the system and displays all of them up to a total of 6 2 4 6 Motif Resources Various colours and modes including the chosen font for the display may be changed by editing the file u prog version app defaults AcbDisp This file is delivered with your release and sets up a default session s characteristics It may be changed at any time according to your personal preferences 2 5 Pulse program pulsdisp The command pulsdisp displays pulse programs written for Avance type spectrom eters It requires that the cf configuration command was executed for an Avance The spectrometer executes the timing of pulses on a processor called TCU timing control unit while the frequencies phases and power levels of pulses are handled by the freque
253. re the phase for any pulse will be set 3 microseconds before the pulse begins If you would change PHASPR3 to 4 microseconds the phase of all pulses executed on channel 3 would be set 4 micro seconds before the pulses begin Consider the following section of a pulse program which executes two pulses in a row i e without a delay in between on the same channel but with different phases 10up ph8 f2 20up ph9 f2 Assume that PHASPR2 3 microseconds Phase setting for the second pulse would be initiated before the first pulse is finished namely 7 microseconds after its beginning Phase setting independent of pulse commands XWIN NMR allows you set the phase for a particular spectrometer channel inde pendent of pulse commands For this purpose you must specify a phase program behind a delay Examples d1 ph1 f3 0 1u ph3 f2 4 5 Pulse generation commands P 203 4 5 3 10 4 5 4 4 5 4 1 The 4 phase modulator The phases for the spectrometer channels f1 f8 as presented so far are realized in the FCU Frequency Control Unit hardware of the acquisition system during dig ital frequency generation For special applications such as certain solid state exper iments an accessory is available called 4 phase modulator This device permanently provides four phases of the current frequency 0 90 180 and 270 degrees It therefore allows for faster switching between these phases The follow ing example shows the phase
254. re you want to be and then by clicking once on the middle button the chosen value is set The third possibility is is by placing the mouse on either side of the slider button and holding down the left 1 6 Interface control commands P 93 1 6 9 4 mouse button This has the effect of moving the slider in the desired direction in steps according to the step value shown at the rightmost end of the slider which can be changed via the two arrow buttons on either side of the step value The input field between the slider itself and the step control field is used to enter directly the desired value of the slider The option menu to the left of the slider is used to set the time base for the corre sponding time silder Changing time base changes also the time slider limits and step size but not the time slider value in milliseconds except in the case where the time value becomes larger than the maximum limit then it is truncated The pushbuttons There are five pushbuttons under the sliders with functions equivalent to popular pocket calculators Store store current slider and option menu values for the current preemphasis channel in memory for later use The offset impedance and loop parameters of GREAT are also put in memory Recall recall previously stored values from memory set the sliders and hardware accordingly Exchange swap the values stored in memory and in the hardware to see which set is better Undo undo sli
255. red there The files are stored in the directory u exp stan nmr loc_win read The purpose of this command is to read in the lock window settings saved in a file generated with the store command described above A list of available files is displayed from which you may select the desired one quit Terminates the lockdisp command and closes the lock window Amplifier control acbdisp Introduction The acbdisp Amplifier Control Board Display XWIN NMR command represents another new digital control approach improving the functionality of Bruker Spec trometers It is available for the Avance spectrometer series The program allows all amplifier activity to be monitored at the workstation terminal Functionality Decide which amplifiers to display with the aid of the Transmitters pulldown menu It contains a list of all currently activated amplifiers An amplifier is said to be active when it is used in a particular routing arrangement which has been acti vated by means of the edasp or edsp command The system is completely flexible The Windows Menu P 106 2 4 3 2 4 4 2 4 5 and able to monitor any of the 48 possible amplifiers in any given spectrometer Amplifier type and maximum output power is also displayed Not only that but depending on the type of experiment the correct set of amplifiers will automati cally be monitored by the program Initialization The aquisition startup routine informs acbdisp which amplifiers
256. rees 1 go 2 ph31 Receiver phase ph30 PH_ref realized via the phase of the reference frequency of the observe channel Legal phase values arbitrary 2 go 2 ph30 r Combination of 1 and 2 The receiver P Pao a POE phous phase is the sum ph31 ph30 PH_ref Decoupling starts at the same time the 4 go 2 ph31 ph30 r cpd1 f2 receiver is opened and stops automatically when the loop is executed Like example 4 with a phase program for 5 o 2 ph31 ph30 r cpd1 f2 ph29 BOTS Paap p k the cpd sequence Table 4 16 Ways to specify a go or gonp command The commands rcyc label recycnpzlabel The command rcyc executes step 5 of the actions performed by go abel and gonp label cf the previous section The rcycnp command skips step 5c The commands are provided for programming acquisition loops based on adc rather than go abel and gonp label You must not specify phase programs behind rcyc and rcycnp However decoupling commands are legal although it is not meaningful to use them here Table 4 18 displays an example of an acquisition loop based on rcyc The rcyc commands may also be specified behind a delay e g 100u reyc 2 In this case they are executed during the specified delay instead of the default 3 millisec onds The delay must not be shorter than 100 microseconds The commands eosc eoscnp The command eosc executes steps 5a 5c of the actions performed by go abel and gonp
257. rent date during set Please note that the header text of a section may be arbitrary The leading characters indicate the start of a section Experiments The section Experiments is the list of experiments this user is permitted to run Each entry consists of a number a name and a comment The number speci fies the experiment type according to Table 1 8 The name must denote a parameter set in the directory XWINNMRHOME exp stan nmr par Experiments of type 1 or 2 require one or two preparation experiments to be performed before the experiment itself can start e g a 1D preparation experiment determining the optimized sweep width for a subsequent 2D experiment T characterizes a variable temperature experiment If such an experiment is selected during set the initial temperature the temperature increment and the number of increments are requested The corre The Acquire Menu P 22 Example user permission file Data set names DATE Namel Name2 Experiments 0 PROTON128 1H experiment 128 scans 0 PROTON 1H experiment 16 scans 0 C13CPD C13 exp comp pulse dec 1024 scans ONIS5IG 15N exp inverse gated 1 INV4SW sw opt inv 4 pulse MC 1 INV4NDLRSW_ sw opt inv 4 pulse MC long range 2 HCCOSW sw opt CH correlation 2 HCCOLOCSW sw opt COLOC Permissions urgent editPAR composite exit qnmr no yes no no Figure 1 3 Example of a user per
258. riment in set run will invite you to answer the following questions 1 Enter set up file name 1 7 Starting and stopping data acquisition P 99 run will execute the experiments stored in the specified file The file is created and filled with experiments either by the commands set or extset or from the information read from bar code labels It is stored in the directory XWINNMRHOME prog curdir changer 2 Enter sample changer AU program run will start up an AU program which takes over control of data acquisition processing and plotting Please enter a single_sx for spectrometer operation with manual sample handling Before run will execute the next experiment s corresponding to the next holder number in the set up file it will invite you to insert the next sample See b how to terminate run b wm stan_sx for sample changer operation run will move the sample carousel to the position corresponding to the next holder in the set up file taking into account samples with priority change the sample execute the experi ment s defined for this sample and carry on with the next holder number in the set up file If no more experiments are defined run will not terminate but wait until new experiments are inserted into the set up file with set or extset In order to terminate the run command type in run again run will realize that it is already active and ask you whether to terminate c wa barcode_sx for sample ch
259. rint help messages Table 1 9 Command buttons in edlock dialog window special commands Itime Igain lfilter from which you may load the hardware directly by ignoring the values of the edlock table These commands also availa ble in the Acquire gt Interface control gt BSMS unit submenu request the numbers to be entered on the keyboard or they may be specified on the command line For SCM units only LPower is available stored in the 2Hlock or 19Flock file In the right half of the dialog window for each solvent and a selected nucleus the shift of the lock from 0 ppm distance the chemical shift value of the reference signal Ref O ppm for TMS and a width value may be specified They are stored in the 2Hlock or 19Flock file The Acquire Menu P 26 The Bruker standard 2H ock file contains default values for lock power loop gain loop time and loop filter for each solvent If a spectrometer installation is started from scratch these values are automatically read when you do edlock the first time If the 2Hlock file already exists and the lock loop parameters were already defined then these values are displayed and the values from the default file are not used The LOADSTAN button in edlock will read the default file and overwrite all previous settings Please make sure before you use LOADSTAN that you have a print out or disk copy of the original settings The table shown with the command edlock contains an additio
260. rom exiting the setpre module via Cancel On startup of setpre the Z channel is chosen for adjustment as the default The Enable pulldown Gradients generation enable gradient generation If disabled no gradient reaches the gradients amplifiers and the probe This feature only exists for the BGU II Preemphasis bypass enable preemphasis bypass If enabled preemphasis will not be applied to the gradients and they will be directly connected to the amplifiers as they come from the gradient controller BO compensation enable BO compensation This feature only exists for the BGU II Amplifier modules enable gradient amplifiers If disabled no gradient reaches the probe Reset protection reset protection circuit after dangerous rising of the gradient coil temperature or some other erroneous state of preemphasis Offset adjustment start autoadjustment of DC offsets for all channels simultane ously This feature only exists for the GREAT preemphasis units For older GREAT units which do not have auto offset adjust feature this command is disa bled Impedance amp loop editing enable editing of impedance and loop parameters for GREAT Wrong settings of these important parameters can damage the hardware therefore editing is disabled by default To enable it the NMR superuser password must be known If enabled the corresponding sliders and option menu appear in the setpre window 1 7 Starting and stopping data acquisitio
261. s for spectrometers using an intermediate frequency This corresponds to the execution of the command sytra which is inverse to syrec c The phase program pointers are incremented to the next phase in the lists corresponding to the execution of the commands ipp0 ipp31 for the phase programs present in the pulse program This step is skipped by gonp label and goscnp d The commands go label and gonp label perform a loop to label whereas gosc and goscnp do not loop The pulse program commands between label and go or gonp are executed DS NS times During the first DS loops dummy scans to achieve steady state conditions the digitizer is not acti vated otherwise the dummy scans are identical to the NS data acquisition scans If no dummy scans are desired DS must be set to 0 Please note Even if DS gt 0 no dummy scans will be executed if the pulse program command zd rather than ze was executed before a go loop is entered cf the description of ze and zd This feature is for example employed in 2D experiments where dummy scans are only required before the first fid is measured Table 4 16 shows that the go commands can be specified in conjunction with other commands PH_ref is an acquisition parameter to be defined by the user 4 13 Commands to start data acquisition P 239 4 13 2 4 13 3 Receiver phase ph31 realized via add subtract and channel A B switching Legal phase values 0 90 180 270 deg
262. s of NMR experiments defined with the com mand set A typical application of run is automated spectrometer operation with a sample changer b quicknmr Execution of experiments based on standard parameter sets pro vided by Bruker or defined by the spectrometer administrator for routine P 1 The Acquire Menu P 2 applications Requires only solvent and experiment to be specified before execution can start 1 2 Preparing for data acquisition 1 3 Before you can start with data acquisition the following preparations are neces sary 1 Execute the configuration suite command config This is a sequence of com mands which allows you to define your spectrometer environment It is required once after program installation or if the environment changes 2 Set up sample experiment specific acquisition parameters commands eda wobb gs rga set ased Required for every experiment Set up depends on acquisition command to be used zg go run quicknmr Display the lock and fid windows Required to observe fid signal and lock 3 Start acquisition zg Starts an experiment based on free parameter set up with eda iconnmr routine execution of standard experiments Older commands quicknmr Executes experiments based on standard parameter sets run Executes a series of experiments defined with the command set based on standard parameter sets may use a sample changer The configuration suite config Please ex
263. set Otherwise a warning message will be printed even though the experiment can still be executed It is the responsibility of the user to set the TD values of the respective dimensions to match the ser file size since they are used later for the Fourier transform and other processing routines It is important to set the correct values before the experiment starts because XWIN NMR will update the status parameter files at the end of acquisition accordingly If for any reason the TD values in the status parameter files are incorrect after acquisition check with dpa you can still adjust them using the commands 1s td 2s td and 3s td When designing 3D pulse programs the acquisition status parameter AQSEQ describes the order 32 or 312 in which the 1D fids of a 3D acquisition are written into the ser file 3 the acquisition dimension 1 and 2 the orthogonal dimen sions AQSEQ will be set automatically and stored in the parameter file acqu if td and tdl are used consistently within the 3D pulse program However you may explicitly define AQSEQ in the pulse program For this purpose insert one of the following statements in the pulse program header aqseq 321 or aqseq 312 You can also set or modify AQSEQ using the keyboard command 3s aqseq before start ing the transform 4 16 A shortcut for acquisition in higher dimensions using the mc command A typical 1D sequence has a framework similar to the following sequence ze initialis
264. set window will scroll to the corre sponding holder EditPar Clicking on this button will open a list box containing parameter editing com mands acquisition parameters eda processing parameters edp plot parameters edg output device parameters edo information file edinfo Their execution requires a permission to be set with eduser Acquisition parameters are normally defined by the selected experiment At the time the experiment is started the sol vent and probehead dependent parameters are inserted see prosol solvloop Finally the acquisition parameters you have defined with eda are applied and therefore obtain the highest priority If the experiment you have selected is a composite experiment indicated by the 1 5 Setting up acquisition parameters P 81 letter C in the first column of the experiment table and you want to modify parameters of its component experiments you must click on the n EXPERIMENTS button select the component experiment by clicking on its holder number and then invoke EditPar Leave the dialog window with the component experiment via the Return button Quit Terminate set requires a permission to be set with eduser You may terminate set at any time Everything you have set up will be preserved in the set up file If you re enter set at a later time by specifying the same set up file name the dialog box will be filled in with the correct information You may also leave set while run is in progr
265. shape For further information see NMR SIM manual 3 5 The Interactive Display Command stdisp P 169 3 5 5 The Manipulate Menu To manipulate a shape cf Chapter 3 3 Manipulate existing Shape on the display use the Maniplulate menu Figure 3 8 Figure 3 8 The Manipulate Menu 3 5 5 1 Frequency Encoding To calculate a phase and amplitude modulation encoding one or several frequen cies use the offs command Phase Modulation according to Offset Freq To define the parameters needed by the command an editor is available Figure 3 9 In the first radio button box the alignment for the phase is defined phase 0 at the beginning middle or end of the shape In the second radio button box you select whether the reference frequency is taken from the first entry of the frequency list or from O1 of the current data set The Shape Tool P 170 The check button box provides options for the offs command If the frequencies should be taken from a frequency list please use XWIN NMR to define a fre quency list The shape tool reads the frequency list from the directory XWINNMRHOME exp stan nmr lists f1 Figure 3 9 Editor for offs Command After entering the length of the pulse and either the number of frequencies or the name of the frequency list and clicking OK a second Editor Window appears In this window the Reference Frequency and the frequencies from the Frequency List with their differences to the reference freq
266. sidered to be undefined The command ifdef aFlag will ignore all pulse program commands until the next endif if aFlag is unde fined and accept them if aFlag is defined The command ifndef aFlag works conversely In Table 4 11 define PRESAT enables the presaturation command block Com menting out this line in C syntax style define PRESAT would make the PRESAT flag undefined and the presaturation block would not be executed Com ments which begin with a semicolon define PRESET are not evaluated by the precompiler and lead to a syntax error when used together with define and include statements The ifdef and ifndef statements are evaluated by a pre processor The pulse pro Writing Pulse Programs P 232 gram compiler will take over the pre processed pulse program For this reason these statements do not introduce any timing changes It is easy to view a pre proc essed pulse program where all conditional statements beginning with a have been removed Enter the pulsdisp command and click on the button Show pro gram The example could be extended to include double quantum filtering For this pur pose an additional flag e g define DQF could be defined The right part of Table 4 11 shows the same pulse program in a more condensed form The presaturation block is now contained in a separate file Presat incl which is invoked with the include statement Please note All statements beginning
267. stem To specify another font add a font resource on the command line as for example bsmsdisp xrm XBsmsDisp fontList helvet ica bold r normal 10 The Main Panel When starting the BSMS display tool a first window the so called main panel comes up a window with the following layout Main Panel ay Menu Bar Pulldown Menus p ma a a Control Buttons Figure 2 9 Layout of the Main Panel In the upper part of the panel a menu bar with pulldown menus labelled Dis play Options Service as well as a Help menu provide commands control ling the general behaviour of the display tool The lower part offers 5 so called control buttons to open the control panels refer to Chapter 2 7 3 1 Opening and Closing Control Panels The main panel is intended to control the general tool operation Therefore this panel is always open when working with any one of the control panels The latter can however be opened and closed individually to provide just the functionality currently needed 2 7 BSMS panel bsmsdisp P 123 2 7 3 The Control Panels 2 7 3 1 Control panels are used to invoke commands on the BSMS unit For each subsys tem of the BSMS a separate control panel exists offering functions referring to that subsystem Due to the extensive functionality provided by this tool the BSMS functions are distributed to 5 different pa
268. strument name gt A description may be found in Table 1 2 There are several subdirectories whose descriptions are shown in Table 1 3 The hardware _list file All AMX ARX and ASX spectrometers and all non standard Avance spectrome ters need the text file XWINNMRHOME conf instr lt Instrument Name gt hardware _list which is set up by the service engineer at installation time of the instrument and contains information about the hardware equipment of the spectrometer The file 1 3 The configuration suite config acqu conf text file created by cf containing information about the Aspect 3001 hardware configuration not for Avance spectrometers acqu conf_info text file created by cf containing an explanation of the numbers found in acqu conf not for Avance spectrometers bacs_param text file created by cf containing information about the sample changer bbis_bla lt x gt text file created by cf containing information about the specific linear amplifier Avance only bbis_fcu text file created by cf containing information about the FCU s installed in the spectrometer Avance only bbis_rcu lt x gt text file created by cf containing information about the specific RCU and other boards connected to this RCU Avance only bsmsdisp calibr text file created as empty file by cf and filled in or used by bsmsdisp Avance only bsmsdisp calibr bak backup file for bsmsdisp cal
269. t lt cycnum gt lt phase gt int lt size gt shape size in number of points int lt cycnum gt nunber of cycles to calculate double lt phase gt phase angle in degree 0 0 lt p lt 360 0 Example st generate Sinus 256 8 180 0 If only amplitude data are needed The call is st generate Sinus 256 false 8 180 0 The Shape Tool P 138 3 2 1 4 Trapezoid Shape Syntax st generate Trapezoid lt size gt lt startAmpl gt lt leftLimit gt lt centerAmpl gt _ lt rightLimit gt lt endAmpl gt int lt size gt shape size in number of points double lt startAmpl gt Amplitude at Start of Shape in double lt leftLimit gt Left Limit of center region in Points double lt centerAmpI gt Amplitude at Center of Shape in double lt rightLimit gt Right Limit of center region in Points double lt endAmpl gt Amplitude at the End of Shape in Example st generate Trapezoid 1000 0 300 100 700 0 If only amplitude data are needed The call is _st generate Trapezoid 1000 false 0 300 0 100 700 0 3 2 1 5 Triangle Shape Syntax st generate Triangle lt size gt int lt size gt shape size in number of points Example st generate Triangle 256 If only amplitude data are needed The call is _st generate Triangle 256 false 3 2 2 Classical Shapes 3 2 2 1 Burp Shapes Syntax st generate lt shape type gt lt size gt or st generate lt shape type gt lt size gt
270. te it extset periodically every 60 sec onds checks the directory XWINNMRHOME prog tmp for new ASCII experiment files Any new file will automatically be inserted into the desired setup file The Acquire Menu P 82 The result is the same as if the user had entered the information directly on the spectrometer with the command set Once entered into the setup file the ASCII file is deleted from the temporary directory XWINNMRHOME prog tmp It is therefore the user s responsibility to keep a backup copy of this file if needed If several ASCII experiment files are found by extset they are proc essed in the order of their file name extensions NNN When extset is called a dialog window appears first with the question Allow permanent access to setup If the OK field is clicked extset will become per manently active in the background and will enter all arriving ASCII experi ment files into the desired setup file If CANCEL is selected a single ASCII experiment file may be specified for insertion into the setup file and extset will terminate extset may be entered on the keyboard with arguments extset_ lt path of an ASCII file gt Example extset usr people guest expdat 234 In this example extset will only insert the ASCII experiment file expdat 234 into the desired setup file and performs no other task In particular extset will not be active in the background afterwards Figure 1 9 illustrates the major proper
271. te power level compared to hard pulse Syntax st analyze _ lt shape type gt integr2 lt pulDurShape gt lt pulDurHard gt double lt pulDurShape gt length of shaped pulse in us double lt pulDurHard gt length of reference hard pulse in us Example st analyze Gauss integr3 10000 6 6 180 Result integral ratio compared to a square pulse of 100 corresponding difference in dB change of power level compared to level of hard pulse in dB The commands integr and integr2 have been combined to integr3 3 4 Analyze existing Shape P 159 3 4 10 3 command calcb1m calculate yB1 max on resonance e Syntax st analyze Gauss bandw2i lt rotation gt double lt pulDurShape gt length of shaped pulse in us double lt rotation gt total rotation in degree e Example st analyze Gauss calcblm 100 180 e Result maximum yB1 on resonance corresponding 90 degree square pulse The command calcb1m is a special case of calcblmo with offset 0 The Shape Tool P 160 3 5 The Interactive Display Command stdisp The Shape Tool can be started from XWIN NMR by selecting Shape Tool from the Windows Menu or by typing stdisp on the command line The command stdisp opens a new window that allows you to work interactively with the Shape Tool The shape is displayed as amplitude and phase component To convert this to a real imaginary display use the Cartesian Coord button on the button panel F
272. th the display tool calibration the ranges are saved into a defaults file If you think function maxima minima are not set correctly in the control panels due to hardware exchange just start a calibration 1 Only the control panels show an immediate effect The main panels colors change when you restart the application The Windows Menu P 134 2 8 Temperature monitor temon The command temon opens a window and displays the sample temperature in Kel vin or Celsius depending on your selection The last setting is saved in the text file SHOME xwinnmr lt host gt temon where HOME is the XWIN NMR user s home directory and lt host gt the compu ter s network name If the feature Write log file is enabled the temperature is writ ten into a text file in regular selectable time intervals The log file name is DU data lt user gt nmr NAME EXPNO temperatureLog i e in the acquisition directory of the data set from where temon was started The temon window has two modes The first one displays the temperature along with the time it was measured In addition it shows the minimum and the maxi mum value measured during the period the temon window was open The second mode only displays the temperature in a larger font 2 9 MAS rate monitor masrmon The command masrmon opens a window and displays the Magic Angle Spinning Rate in Hertz Its behaviour is similar to the temon window of the previous section The respective
273. that more than one experiments have been set up for this sample F finished All experiments with this sample are complete the holedr may be used for a new one Click on the HOLDER field if you want to re activate the last parameters used HOLDER You must fill in the entry field for a particular holder in order to define the experi ment for the sample in this holder Click on the holder number to anable this entry for editing Clicking on the next holder position will terminate the parameter set up for the current one and switch its status to R or nR In non sample changer mode after the experiments for a holder are terminated by run the operator is invited to insert the next sample manually NAME Define data set NAME parameter for this experiment up to 10 characters See eduser how to set up predefined names You may use the same NAME for all sam ples EXPNO Define data set EXPNO parameter for this experiment a number with possible val ues 10 20 Used to differentiate data sets with the same NAME parameter The increment must be 10 to allow for multiple up to 10 experiments defined on the same holder position SOLVENT Define solvent for this sample The solvent table was set up with edsolv EXPERIMENT Define experiment for this sample Bruker standard experiments were installed with the expinstall command The system administrator may have installed own experiments and copied them to the experiment directory with
274. the button 8 Using the slider 9 Using the right display field In the following paragraphs each method is discussed Changing the Current Value Using the Button By clicking on the button with the left mouse button the current value dis played in the right value field is decreased unless it has already reached its lower The Windows Menu P 128 limit value decreased Click with left mouse button 2 7 3 9 Figure 2 13 Usage of the Button If you click on the button with the middle mouse button the button label will toggle from to and the value will be increased instead of decreased The size by which the value is in decreased is displayed next to the label Step It is currently set to two units in the figure above but can be changed by using the 2 2 button see paragraph 2 7 3 11 Function Sensitivity When holding down the mouse button on the key for a longer time continu ous adjustment of the function value is possible This button has an auto repeat behaviour Changing the Current Value Using the Slider Seiting Values by Dragging the Slider Button The slider provides a method to change a value by using the slider button Push hold down the left mouse button with the mouse pointer onto the slider button and move the mouse to the left or to the right You will
275. the following way The plane which is orthogonal to the gradient direction and which contains the center of the receiver coil will see no gradient field while the two most distant parts of the receiver coil in the respective direc tion will see the negative minimum and the positive maximum of the gradient field The absolute value of the maximum gradient field for either dimension is described by a parameter the gradient strength which can be set by the operator see below A gradient can have a constant strength during the time it is applied or a variable strength Formally this is treated by XWIN NMR similarly to executing rectangular and shaped high frequency pulses Writing Pulse Programs P 262 4 22 1 Rectangular gradients A rectangular gradient has the same constant strength while it is turned on Example 300u gron2 lm 100u groff The command gron2 turns on a gradient with the beginning of a 300 microsecond delay The gradient remains active until explicitly disabled with the command groff In this example the gradient is on during a period of 1 3 milliseconds The gradient strength in either dimension is given by the parameters GPX2 GPY2 and GPZ2 In general the commands gronQ gron31 are provided to enable a gradi ent using the strength values GPX0 GPYO GPZO GPX31 GPY31 GPZ31 respectively The numbers must be in the range 0 100 You can set the parameters by typing gpx0 etc on the keyboard or by ope
276. the increment IN10 in F2 of a 3D data set value must be a FLOAT variable storepar1 SWH value to change the sweep width in Hz in F1 of a 2D data set value must be a FLOAT variable storepar3 SWH value to change the sweep width in Hz in F1 of a 3D data set value must be a FLOAT variable storepar1 SWH value to change the sweep width in Hz in F2 of a 3D data set value must be a FLOAT variable storepar1 SW value to change the sweep width in ppm in F1 of a 2D data set value must be a DOUBLE variable storepar3 SW value to change the sweep width in ppm in F1 of a 3D data set value must be a DOUBLE variable storepar1 SW value to change the sweep width in ppm in F2 of a 3D data set value must be a DOUBLE variable 1 5 Setting up acquisition parameters P 51 SW SWH sweep width in ppm Hz The sweep width may be specified in ppm or Hertz units by setting one of the parameters SW or SWH The other parameter is calculated automatically SWH SW SFO1 The sweep width is the spectral range to be observed SW in conjunction with TD or the desired scan time AQ define the dwell time DW which triggers the digitizer to sample the individual data points The digitizer hardware only allows for discrete values of DW and therefore for SW This explains the observation that the program often changes SW slightly if you enter an arbitrary value SW may also be set interactively
277. the intermediate frequency if required is added to the fre quency of the observe channel This corresponds to the execution of the com mand syrec 4 At the end of DE2 the phase of the receiver channel is set to 0 5 At the end of DEADC delay for ADC blanking the digitizer is enabled Writing Pulse Programs P 238 6 After a total delay of DE the digitizer is started Please refer to the description of the parameters DW DWOV DIGMOD on how the sampling rate is selected The result will be a digitized fid signal of TD data points where the time domain size TD is defined by the user from eda or by typing td The fid will be placed into the current memory buffer The contents of memory buffers can be transferred to disk by means of the wr pulse program command or the tr key board menu command The section Working with acquisition memory buffers discusses the usage of memory buffers and the size restrictions of TD 7 The same time the digitizer is started a delay AQ is executed This is a delay until the digitization of the fid is finished 8 A delay of 3 milliseconds is executed During this time the acquisition software prepares for the next scan a The scan counter visible during real time fid display is incremented to inform the user about the number of scans performed since the last executed ze or zd statement b wm The frequency of the observe channel is switched back to the frequency of the observe nucleu
278. the type of digitizer installed in your instrument The answer is stored in the DIGTYP acquisition parameter of the standard acquisition parameter files Finally for AMX instruments you may initialize the parameters XL and YL with the BSV 10 attenuator setting 3 to prevent probe head damage Parameter set conversion will now start and take a few minutes During this proc ess frequencies are adapted to your spectrometer the sweep width and 2D incre ments are corrected and for Avance type spectrometers the default frequency routing is initiated Update user permission files Enable this item if you intend to use XWIN NMR s automated spectrometer opera tion features commands set run or the commands quicknmr setexp and runexp For any XWIN NMR user a permission file may be created by the system adminis trator using the eduser command Such a file contains the standard experiments which may be carried out by this user and other possibilies see eduser command an example file is XWINNMRHOME exp stan nmr lists sam_users_exam Usually a The Acquire Menu P 40 1 3 15 9 1 3 15 10 new XWIN NMR version includes new standard experiments stored in the file XWINNMRHOME exp stan nmr par 300 News This part of expinstall displays a dialog box of all users If you click on a user expinstall merges the new experiments into his her permission file If you click on the Select all button all users will be updated Install
279. this application The primary user interface has been up to now an additional hardware control unit a keyboard attached directly to the BSMS The tool provides an alternative user interface with the additional capability to access the BSMS from any remote host connected by a network The BOSS 2 keyboard is an extension of BOSS 1 its complete functionality is not supported by the display tool version 1 0 Spectrometers equipped with the newer BOSS 2 keyboard cannot fully be controlled by this software as some of the BSMS functions are missing some shim currents cannot be accessed Getting Started How to Start the BSMS Display Tool The BSMS display tool can be started from either the XWIN NMR package or from a UNIX command shell by entering the command bsmsdisp An amp typed after the command in a UNIX shell allows to continue operation with the shell immediately Starting the Display Tool after a New Installation When the tool is started up the first time after a new installation an automatic cali bration process is invoked checking the BSMS hardware for the limits of the func The Windows Menu P 122 2 7 2 2 tions supported by the display tool The values displayed on the BSMS keyboard if connected during this calibration process may be neglected BSMS parameters are left unchanged Start up Options Start up options are not recognized by the BSMS display tool directly they are passed to the X Window Sy
280. ties of ASCII experiment files Lines start ing with the character are comment lines which are ignored The file consists of a series of keywords one per line combined with information SETUPNAME Specifies the setup file into which extset should enter the following experiments This is the file from which run extracts the experiments to be executed USER Defines the USER parameter of the data set specification a data set is defined by NAME EXPNO PROCNO USER DU SAMPLES Between this keyword and the keyword END experiment names for the holder positions may be listed The holder positions must be empty at the time extset tries to enter the experiments into the setup file Otherwise an error situation occurs extset logs errors in the protocol file generated by run 1 5 Setting up acquisition parameters P 83 SETUPNAME set20 USER guest SAMPLES HOLDER 19 NAME Feb25 EXPNO 50 SOLVENT CDCI3 EXPTITLE created by setd HOLDER 7 SOVENT Aceton EXPERIMENT double END Figure 1 9 Example of an ASCII experiment file An experiment is defined by the keywords HOLDER NAME EXPNO SOLVENT EXPERIMENT TITLE They correspond exactly to the fields of the set dialog window NAME EXPNO and TITLE are optional i e they may be omitted In that case XWIN NMR uses standard default values EXPNO 10 no title NAME is formed from the name of the experiment file the extension being replaced by the H
281. to a form suitable for the spectrometer hardware and load them into the hardware for execution of the experiment The next section describes all the acquisition parameters in detail Some of them depend on the spectrometer type and are required e g for an AMX but not for a DMX The contents of the eda dialog box may therefore differ accordingly Actu ally the parameters appearing in this window are taken from the so called format file XWINNMRHOME exp stan nmr form acqu e which is linked made identical to a format file suitable for your instrument at the time of spectrometer configuration with cf Format files are text files which you may adapt to your requirements e g remove parameters you will never use or change or change their output format If you re arrange the sequence of parame ters in a format file the eda display will change accordingly Please note Before modifying a format file make a copy Format files do not only define the arrangement of parameters in the eda window Some parameters such as DW AQ FIDRES SWH are defined in the format file by means of an equation expressing the relation to other parameters e g SWH SW SFO1 Parameters defined in a format file in this way are called tem porary parameters since they are not stored in an acquisition parameter file acqu which only contains parameters not depending on each other You may insert own 1 5 Setting up acquisition parameters P 45 1 5 2 2
282. to investigate the fine details of the pulse program Particularly text labels indicating the length of dura tions power levels in db or per cent units phases in degrees or pulse program text will not appear before you zoom in deep enough so as to create space for the text The Zoom out button reverses Zoom in and allows you get an overview of the entire simulation You may create an additional pulse program window a copy of the current one from the New display button You can use the one window as an overview and the second one to zoom in The procedure is not limited to two win dows Use the Kill display button to close a window If you want to get a print out The Windows Menu P 110 Sa een SS 8 a es ee a y i E eee al EE Figure 2 4 Display Window of the current display click on the Print button The print dialog box allows you to start printing or to preview the output The printer type paper format layout parameters the preview command and the plot command must be specified in the print setup dialog box It is not always possible to output a long simulation on a single sheet of paper with enough resolution The print setup dialog therefore allows you to expand the output in x and y direction across several pages This is achieved by filling the Split to X Y pages entry with the desired numbers Finally the Options menu of the main pulsdisp window contains the commands Scale setup and FCU simulator set
283. ts 4 5 Pulse generation commands P 205 number in square brackets like pwl 2 Note List indices start with 0 All index calculations are performed modulo the length of the list so in the above example pwl 3 pwl 0 6 0 Caution Take care when changing power levels for several channels within one duration d1 pwl f1 pwl f2 will set both channels to the same power level as index manipulation commands are evaluated only at the end of the duration As an alternative way to initialize a list you can substitute the list definition in braces by a reference to a file given in angles e g lt myfile gt Files are searched for in the 8XWINNMRHOME exp stan nmr lists va directory If you specify VALIST as a filename the actual name will be taken from the VALIST acquisition parame ter Note The number of user definable lists is limited at the moment to 32 for each list type The length of the name is arbitrary but only the first 7 characters are sig nificant A final example shows the use of the above described features Example define list lt power gt pwl 10 30 50 70 definition from file XWINNMRHOME exp stan nmr lists va pwlist define list lt power gt fromfile lt pwlist gt definition from file defined in VALIST define list lt power gt fromva lt VALIST gt ze set power of channel 1 2 3 and 4 using list pwl 1 d1 pwl f1 pwl inc set power to 10dB in first scan d1 pwl f2 pwl dec set power to 20dB i
284. tures unavailable for this particular hardware are excluded from the menus and from the main window If the setpre command is given while an instance of setpre is already started then the preceding instance of setpre is deiconified if necessary and its window is raised to the top of the screen If the user exits setpre via the Close or Exit command of the window manager menu then the module exits leaving the preemphasis unit in its current state If the spectrometer has no preemphasis unit connected the setpre module starts in such a mode where only reading writing and editing parameters is supported This can be useful if somebody is using GAB board or some other gradient hard ware not directly controlled by setpre but wishes nevertheless edit gradient calibra tion constants and scaling factors which are written into disk files and therefore do not require preemphasis hardware The sliders and option menus As with all X sliders there are three possible ways of employment The first and easiest way is by placing the mouse on the slider knob pressing the middle mouse button and moving the mouse sideways to achieve the desired result The sliders have the rolling feature It means that if the slider reaches its rightmost leftmost side but not the numerical limit of its value then the slider rolls over to the other side and continues moving to the given direction Another possibility is to move the mouse to the position on the slider whe
285. uc and type 2H or 19F to define the lock nucleus edlock opens a dialog window according to Figure 1 4 Table 1 9 describes its command buttons For instruments equipped with a BSMS unit the lock parameters are stored in two files The first one contains those parameters depending on the lock nucleus acquisition parameter LOCNUC and the solvent For deuterium its file path name is XWINNMRHOME confinstr lt instrument name gt 2Hlock For a fluorine lock i e the acquisition parameter LOCNUC is set to 9F before calling edlock the file name is 9Flock in the same directory The second file contains parameters depending on the solvent and on the probehead The name of the directory where it is located is the solvent name with the probe head identifi cation number see edhead command as a name extension e g Acetic 03 The file name itself is param XWINNMRHOME conf instr lt instrument name gt prosol lt solvent probeID gt param The first line of the edlock dialog window shows the 2Hlock or 19F lock file names and the current probe head including is ID number as defined with edhead The second line shows the lock frequency the field value and the basic spectrome ter frequency BFREQ The lock frequency is calculated by the software from the BFREQ and the nucleus table The Acquire Menu EERE I ae ane Ji be
286. uency will be shown Figure 3 10 3 5 The Interactive Display Command stdisp P 171 3 5 5 2 Figure 3 10 Editor for Frequency List If no reference frequency is used the values entered as frequencies have to be dif ference frequencies already With the Additional Scaling option the relative power distribution to each signal can be adjusted Scaling factors are in with 100 being the maximum The final amplitude will be rescaled according to the number of frequencies In the above example each frequency will receive 33 of the power Click the OK button to start calculation Calculate Shape from Excitation Region A shape can be modulated according to specific regions in a spectrum The excita tion region may be specified using the interactive integration command in XWIN NMR and saving the regions as intrng file Left and right limits for the different regions are taken from this intrng file If no intrng file is available the number of regions and the carrier frequency O1 must be entered Then the fields for Left Limit and Right Limit Figure 3 11 are empty and must be edited The values must decrease from left to right and overlap ping of the regions is not allowed The Shape Tool P 172 Figure 3 11 Editor for Calculate Shape from Excitation Region The default setting for flip angle alignment and type of 180 degree pulse are shown in Fig 3 11 Depending on the application these settings hav
287. ulse command to refer to entry 0 15 The examples indicate that a phase program may be appended to a shaped pulse just as to a rectangular pulse The current phase of the phase program is added to the phase of each component of the shaped pulse Each entry of the shaped pulse parameter table has 3 parameters assigned A power value an offset and a file name File name The name of a shape file A shape file can be generated using the command st Shapes are stored on disk in the so called JCAMP format Its file format is described in the Chapter File Formats The specified file must be located in the directory XWINNMRHOME exp stan nmr lists wave Offset frequency The offset frequency allows you to shift the frequency of the shaped pulse by a cer 4 5 Pulse generation commands P 207 tain amount in Hertz This shift is internally realized by applying phase changes during the shaped pulse s time intervals This method was chosen to maintain phase coherency of the frequency Power value dB This is the absolute power value which is assigned to the 100 relative power value in a shape file If the shape file contains a relative power less than 100 its absolute power including that of all others in the file will be reduced accordingly With some restrictions also the power level specified last recently for the channel can be used for the shape Use the currentpower modifier after the shape speci fier to achieve this behav
288. up The Scale setup allows you to select loga rithmic scaling of the time axis versus linear scaling Linear scaling will cause a duration to be drawn in dashed lines if it exceeds a certain limit which may be specified The length of the drawing corresponds to the specified limit The reason 2 6 Pulse and Gradient Program Display P 111 for this feature is the fact that pulse programs usually contain microsecond pulses and millisecond or second delays A reasonable display of the pulse sequence can only be obtained by artificially limiting the width of long durations on the screen Logarithmic scaling although distorted often results in an appealing presentation of a sequence The FCU simulator setup allows you select the pulse power units db a logarithmic unit or a linear unit 2 6 Pulse and Gradient Program Display 2 6 1 Introduction The Pulse and Gradient Program Display Tool further ppgDisplay can be accessed via the pull down menu Tools of the Spectrometer Control Tool in the ParaVision mode or via the ppg keyboard command in the XWIN NMR High Resolution mode The following abbreviations apply throughout the present section pp will denote the current pulse program gp will denote the complete set of current gradient programs for read phase and slice or x y Z ppg will denote both pulse and gradient programs as a whole The ppgDisplay contains a menu bar with five menu items on top a slider area and ppg i
289. uration suite config P 27 1 3 12 Avance spectrometer constants edscon The command edscon is only available for Avance type spectrometers It opens a dialog window where you may change the default value of certain spectrometer constants Unlike the normal acquisition parameters these constants are not part of a particular data set If changed the modifications will influence all further meas urements on this spectrometer The constants are stored in the file XWINNMRHOME conjf instr lt instrument name gt scon They define the timing of transmitter blanking ASU blanking preamplifier blank ing phase presetting and shaped pulse presetting with respect to the transmitter gating pulses Furthermore the pre scan delays DE1 DE2 DEPA DERX and DEADC may be changed The pulse blanking constants are explained in Figure 1 5 TGPCH 1 8 pulse BLKTR 1 15 ne oo transmitter blanking BPCH 1 8 ASU blanking TGPPA I 5 eal ole preamplifier blanking PHASPR 1 8 3 a zi phase presetting SHAPPR 1 8 t4 s shape pulse presetting Figure 1 5 Presetting of blanking pulses TGPCH 1 8 transmitter gating pulses The Acquire Menu P 28 They are generated on the TCU word3 Bits 24 31 with the pulse program com mands p1 f 1 8 or cw f 8 Routing is done according to TGPCH FCUCHAN channel BLKTR 1 8 transmitter blanking pulses The transmitter blanking ma
290. ust F1 and F2 edprosol provides additional buttons F3 F4 FS Just as F2 W10 if your system consists of a 10W amplifier F2 routed to the 10W amplifier A4 These buttons show the prosol parameters for the selected Nucleus connected to the correspond ing channel F3 F4 F8 The button Global shows the five global prosol parameters D_grad P_gradl P_grad2 P_trim_mlev and P_trim_hsqc The global prosol parameters are valid for all channels The button standard hard shows the standard hard pulse length and power levels for the selected nucleus Nucleus on the selected channel Fx The button standard soft shows the prosol parameters for the standard soft pulses pulse length power 1 3 The configuration suite config P 19 1 3 6 3 levels shapes and phase alignment To edit the user defined hard or user defined soft pulses click on the corresponding buttons at the bottom of the edprosol win dow These buttons are only available in the Advanced Mode which you may activate using the File Menu Once a prosol parameter set is selected and edited for a channel Fx the Save button stores each prosol parameter set with the filename Nuc Fx Ay Where as Nuc is the selected nucleus e g 1H 13C Fx the selected logical channel e g F1 F2 and Ay is the default routed amplifier of Nuc on ch
291. ustment of acquisition parameters gs The command gs executes like zg the pulse program defined by the acquisition parameter PULPROG in order to perform a data acquisition In contrast to zg only the first acquisition loop in the pulse program plays a role e g up to the first go n or rcyc n pulse program command Data is not accumulated by gs but each new scan replaces the data of the previous one Phase programs are also not executed every scan uses the first phase of a referred list The purpose of gs is to observe the effect of a changed acquisition parameter on the signal thereby optimizing this parameter gs is terminated immediately either by stop or halt and in contrast to go no data is saved on disc with halt gs on AVANCE spectrometers As soon as gs has been activated the acquisition starts and the fid is displayed in the acquisition window while the fid integral is displayed in the information win dow The iconified XWinNmr gs gsdisp appears on the desktop After klicking on it or activating modify gsdisp appears allowing the manipulation of parameters with sliders see Figure 1 8 On startup the frequency offset parameter group O1 8 is active allowing all frequencies used by the current pulse program to be varied On 13C observe 1H decoupling experiments for example O1 and O2 are dis played 1 The preamplifier controller is a microcontroller located in the top of the HPPR housing which is connected to the CC
292. ut the expression into the following line Expressions do not introduce a delay in the pulse program Pre evaluation is applied before the pulse program is started and the result is stored in the available buffer memory to be accessed at run time At run time pre evaluation is performed during the cycle time of the loops in which the commands are embedded If loops are executed too fast in a particular pulse program a run time message is printed 4 5 Pulse generation commands P 193 d0 d31 sec p0 p31 microsec 10 131 loop counters in0 in31 sec inp0 inp31 microsec aq sec dw microsec dwov microsec del de2 depa derx deadc microsec vd sec vp microsec nbl ds ns nsdone td td1 td2 decim cpdtim 1 cpdtim8 sec cnst0 cnst31 Table 4 3 Parameters which may be included in expressions 4 5 1 9 Manipulating the durations of user defined pulses Users may define their own pulse commands using a statement such as define pulse p30d1H at the beginning of the pulse program The pulse would be executed by the com mand p30d1H The duration of the pulse can be defined by a pulse program line such as p30d1H p1 0 33 For such an expression the same rules apply that are valid for the manipulation of p0 p31 described in the previous section Note The defining expression of a user defined pulse must occur before the actual start of the pulse sequence It is evaluated at compile time of
293. ve OK will in addition to Apply close the table Cancel will close it without The Windows Menu P 108 Avance Spectrometer TCU FCU Hardware Timing Frequency Control Control Unit Unit XWINNMR TCU FCU Pulse Program Source Code Memory Image Compiler Pulse Program TCU FCU Simulator Simulator Pulse Program Simulation Programs Display Figure 2 2 TCU and FCU simulator Figure 2 3 Pulse Progam Display changing the last settings If the RCUGO channel is enabled the pulse program display window will contain a section with the RCUGO pulse whose purpose is to start the receiver control unit RCU This is equivalent to the start pulse given to the 2 5 Pulse program pulsdisp P 109 digitizer If you enable the Receiver checkbox a receiver field will be displayed showing the on off times of the receiver and its phase Finally enabling the Prog checkbox will cause the pulse program line responsible for the generation of a cer tain duration to be displayed in the same column as the graphical representation of the duration Next you must specify the duration of the simulation Click on Time or Scans in the main pulse program display window depending on whether you want to spec ify a time or a scan interval to be simulated Insert the time or the scan number where simulation should start in the Start entry field and the stopping time or the last s
294. witching to another function will also switch to the other functions private step size These function sensitivities can be saved with the Save Function Sensitivity command The Differential Mode Diff Mode For normal operation the panels display absolute numbers for value functions in the left and right display fields In differential mode the PREVIOUS field displays the change made the last time the function was accessed The ACTUAL field contains the total change made since the function was selected to be the current function Display Tool Commands Terminating the Display Tool from within the BSMS Display Tool Exit the BSMS display tool with the Exit command in the Display pulldown menu or by using the window managers Quit or Close command It is recom 2 7 BSMS panel bsmsdisp P 131 2 7 4 2 mended to terminate the BSMS display tool always this way If this method does not work the tool does not react on inputs any more the application must be killed from outside by a UNIX shell see below from XWIN NMR When the BSMS display tool has been started from XWIN NMR next to the built in exit and quit command the tool can also be terminated with the kill cmd command entered on the XWIN NMR command line from a UNIX Shell This method should be used only when the methods explained above fail Terminate the tool from a command shell with the command kill
295. with a character must start at the beginning of a line No spaces or tabs are placed in front of the You can use define not only to define aFlag but as known from the C language preprocessor to define complete macros Example 1 define macrol p1 d1 p2 f2 macrol This pulse program is equivalent to p1 d1 p2 f2 Example 2 define macro2 p1 d1 n p2 f2 macro2 This pulse program is equivalent to p1 dl p2 f2 The definition of macro2 is continued on a new line using the n character sequence In example 1 p1 and p2 start at the same time while in this exam ple p2 start at the end of the sequence p1 d1 4 11 Conditional pulse program execution P 233 Example 3 define macro3 p1 d1 n p2 f2 macro3 This pulse program is equivalent to p1 dl p2 f2 The definition of macro3 only requires one line However the n character sequence enforces a new line when the macro is invoked For this reason the pulse programs of the examples 2 and 3 are identical 4 11 2 Conditions evaluated at compile time Program compilation can also be controlled by the parameters LO L31 The fol lowing conditions can be evaluated at compile time if 17 is executed if 17 is not 0 if 118 is executed if 18 is 0 if 19 op number op may be gt lt gt or lt Table 4 12 The condition must be followed by an if block and optionally can be followed by an else b
296. y be switched on a time t1 before the pulse Up to 8 different times can be used for the 8 different ASU channels The same blanking is applied to the amplifiers They are generated on the TCU word 3 Bits 0 7 and NMR2 Bits 5 and 6 together with the transmitter gating pulses TGPCH 1 8 but prolonged at the beginning by the times BLKTR 1 9 Routing is done according to BLKTR RSEL FCUCHAN channel The routing according to RSEL is done by setting setting the RSEL parameters on the digital routers This routing can be switched at runtime by setting the corre sponding NMR control words NMRI Bits 0 3 for RSEL 1 NMRI Bits 4 7 for RSEL 2 NMR Bits 8 11 for RSEL 3 For more than 3 FCUs NMRI Bits 12 15 for RSEL 3 and if RSEL 3 lt 6 NMRI1 Bits 8 11 NMR7 Bits 0 3 for RSEL 4 4 NMR7 Bits 4 7 for RSEL 5 aa For more than 5 FCUs NMR Bits 8 11 for RSEL 5 and if RSEL 5 lt 10 NMR Bits 4 7 NMR7 Bits 12 15 for RSEL 6 6 NMR amp Bits 0 3 for RSEL 8 7 i The corresponding routing of BLKTR BLKPA and BPCH will follow these set tings Examples setnmrl 3 2 1 10 set RSEL 1 3 setnmrl 7 6 15 4 set RSEL 2 2 BPCH 1 8 ASU blanking pulses 1 3 The configuration suite config P 29 1 3 13 They are generated on the TCU word 3 Bits 16 23 together with the transmitter gating pulses TGPCH 1 8 but prolonged at the beginning by the times BLKTR 1 5 Routing is
297. z and My respectively Further routines for evaluation of different components of the magnetization are available under Special Bandwidth Calculations Calculate yB1 max There are two routines to calculate the maximum Rf field strength for classical and for adiabatic pulses For classical pulses the result is given as the field strength yB 1max 27 as well as the corresponding 90 degree pulse length for a square pulse at this field strength To obtain this result the integral of the shaped pulse is compared to that of a square pulse of same length with the latter being normalized to 1 With YB 1 27 square pulse of same length 1 length of pulse 360 deg flip angle 3 5 The Interactive Display Command stdisp P 167 3 5 4 3 3 5 4 4 the result is calculated as YB 1 max 2m yB1 27 square pulse of same length integral ratio For adiabatic pulses the calculation is done completely different by evaluating the sweep rate of the pulse The result is yB 1 max 27 V Q with Q being the quality factor After entering the appropriate value for Q the value for yB1 max 27 is obtained As a rule of thumb Q 5 for inversion pulses and for decoupling pulses Q is between 2 and 3 Calculate average power level This routine integrates the shape and compares it to a square pulse of the same length not only with respect to the amplitude but also with respect to the power Integration of Shapes For classical pulses

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