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Getting Started - Center for Structural Biology

1. Getting Started Varian NMR Spectrometer Systems With VNMR 6 1B Software Pub No 01 999083 00 Rev A1298 varian CO EARS nuclear magnetic resonance instruments Getting Started Varian NMR Spectrometer Systems With VNMR 6 1B Software Pub No 01 999083 00 Rev A1298 Applicability of manual Varian NMR spectrometer systems running VNMR 6 1B software Technical contributors Krish Krishnamurthy Evan Williams Steve Cheatham Frits Vosman Dan Iverson Technical writers Michael Carlisle Dan Steele Technical editor James Welch Revision history A1298 Initial release for VNMR 6 1B software Copyright 1998 by Varian Associates Inc All rights reserved Printed in the United States The information in this document has been carefully checked and is believed to be entirely reliable However no responsibility is assumed for inaccuracies Statements in this document are not intended to create any warranty expressed or implied Specifications and performance characteristics of the software described in this manual may be changed at any time without notice Varian reserves the right to make changes in any products herein to improve reliability function or design Varian does not assume any liability arising out of the application or use of any product or circuit described herein neither does it convey any license under its patent rights nor the rights of others Inclusion in this document does not imply that any p
2. 00 4095 16 to 63 dB steps of 1 i steps of 1 dB DS ct E a ca ee tee E Optional tpwrf dpwrf dpwrf2 tpwr dpwr dpwr2 r VXR S for systems with class C amplifiers observe channel 0 to 255 non linear hetero pe steps of 1 decoupler channel dhp l 0 to 39 dB homo steps of 1 dB 1 W max dlp if dhp n Figure 58 Attenuator Configurations Part 1 of 2 modulation sequence Similarly setting dm to s specifies the synchronous mode in which the decoupler rf is gated on and modulation is started at the beginning of the modulation sequence The s and a values have meaning only on UN TYINOVA and UNITYplus systems On UNITY and VXR S systems s and a are equivalent to y The parameters dm2 dm3 and dm4 function analogously to dm except dm2 works on the second decoupler dm3 on the third decoupler and dm4 on the fourth decoupler ANTYINOVA or UNITY system is configured with transmitter fine power control This fine power level is controlled by the tpwrf or tpwrm parameter The attenuation is linear and spans 60 dB A UNITY or VXR S system can be optionally configured with fine power control This fine power level is controlled by the tpwrf parameter The attenuation is linear and spans 6 dB The parameter homo sets the homonuclear decoupling control for the first decoupler On UNITYINOVA or UNITYplus systems setting homo to y specifies that the receiver is gated which is done by
3. parameter control process in order to find the exact resonance and the optimum parameters phase power gain automatically and quickly with high reliability Fuzzy rules are used in the program to find the exact resonance frequency and for adjusting power and phase The fuzzy rules are implemented at different stages of the auto lock process First the software finds the resonance If the exact resonance cannot be found phase and power are adjusted and the software looks for the exact resonance again The software then optimizes the lock power to avoid saturation optimizes the lock phase and optimizes the lock gain to about half range Figure 36 Lock Frequency Acquisition Window RF frequencies decoupler status and temperature are also set during full optimization Using the Input Window e Enter lock Note that the full optimization is the only automated method for optimizing the lock phase If alock a or s is entered only power and gain is optimized Lock Level and Spin Speed Error Handling The in parameter controls error handling based on lock level and spin speed and specifies the action to be taken based on lock level failure or spinner failure 134 Getting Started VNMR 6 1B 01 999083 00 A1298 6 9 Adjusting Shims e n stops any system checking so that acquisition continues regardless of the lock channel or spin speed e w makes the system check the lock level and the spin speed A warning message is add
4. File Protection Two different processes two different users or one user doing two different things simultaneously should not access the same experiment at the same time To prevent this simultaneous access VNMR has an experiment lock system The primary lock is a file in the user s VNMR directory named lock_N primary where N is the experiment number 1 to 9 The directory contains the lock mode the host name and the ID of the process which has a lock on that experiment The lock mode is a small number that distinguishes between foreground background and acquisition processing Since there is a possibility of a collision between two processes if each finds the experiment available and each attempts to access it at the same time each process must first obtain a secondary lock creating a file named lock_N secondary This file can only be created once so it enforces a sequential access on the primary lock system Since it is only accessed briefly and is deleted once the access is complete you never see this file present under normal circumstances Getting Started VNMR 6 1B 01 999083 00 A1298 7 4 Performing Acquisition To override this protection system on an experiment enter the command unlock exp_number where exp_number is the number of the experiment e g unlock 3 Use unlock only if you know the primary lock on the experiment is stale that is the process that has a lock on the experiment no longer exists Should
5. Hardware Overview The system uses a matrix of 48 channels to provide current into 49 coils within the room temperature shim tube from which 38 or 39 shim gradients are generated Each of the axial shim gradients is produced by applying currents simultaneously in up to 12 different channels and each of the radial gradients in up to 6 different channels with the 48 channel matrix system The distribution of current within the allowed channels for each gradient is under computer control and is calibrated to produce the purest most orthogonal possible single shim gradient For example the distribution of current for the Z2 gradient is adjusted so that the Z2 gradient produced has minimal amounts of other gradients such as Z Z1 or Z0 An interface box provides five user selectable optically encoded knobs to control the shim gradients The interface box also provides the user with a means of storing viewing and recalling up to 63 shim sets on a floppy disk Each of the shim gradients has both coarse and fine controls with each control having a range of 32767 DAC counts The following gradients are controlled Axial ZO Z Z2 Z3 Z4 Z5 Z6 Z7 Z8 Radial X ZX Z2X Z3X Z4X Z5X Y ZY Z2Y Z3Y ZAY Z5Y C2 ZC2 Z2C2 Z3C2 Z4C2 where C2 XY S2 ZS2 Z2S2 Z3S2 Z4S2 where S2 X2Y2 C3 ZC3 Z2C3 Z3C3 where C3 X3 S3 ZS3 Z2S3 Z3S3 where S3 Y3 Interface Box The interface box see Figure 48 has a small displa
6. If labeled AV switch to the absolute value mode If labeled PH switch to the phase sensitive mode The value of the parameter dmg determines the button label Reference in both dimensions set cursor positions to zero chemical shift on the scale Allow 2D analysis including line listing and automatic COSY correlation map Return to the 2D Data Display menu page 79 01 999083 00 A1298 4 11 Analyze Menus 4 11 Analyze Menus A variety of data analysis tools are provided in VNMR including exponential analysis automatic DEPT and COSY analysis spectral add subtract spin simulation deconvolution and regression analysis Analyze Menu The Analyze menu is activated by selecting the Analyze button in the Main menu or by entering the command menu analyze Button Description Exponential Display the Exponential Analysis menu below DEPT Display the Automatic DEPT Analysis menu page 81 for full spectral editing capabilities COSY Display the Automatic COSY Analysis menu page 82 Add Sub Display the Add Subtract menu page 82 Simulation Display the Spin Simulation Main menu page 83 Deconvolution Display the Deconvolution menu page 85 Regrs Display the Regression 1 menu page 86 and run the command expl regression Exponential Analysis Menu The Exponential Analysis menu is activated by selecting the Exponential button in the Analyze menu or by entering the command menu t1lt2anal B
7. Shimming Criteria for Autoshim on page 140 for more information AUTOSHIM menu holds the selections of shim combinations that can be adjusted Choices on this menu include Z1 Z2 Z1 Z4 and ALL NONSPINS A selection is made with the mouse in the normal way the criteria set then shimming is started When the autoshimming reaches the end criteria the label on the STOP button automatically changes back to START On completion of shimming and or locking operations click the CLOSE button at the top of the screen to leave the acqi program New parameter settings are written to the experiment at this time and normal acquisition is enabled again Shimming on the Lock Signal When shimming on the lock you monitor the intensity of the lock signal as you adjust the shim settings Each shim setting controls the current through shim coils that control magnetic field gradients in different directions It is important to know that the Z direction is parallel to the vertical direction of the probe and it is for this reason that the height of the sample in the NMR tube affects the Z shim settings rather dramatically 1 The shim settings could be way off the mark e g if the temperature has changed and in this case the shim settings that have been most recently established for the particular probe you are using should be retrieved from the shims directory as a starting point To retrieve the settings enter rts file where file is the name of
8. revel Al w mi directories and choose a i EREE E A directory You can also enter RER ae a path for your file in the f PS en N ea 74 Directory field Directory export home vnmr1 vnmrsys 3 Select a Data format for ire your file and enter a Data save clone resolution Figure 79 Plot Save Window 4 Label your file by entering a name in the File field 5 Click Close to exit the window Printing Your Plot To print your plot click on the print tool Getting Help Click on the Help option for descriptions of Plot Designer features Getting Started VNMR 6 1B 01 999083 00 A1298 9 9 Printing Exiting Plot Designer To exit the program click on File Quit If you leave a design in the window when you exit Plot Designer your design will automatically appear in the workspace the next time that you use the program 9 9 Printing Table 44 lists printer associated commands and parameters Table 44 Printer Associated Commands and Parameters Commands killprint Stop print job and remove from print queue printoff lt clear file gt Stop sending text to printer amp start print operation printon Direct text output to printer ptext file Print out a text file showplotter Display currently defined plotters and printers showprintgq Display print jobs in print queue vnmrprint Print text files UNIX vnmrprint printfile lt printcap gt lt printer_type lt clear file gt gt Parameter printer strin
9. 2 Ifthe Acquisition Status window is still open click on the EXIT button in the window to close the window and quit the program You are now out of VNMR but still in the UNIX windowing system logged in under your user name In addition to the workspace the background area not covered by any windows you may yet have windows for some programs like a clock or a text editor still open and some icons on the screen for closed programs 3 To close the windowing system move the mouse arrow over the workspace and then press and hold down the right mouse button until a pop up menu appears Drag the mouse downwards until the Exit option at the bottom of the menu is highlighted and then release the mouse button A dialog box appears with the prompt Please confirm exit from window system and two buttons Exit and Cancel 4 Click on Exit with the left mouse button The UNIX prompt for the current user appears for example NMRlab vnmrl gt 5 Enter the command logout The login prompt appears for example NMRlab console login You are now logged out of the system 2 2 Working with VNMR on the Host Computer This section describes how the operator interacts with the system through a number of devices the mouse the keyboard remote status module not on all systems and the display monitor Each part of the VNMR screen is described in detail along with an introduction to working with Solaris and OpenWindows or CDE Table 2 lists the
10. Many users operate their system with just one or two operators and might want to operate solely as vnmr1 without concerning themselves with creating additional files for additional operators In this case we recommend leaving the vnmr files to hold the software provided by Varian pulse sequences macros etc while you put your own modifications into the export home vnmri vnmrsys files Other system administrators might want to set up a system in which each operator or group has an individual directory This can result in for example a series of files organized in a directory such as export home george where george could be userA in Figure 7 which contain the same series of files as found in export home vnmr1l The obvious question is where should data be stored You can create a directory at almost any location in this tree structure in which you can subsequently store data in a permanent fashion or at least before you transfer it to tape A logical place however is within the user s subdirectory Another alternative is to store data in a directory called data within export home username vnmrsys In Figure 7 for example the directory my fids has been created within the home directory of user vnmr1 and has been used to store two different FIDs A FID is not a single file but a directory with the following files e fid contains the raw data for the FID a binary file e procpar contains parameters used to acquire and proce
11. which can be 1 2 on up to 9999 We refer to these experiments as exp1 exp2 exp3 and so on Different experiments can hold different sets of data The exp1lib program gives a view of the experiments on a system by displaying a list of the experiments that exist their size and information about the current data contained in that experiment An experiment has room simultaneously for both the raw data the FID and the processed data the transformed spectrum Thus it is not necessary to remember to save the data before performing an FT or other processing the original data is always unaffected Each experiment always contains some data namely the last data that was collected in that experiment just like parameters always contain the last value that was entered Data remains in an experiment until you return to that experiment and begins a new acquisition Thus an experiment is basically the mechanism for temporary data storage a place for the data while it is being acquired processed or plotted When done with the data it should be saved in a permanent file freeing the experiment for another set of data Multiple Related FIDs Many experiments require obtaining a series of FIDs related to each other through the variation of one or more parameters For example suppose it is necessary to run a series of spectra at four different temperatures 30 C 50 C 70 C and 90 C Instead of acquiring four separate sets of data
12. 162 Interactive Add Subtract menu 83 Interactive button 77 interactive display programs 231 Interactive Mode button 82 interactive programs with menus 60 Interactive Weighting menu 71 72 interface board 192 interleaving FIDs 229 interlock parameter 128 intermodulation distortions 205 Internet Protocol IP 281 intmod parameter 78 249 252 inverted lines spectra 225 io parameter 232 240 242 ionic samples 114 IP Internet Protocol 281 IPA interactive parameter adjustment 159 IPA button 159 ipulse statement 159 160 is parameter 239 242 253 isadj macro 253 iterate button 85 iterative optimization 85 J jdesign macro 264 jexp command 32 207 join an experiment 32 join experiment 67 jplot command 262 264 J resolved 2D 70 80 K k suffix 95 K symbol 223 kermit directory 34 kermit program 34 kermit doc file 34 keyboard 27 42 keyboard entry of macros 33 kill command UNIX 208 286 killplot macro 255 L L shimming criterion 140 L1 to L10 keys 43 L7 function key 50 Label button 76 Laboratory Information Management Network 281 landscape view plot configuration 270 Large button 72 74 01 999083 00 A1298 LARGE button acqi 149 large command 47 large graphics window 46 large transform with zero filling 72 74 LaserJet Plus printer 255 Ib button 72 223 lb parameter 221 222 Left button 78 79 left button of mouse 42 59 left command 25
13. Exp 3 in Figure 10 This number refers to the experiment currently displayed on the screen which is the experiment the operator can currently control How the data system defines an experiment is discussed below Short messages frequently appear on the right end of status line to identify the particular program that is executing such as FT when a Fourier transform is in progress or CONT when a contour plot is being drawn e The second line displays the current plane during 3D data display In the absence of 3D data the second line is blank e The scrollable window is generally used to display system messages such as Acquisition Complete or the value of a parameter or to display error messages such as Error in Input from Terminal The advantage of a scrollable window is that if a message has scrolled out of view it can be retrieved by clicking on the scroll bar along the side of the window You can edit text in this window by highlighting the text you want to copy or move using the left mouse button and then pressing the right mouse button to pop up an Edit menu Only VnmrxX installations feature the scrollable window Other systems display a single line only If VnmrX is installed on your system you may want to change the size or even the existence of this window To change the number of lines in the window open the export home username vnmrsys app defaults vnmr file or vnmr app defaults Vnmr with a
14. Parameter shimspath string Path to user s shim directory Experiment Files An experiment such as exp1 consists of one or more FIDs one or more spectra various parameters including nine saved displays a text file and a number of other files Because the FID is maintained separately from the spectrum it is not necessary to save data permanently before performing the Fourier transform or other data processing In general the recommended course of action using a VNMR data system is to save the data in a permanent file as the last action that you perform on the data In this way the result of operations performed during data processing choice of weighting functions referencing phasing scaling etc are preserved with the data and should the data be recalled later it will incorporate all of this information automatically Saving Data Data are saved using the sv lt file gt macro Ifa file name is not entered as an argument svf asks for one Only the FID is saved not the spectrum since the spectrum can always be reconstructed from the FID 01 999083 00 A1298 Getting Started VWMR6 1B 277 Chapter 10 Storing Retrieving and Moving Data 278 The svf macro creates a directory with the suffix fid that contains the following four files each with a special purpose e File fid contains the raw data the FID e File procpar contains the parameters e File Log contains the acquisition log e File text c
15. The following codes enable control of other aspects of automatic shimming e 1sets shimming on the lock instead of the FID default e fsets shimming on the FID instead of the lock background FID shimming is not available on MERCURY VX MERCURY and GEMINI 2000 systems e 0 90 sets shimming on the FID with limits for the FID evaluation range Full range is 0 to 100 percent of the duration of the FID Sensitivity to higher order spinning gradients is increased with a start of 0 and a finish limit of about 5 or 10 which weights the evaluation to the front of the FID e ry rotation yes turns the spinner on e xn rotation no turns the spinner off e dxsets a delay x hundredths of seconds between lock samplings Variations in lock solvent T and D relaxation times affect the ability of automatic shimming to attain good resolution in reasonable times If too short automatic shimming will not perform properly If too long the shimming will become unacceptable in duration dx allows setting an appropriate delay and can be used one or more times within a text string If no entry is made using dx the system automatically measures the lock response and sets a delay accordingly e tx sets the maximum shimming time to x seconds Once t x is set it governs all future shim elements within a method string just as dx governs the lock sampling interval for all shim elements until changed If t x is not set the shimming will proceed based o
16. cccecessesscescsseeeeeecsecseescenecaecaeesesaeeaseeesaesaeensenenes 260 Figure 72 Plot Designer Window 0 sssessssecsseccesesseecceeceseseescenecneescesecnecasencssecaeeaseeesaeeeseneee 262 Figure 73 Window Preferences Panel 0 cseesseccssssseeeceeceseeeseceecsceseesecnecaeeeeaecaseeeeecsaecasseeaes 263 Figure 74 Window with Data and Without Borders and a Grid oo eee ceeeeeeeeecneeeeeeeeaeeeeeeeens 264 Figure 75 Region Editor Window tices ie A oe ei 266 Figure 76 menu File sisser aoe ea aeaee a aeea EE nieve et be E EEEE Ea CaTa 267 Figure 77 Item Preferences Window ssscessccsseseseeceseseesceseenecoeeecenecaseaseeesaecasnsseeneeeserens 268 Figure 78 Text Input Window 00 eecssssesessecsseccesesseeeceeesceseescseecncescesecnecaceeessecaseaseeesaeceseneees 269 Figure 79 Plot Saye Wi dOW dscacueiediiiindsiiiia nia auiudiga Gail din aniiaiiian 270 14 Getting Started VNMR 6 1B 01 999083 00 A1298 Table 1 Table 2 Table 3 Table 3 Table 3 Table 3 Table 4 Table 5 Table 6 Table 7 Table 8 Table 9 Table 10 Table 11 Table 12 Table 13 Table 14 Table 15 Table 16 Table 17 Table 18 Table 19 Table 20 Table 21 Table 22 Table 23 Table 24 Table 25 Table 26 Table 27 Table 28 Table 29 Table 30 Table 31 Table 32 Table 33 Table 34 Table 35 Table 36 Table 37 List of Tables Entering and Exiting VNIMIR seccciesccegstconse covecescstsacscdnsanscbssseseastvssscodnseioesadonsscadedaseebsad
17. directory gt ls lt directory gt mkdir directory mv from_file to_file pwd lt directory gt rename from_file to_file rm filel lt file2 gt rmdir directory Parameters curexp string defaultdir string Display one or more text files in text window Change working directory Copy a file Copy a file Delete file parameter directory or FID directory List files in directory List files in directory List files in directory Create new directory Move and or rename a file Display current working directory Move and or rename a file Delete file Remove directory Current experiment directory Default directory for the files menu system Creating and Manipulating Directories A new directory is created by the mkdir directory command If a directory is no longer needed the rmdir directory command removes one or more empty directories i e the directory does not contain files The mv old_name new_name command renames a directory and the copy old_name new_name command makes a copy of the directory entered as the first argument and all subdirectories and files of that directory The new directory name is specified by the second argument The commands 1f 1s and dir list files in the current working directory on the text output window If a directory is specified as an argument to 1 f or 1s the files in that directory are listed instead of the current directory dir can include a st
18. lockte 1 2 4 7 12 48 in sec on UNTYNOVA locktc N A on GEMINI 2000 MERCURY VX and MERCURY shimset 1 2 3 14 on YNTYINOVA 1 on GEMINI 2000 shimset 1 2 3 10 on WMERCURY VX and MERCURY z0 2048 to 2047 or 32768 to 32767 Lock Power Gain and Phase Under computer control lock power gain and phase are set by the lock parameters lockpower lockgain and lockphase with the following limits and step sizes e On NTYINOVA and UNITYplus lock power is 0 to 68 dB 68 is full power lock gain is 0 to 48 dB and lock phase is 0 to 360 degrees Step size for power and gain is dB step size for lock phase is 1 4 degrees On MERCURY VX and MERCURY lock power is 0 to 40 dB 40 is full power lock gain is 0 to 39 dB and lock phase is 0 to 360 degrees Step size for power and gain is dB step size for lock phase is 1 4 degrees e On GEMINI 2000 lock power is 0 to 40 dB 40 is full power lock gain is 0 to 30 dB and lock phase is 0 to 360 degrees Step size for power is dB and step size for gain is 10 dB step size for lock phase is 1 4 degrees e On UNITY and VXR S lock power is 0 to 63 dB 63 is full power lock gain is 0 to 70 dB and lock phase is 0 to 360 degrees Step size for power and gain is 1 dB step size for lock phase is 1 4 degrees 01 999083 00 A1298 Getting Started VNMR 6 1B 131 Chapter 6 Preparing for an Experiment On all systems except UN TYINOVA MERCURY VX and MERCURY a
19. solvent string in vnmr solvents sw number in Hz tn string in vnmr nuctables tof number in Hz Move cursor to center of spectrum Reduce spectral width to minimum required Move spectral window according to cursors Move transmitter offset Set decoupler frequency to cursor position Set decoupler frequency array Set frequency of rf channels Set spectral width Current cursor position Difference of two frequency cursors Transmitter frequency of decoupler Nucleus of decoupler Frequency offset for decoupler Lock frequency RF band in use Independent control of rf channel selection Transmitter frequency of observe nucleus Lock solvent Spectral width Nucleus for observe transmitter Frequency offset for observe transmitter 184 It is essential that 1ock f req parameter for lock frequency be set correctly in order to observe NMR signals On MERCURY VX MERCURY YNTYINOVA UNITY plus and GEMINI 2000 systems Lock freq must be set to the actual deuterium frequency See the description of Lock f reqin the VNMR Command and Parameter Reference for values On UNITY and VXR S 300 400 and 500 MHz systems the lock transmitter is equipped with a series of thumbwheel switches These switches are used to adjust the lock frequency if the field drifts out of the range of the field offset control the zO parameter The starting value of these switches varies 200 MHz systems typically start at 1 210 300 MHz at 1 206 400
20. the spectral region displayed is determined by the parameters wp width of plot and sp start of plot These parameters are entered in seconds and Hz respectively e g wp 1000 Display of these parameters is controlled by the parameter axisf for FID display or axis for spectrum display these are also used to regulate the labeling of plot scales peak frequencies etc axisf is typically in seconds axis is typically in either p ppm h Hz or k kHz For FID display the parameter vf affects the vertical scale of the display For spectrum display the parameter vs affects the vertical scale Scale intensities depend on the display mode e Inthe normalized nm display mode the largest peak in the spectrum is automatically found then the display is normalized to make the peak vs mm high on the plot e In the absolute intensity ai mode the appearance on the display screen is used as a guide to adjust vf or vs to produce the desired vertical scale This mode enables comparing intensity from one experiment to another a necessity for all arrayed experiments The position of the display on the screen and the plotter is governed by the chart parameters wc width of chart and sc start of chart Both are entered in units of millimeters For FID display the parameter vpf positions the FID display vertically for spectrum display the parameter vp positions the spectrum vertically and io integral offset positions the integ
21. 213 218 first button acqi 156 first order baseline correction 242 252 fit a line to data points 86 Fit button 85 fit current spectrum 85 fit line to data points 86 five spin system 84 fixpar macros 109 flag parameters 96 flammable gases warning 18 Flip button 47 65 flip command 47 flip time 188 floppy disk drive 291 fn parameter 223 253 FN Small button 72 74 Fold buttons 80 format of text files 286 306 Getting Started VNMR 6 1B Fourier number 72 74 95 Fourier transformation 221 223 complex 227 data processing 227 in progress 45 number of points 223 output data 224 real 227 spectra 71 four spin system 84 fourth rf channel parameters 110 fr macro 243 FRED software package 33 free induction decay See FIDs free form arguments 94 frequency referencing 247 frequency shift of spectral data 227 frequency dependent phase shift 216 frequency shifted quadrature detection 218 fsq parameter 218 ft command 221 223 227 FT message 45 ftp command 282 Full Analysis button 82 Full button 71 73 74 76 83 234 239 243 full command 250 full display of plot image 250 Full Integral button 73 full optimization of lock 134 Full Screen button 78 79 full screen page 78 79 full set of transforms 73 Full Transform button 73 Full with Traces button 79 fully automatic Autoshim 139 function key actions 231 function keys 43 function keys to select menu choice 59 fuzzy log
22. 4 9 Processing Menus Button Description Go Periodic Wft Automatic Begin an acquisition and weight and Fourier transform the FID periodically after each bs transients are completed Begin an acquisition and process data according to the parameters wbs wnt and wexp 4 9 Processing Menus Two different data processing menus are possible depending upon whether a 1D or 2D experiment is active 1D Data Processing Menu The 1D Data Processing menu is typically entered by selecting the Process button in the Main menu when a 1D experiment is active by selecting the Reprocess button in the 1D Data Display menu or by entering the command menu process_1D Button Display FID Select Params Adj Weighting Transform Weight Transform Description Display the Interactive 1D FID Display menu below Display the 1D Processing Parameter Setup menu page 72 Display the Interactive Weighting menu page 72 Perform non weighted Fourier transformation of all spectra and then display the Interactive 1D Spectrum Display menu page 71 Perform weighted Fourier transformation of all spectra then display the Interactive 1D Spectrum Display menu page 73 Interactive 1D FID Display Menu df Program The Interactive 1D FID Display menu part of the df program is typically entered by selecting the Display FID button in the 1D Data Processing menu or by entering the command df lt index gt If called wi
23. 79 Set Int button 76 set nucleus 68 Set Params button 83 set solvent 68 01 999083 00 A1298 setallshims macro 136 setfrq command 183 sethw command 124 132 setint macro 253 setoffset macro 249 setpen macro 255 setplotdev macro 257 setref macro 248 setrefl macro 249 setref2 macro 249 sets integral value 253 setsw macro 185 Setup button GLIDE 55 66 setup macro 68 111 Setup menu 67 sf parameter 232 sf wf button 71 234 sfrq parameter 24 152 183 247 Sh All button 77 Sh Box button 76 Sh Lbl button 77 Sh Pk button 76 shaped pulses 189 shapelib directory 36 shared use of an experiment 207 shell command 207 shell in UNIX 91 Shell Tool program 50 shell windows 48 shim adjust 159 shim button acqi program 149 159 shim coil diagram 142 shim coil settings 137 278 shim coils 135 shim combinations 162 shim command 138 139 144 145 200 shim directory 90 shim gradient combinations 141 shim menu 161 shim method 140 shim methods files 36 shim parameters adjustment 156 shim sets 137 shim settings 279 shim settings sets 36 shim systems 24 shim values 136 SHIM window 201 shimmaps displaying 170 distributing to users 172 loading 172 shimmethods directory 36 139 140 145 shimmethods file 139 shimming acquisition time 140 background Autoshim 145 criterion 139 140 162 lock signal effect 139 methods 139 140 on FID 160 on spectrum 160 on the lock 16
24. Commands dnode List valid limNET nodes VNMR UNIX eaddr Display Ethernet address VNMR UNIX list remote_mode remote_dir List directory of remote system VNMR list remote_mode remote_dir List directory of remote system UNIX eread Transfer file from a remote source VNMR eread Transfer file from a remote source UNIX ewrite Transfer file to a remote destination VNMR ewrite Transfer file to a remote destination UNIX eread local_file remote_node remote_file VNMR eread local_file remote_node remote fil UNIX ewrite local_file remote_node remote_file VNMR ewrite local_file remote_node remote_fil UNIX 01 999083 00 A1298 Getting Started VYNMR 6 18 281 Chapter 10 Storing Retrieving and Moving Data 282 Transferring Data Using Ethernet UNIX commands ftp file transfer program and rcp remote copy program are among the commands available to transfer of files from one VNMR system to another using Ethernet These commands are not supported inside VNMR although a macro can easily be created if this is desirable Since most FID files in the VNMR file system are stored as directories the rcp program is probably the most useful because it can transfer entire directories not just individual files The structure of rcp is identical to that of the standard UNIX cp program except that the remote file name must be preceded by the name of its computer the remote host name followed by
25. Commands and Parameters for Acquiring Data tees ceceeeeeeeeeeteeeeeeeeeeeseeenes 199 Fields in the Acquisition Status Window acqstat Program 00 0 0 ce eeeeeeeeeeeeeneeeeee 205 Digital Filtering Commands and Parameters 000 0 eee eee eseeseceeeeseceeeeeeeeeeeeeeeneeaeeenes 211 Maximum Values for sw oversamp and NP OVELSAMP wo eeeceeecsseeeneeceeeeeteeeeees 212 Weighting and Fourier Transform Commands Macros and Parameters 0 222 Phasing Spectra Commands and Parametersn sssesessssesesseereeereeesterrsessrsrrersrrsreereee 224 Advanced Data Processing Commands and Parameters essseeeeseeresesrererrrsrrrrerreeee 226 Interactive FID Display Commands and Parameters 0 0 eee eeeeeceeeeeeeeeeeeeeeneeenes 233 FID Display and Plotting Commands and Parameters s sesesseseeeeseereseererrsreerrerereeeee 236 Interactive Spectrum Display Commands and Parameters eee eeseeeeeeeeeees 238 Spectral Display Commands and Parameters 0 ec eceeceeeescececseeceeceneeseceseeseeneenaees 244 01 999083 00 A1298 Getting Started VNMR 6 1B 15 List of Tables Table 38 Spectral Plotting Commands and Parameters 0 ssssesesseeeeesesseceeeeceaeeaeeeceeenaeneeeees 245 Table 39 Integral Display and Plotting Commands and Parameters eseeeeseseesecseeeeeeeeeees 251 Table 40 Plotting Commands and Parameters 000 0 cesesesseeseeeceseeeeeeceecneeseeseenecaeeeeeaeceeeeeeeseaees 254 Table 41 Window
26. If experiment control of temperature is selected the two previous selections appear faded because they are inoperative and the selection of the action to be taken after a temperature error is provided by the parameter tin Temperature Related Parameters For systems equipped with the optional variable temperature accessory the t emp parameter sets a sample s temperature between 150 C and 199 C temp n disables the accessory Another parameter vt c sets the temperature cutoff point Above vtc variable temperature gas flows straight into the probe past the heater and then past the sample Below vtc gas is routed first through the heat exchange bucket to be cooled by the heat exchange fluid then into the probe and past the heater vt c should be set depending on the temperature of the gas supply used for VT regulation For further information about temperature related parameters refer to the chapter on variable temperature operation in the manual User Guide Liquids NMR Pulsed Field Gradient Related Parameters For systems equipped with the optional Pulsed Field Gradient PFG module the pfgon global parameter turns the PFG amplifier output on or off for the X Y and Z channels For example setting pfgon nnn tells PFG hardware to turn the amplifier off for all channels and setting pfgon nny turns the amplifier output on for the Z channel only A su or go command must be sent to activate pf gon Another parameter grad
27. Plain l 8 Tuning arrows Figure 77 Item Preferences Window Changing Line Width Change the width of a line by doing the following procedure 1 Highlight the line or region by double clicking on it 2 Enter a new width in the Line Width field 3 Click Apply to change the line 4 Click anywhere in the workspace to deselect the line Changing Fonts Plot Designer has three font families SansSerif Monospaced and Serif Fonts can be Plain Bold or Italic To change the family style and size of a font do the following procedure 1 Highlight the text or region IS a 2 Click on the Item Preferences tool e to open the Item Preferences window 3 Choose a family style and enter a size in the Font field 4 Click Apply to change the text Changing Line Color You can change the color of a line by doing the following procedure 1 Highlight the line or region 2 Inthe Item Preferences window click on the color button green to open a pop up menu showing a range of colors 3 Move either the tuning needle left or right to change a color You can also change a color by clicking on the left or right arrows in the Red Green and Blue fields the values in the Color RGB field automatically change as you move a needle 4 When you are satisfied with a color click Apply 5 Place the cursor anywhere in the workspace and click once to see the color change 268 Getting Started VNMR 6 1B
28. The vnmrsys directory contains a series of essential files One or more experiment files exp1 exp2 etc are used to provide temporary homes for NMR data being acquired or processed these files were previously discussed Several directories that also existed in the vnmr directory are found repeated here seqlib psglib maclib menulib and shims These directories are used to provide user specific pulse sequences macros menus and shim values Thus a user who wishes to develop a personal version of the pl cosy macro which plots a COSY spectrum is free to do so without affecting the software that can be seen by other Getting Started VNMR 6 1B 01 999083 00 A1298 1 4 Introduction to UNIX and VNMR Files users A user who wishes to modify the heteronuclear chemical shift correlation pulse sequence het cor can similarly do so without affecting other users Once the new version is proven to be more desirable the NMR system administrator vnmr1 can copy it into the directory vnmr seqlib where it is accessible to all users Finally a file named global is found in each user s directory This file contains parameters that are common to all of a user s experiments and that do not need to be repeated For example while a user may want to process proton spectra in exp1 and carbon spectra in exp2 that user probably wants to plot them both on the same plotter so the parameter plotter is found in global and not within exp1 or exp2
29. acquired go prompts the user with an appropriate message and aborts the acquisition initiation process To override this function enter go nocheck On TYINOVA UNITYplus and UNITY the pulse sequence language contains a power check for protecting the probe For every timed event during a pulse sequence the power levels of each rf channel are summed for each band high band is IH MR or H low band is the remaining nuclei Each band is associated with a coil in the probe Limits for a coil cannot exceed a predefined safety limit There are two common errors that often damage probes and related equipment One is performing an rf pulse when the pulse width parameter is accidentally defined as a delay in seconds instead of a pulse in microseconds The second common error is to set the power level of the decouple at a high value for decoupler pulses and then forget to reset the power level to a lower level for CW decoupling Both of these conditions can now be set to generate a warning and stop the experiment Because probe protection could prevent performing certain experiments the protection can be turned off temporarily by entering go with the nosafe keyword i e go nosafe Turning off probe protection permanently can be done by setting the parameter probe_protection parameter to n On UNTYINOVA UNITYplus UNITY and VXR S the pulse sequence language contains a gradient level check for protecting the probe from gradients
30. by clicking on certain buttons in the VNMR menu system or by setting values interactively in the GLIDE window When commands macro and parameters are entered in the input window it is called the command mode A command is a request to have an action performed A macro is also a request to have an action performed but the macro action can be customized by users because the source code is readily available making changes to commands can only be done if the user purchases the optional VNMR Source Code Kit A parameter shapes the action that commands take The command mode allows access to all commands macros and parameters while the other two modes menu system and GLIDE allow access to some commands macros and parameters only Thus the emphasis of this section and of the manual as a whole is on providing information about interacting with the system in the command mode Keep in mind however that use of the menu system and GLIDE provide a convenient shortcut to most routine operations and in typical use you may work for minutes or even hours without touching the keyboard For detailed descriptions of all commands system macros and parameters refer to the VNMR Command and Parameter Reference 5 1 Commands Command names contain a variable number of alphanumeric characters e g go jexp1 and dcon Commands can be divided into four types as follows e Commands with no arguments The command eject for example stands b
31. click on the field Use this template as default 3 To insert the template into the Plot Designer window click on Open 4 Click Close to exit the window Removing Templates To remove a template from the list in the Plot Templates window click on Delete A warning appears notifying you that the template will be deleted Click Cancel if you do not want to delete the template Importing a Plot To import a plot from the VNMR graphics window onto the Plot Designer workspace you must first create a region Regions are smaller workspaces in which you can customize a plot Create a region by doing the following procedure 01 999083 00 A1298 Getting Started VWMR6 1B 265 Chapter 9 Display Plotting and Printing 266 4 5 Text Input Area Click on Region in the main menu then New to create a region on the workspace The cursor arrow changes to cross hairs To draw a region press and hold down the left mouse button drag the cursor across the workspace then release the mouse button If a region is not already selected highlight it then click Region Edit to open the Region Editor window shown in Figure 75 Region Editor is a text editor in which you can enter commands to change an imported plot Region Editor Restore Delete Delete All Copy Paste Close Figure 75 Region Editor Window Enter a VNMR command such as p1 or pscale in the text input area Click Preview Selected to impor
32. commands and parameters discussed in this section Mouse Device The mouse is a three button pointing device that can be either mechanical or optical The latest mouse design is a mechanical device with a rotating ball in its base No special tracking board is required for this design however a mouse pad is useful When you move the mouse a cursor correspondingly moves across the display screen The cursor is most often a small arrow that tracks the movement of the mouse that is moving the mouse to the upper left moves the arrow to the upper left of the screen 01 999083 00 A1298 Getting Started VNMR 6 1B 41 Chapter 2 VNMR Basics 42 Table 2 VNMR Interface and Display Tools Command errlog Display recent VNMR error messages flip Alternately uncover and conceal dg program glide Display GLIDE interactive window large Use large graphics window small Use small graphics window Parameter errloglen integer Number of lines in VNMR error message display pslabel string Pulse sequence label shown in status window Menu System GLIDE Open GLIDE interactive window Main Menu Display the Main Menu Flip Alternately uncover and conceal dg program Resize Change size of graphics window Mouse Buttons The three buttons on the mouse which are clicked by pressing down on them briefly are used for different purposes by the software The left button of the mouse the button under the index finger of a right hande
33. dim gt oversamp ss gt Parameters dg string Control dg parameter group display dg1 string Control dgl parameter group display dg2 string Control dg2 parameter display dgs string Control dgs parameter group display file string File name of parameter set Location of Parameter Sets Parameter sets are organized into a number of files and placed in directories e Directory vnmr stdpar contains standard parameter sets for different nuclei For example vnmr stdpar H1 par contains parameters for running routine IH spectra and vnmr stdpar C13 par contains parameters for 13C spectra e Directory vnmr parlib contains parameters sets for particular experiments such as vnmr parlib dept parand vnmr parlib hmqc par e Directory vnmr tests contains parameter sets for the standard system tests such as vnmr tests H11sph for lineshape and vnmr tests C13sn for signal to noise 01 999083 00 A1298 Getting Started VNMR 6 1B 107 Chapter 6 Preparing for an Experiment e Similarly on your system directories stdpar and parlib are standard for every user in vnmrsys These directories are empty at first but grow with parameter sets from experiments that you and other users on your system have saved Normally you save parameter sets into your home directory Chapter 10 Storing Retrieving and Moving Data describes how to save user data To List Parameter Sets You can list parameter sets using the menu s
34. entry in the window A menu appears with choices such as Proton 1D and Carbon 1D 4 Using the left mouse button click on the experiment desired 5 Using the right mouse button click on the triangle to the right of the Solvent entry in the window A menu appears with choices such as CDC13 and Acetone 6 Using the left mouse button click on the solvent desired 7 Click on the Setup button at the bottom of the window Using the Menu System 1 Click on Main Menu gt Setup The Setup menu appears with the following buttons H1i CDC13 C13 CDC13 Nucleus Solvent Sequence App Mode Shim Acquire 2 Ifyou want 1H or Bc experiment with CDCl click on H1 CDCI3 or C13 CDCI3 as appropriate Otherwise click on Nucleus Solvent The Nucleus Selection menu appears with a choice of nuclei H1 H2 C13 N15 F19 P31 Other Return 3 Click on the nuclei desired or if the nucleus you want is not listed click on Other to enter a different nuclei The Solvent Selection menu appears with a choice of lock solvents Getting Started VNMR 6 1B 01 999083 00 A1298 6 3 Retrieving Parameter Sets CDC13 D20 Benzene DMS0 Acetone Other Return 4 Click on the solvent desired or if the solvent you want is not listed click on Other to enter a different solvent Using the Input Window and Menu System 1 Enter setup in the input window The Nucleus Selection menu appears with a choice of nuclei H1 H2 C13 N15
35. escsssscesescsasstssn censctsscstenesbedosszansvabeseasdeduseusescdanstancssapeseases 160 Shimming on the Spectrum oo ee cece csseeeeceeceseceseeseeeeeeeeeeaeesesenseseeeneeaes 160 SHIM Display ceresna E r EEE EO RE 161 6 11 Shimming Using the Ultraenmr Shim System oo eee eee ceeeeeeeeeeeeeeeeeeeeeee 164 ard ware OVERVICW vissini eao AE EE RE Ek 164 Interface BOX cisrenan aa aE E E EE E REEE 164 SODA rieo erare E an E EE E EESE E E 166 Installing th First Probe sssessiesressnresrrtsociropeseiesireesenosr osi insrs ses rapes tapsir itest 166 Floppy Disk USE hiciwatindiahtint Altes bid oE OE E ES 166 Enabling the Acquisition Window eseessesessssesrserersrreerreeerrsrrresrerrsrrererrereersee 167 Turning the System Off and On ou eee ee ecesseneeeeeeecneeseeeeeeecaeeaeesetaetaseeetaesaees 167 6 12 Gradient AutoshiMMIng 0 ccc0 s sccssseecnsersencoscsscensensonsedesenesocussounsensededusteverssesopeoseests 168 Gradient Shimming Method 0 ee eee eeeeeeeecseesseceeeaeceecaececeseeeeeeseeeeeeeeee 169 Configuring Gradients and Hardware Control eee eeeeeecseereeseeeeeeeeeeeeees 169 Mapping th Shims 1 00 50 csstscscesessescassscuteesicsscbbas ctasscusdatocectbvecsecsveessesssbesscbetest 169 Shimmap Files and Parameters 00 0 eececeseceeceseeeeceeeeeeseseeeeseseseeecaeeeaeenee 172 Automated Shimming 0 eee ec eeceeeeeeeeseeeeecaeesaecseesaecaeesaecseceseeeeseeeeseetee 172 Deuterium Gradient Shimming 0 ee eee ceeeseecsees
36. gives single frequency decoupling during the first part of the pulse sequence and WALTZ 16 decoupling during acquisition The parameters dmm2 dmm3 and dmm4 function the same for the second third and fourth decouplers respectively as dmm does for the first decoupler For systems with a waveform generator on a decoupling channel set dmm to p to select programmable decoupling using that waveform generator To specify the decoupling sequence during any period of waveform generator programmable decoupling use the dseq parameter for the first decoupler dseq2 for the second decoupler and dseq3 for the third decoupler The parameters dres dres2 dres3 and dres4 control the tip angle resolution used within a programmable decoupling sequence on the first second third and fourth decouplers respectively See the manual VNMR User Programming for further information on pulse control of waveform generators The following values are typical for decoupling on MERCURY VxX MERCURY YNTYINOVA UNITYplus UNITY and VXR S systems e Homonuclear decoupling with linear amplifiers dm y Decoupler mode on homo y Homonuclear decoupling on dmm c Decoupler modulation mode is continuous wave dpwr 5 to 15 Decoupler power level range dlp dhp nonfunctional e Heteronuclear decoupling with linear amplifiers dm y Decoupler mode on homo n Homonuclear decoupling off dmm w WALTZ 16 decoupling dpwr 40 Decoupler power level dlp dhp n
37. it is possible to create an array in which the temp parameter is given four successively different values temp 30 50 70 90 These four subexperiments are now all treated as a single experiment One go command successively begins acquisition of all four subexperiments One command can be used to transform all the spectra one command to display all the spectra on the screen simultaneously one command to plot all the spectra and one command to save all the spectra Virtually all of the parameters affecting acquisition can be arrayed in this way making for a simple and convenient method of performing pulse width calibrations optimizing parameters etc 01 999083 00 A1298 Getting Started VNMR 6 1B 31 Chapter 1 Overview of Varian NUR 32 Multiple Unrelated Sets of Data Sometimes it becomes desirable to deal with multiple sets of data that are not related to each other simply by arraying some parameter For example you may want to obtain a carbon and a proton spectrum on the same sample where the parameters and the data are completely different You may want to obtain spectra with the same parameters but on different samples Of course it is perfectly possible to acquire one such data set process it plot it save it on disk acquire the next data process plot save and so on But this procedure results in an inefficient use of the system In acquiring one spectrum for example it would be more efficient to start a second acqui
38. magnetic tape operation 289 magnetic tape unit 23 magnetic tapes caution 290 magnetization recovery to equilibrium 188 Main Menu 46 Main menu 46 60 66 Main Menu button 46 65 main processor 24 makefid command 281 manual button 161 manual directory 34 38 manual emulation shimming 138 manual locking 153 manual sample ejection and insertion 103 Manual Shim menu 156 manual shimming mode 161 Mapping the shims 169 Mark button 76 239 mark1d out file 85 239 Massage button 77 79 MasterLog file 208 mathematical expressions 95 maximum transients accumulated 202 maxpen parameter 255 256 257 medium shimming criterion 140 162 medium resolution plotter mode 257 memory overflow from real time DSP 215 menu buttons 46 menu command 60 menu system 44 59 customization 64 help files 34 interactive program menus 60 outline 61 62 63 64 pulse sequence programming 91 menulib directory 34 70 menus library 34 metal objects warning 17 method parameter 139 144 145 207 min button 83 Minimum button 82 minsw macro 185 mkdir command 276 MLEV 16 decoupling 194 mnemonic parameter format 78 261 Mode label 156 modifying the instrument 18 More 1D button 69 More button 60 66 90 mount command UNIX 291 mouse arrow 59 mouse button labels 231 mouse buttons 42 mouse device 27 41 move command 272 move experiment to head of queue 201 move to next command line 97 movedssw macro 217 mo
39. see VNMR User Programming SELECT PHASE Use Previous X Y X Y Fixed 0 More Pulse Sequence Entry Phases Secondary Menu VNMR User Programming 3210 0321 0022 2200 Fixed 90 Fixed 180 Return Pulse Sequence Entry Pulses Menu see VNMR User Programming PW P1 2PW 2PI Other Return Pulse Sequence Entry Decoupler Pulses Menu see VNMR User Programming PP 2PP Other Return Pulse Sequence Entry Status Menu see VNMR User Programming A B C D RevrOn RevrOff Set Rcvr Phase Return Configuration Menu page 92 Show Output Devices Select Plotter Select Printer Hardware Return 4 2 Customizing the Menu System Most of the menus and help files for the menu system can be customized for local use Information on how to customize the menus and help files is provided in the manual VVMR User Programming The description of menus and help files in this manual applies to the default version supplied with the software 4 3 Menu System Step by Step 64 The following example takes you through the process of recalling some stored data processing it displaying it and plotting it Go through it once exactly as described to get a feel for operating the system Then go through it again trying some of the different choices that were available to you along the way You might also try going through the example using the function keys instead of the mouse 1 Inthe Permanent menu click on Main menu 2 Starting from the Main menu the lowe
40. stdpar userlib conpar devicenames usr 01 999083 00 A1298 global Figure 7 File Structure Overview 35 Getting Started VNMR 6 1B Chapter 1 Overview of Varian NUR 36 parlib Contains files that store one parameter set for each pulse sequence so that parameters or parameter values unique to that experiment can be recalled from that file psg Contains source code for pulse sequence statements psglib Contains files holding the source code listings of the pulse sequences supplied with the system These files are not executable pulse sequences and must first be compiled to create a corresponding file in the seqlib directory seqlib Contains compiled pulse sequences ready to be run on the system A pulse sequence must be defined by a seqlib file in order to be run shapelib Contains pulse shape definitions used by the pulse sequence generation PSG software shimmethods Contains files with shim methods by which autoshimming is performed A number of standard methods are supplied see Adjusting Shims on page 135 but these can be augmented so that algorithms of your own choosing can be used shims Contains sets of shim settings Each set might correspond to a particular probe or solvent or perhaps just to a particular date stdpar Contains a series of files each named after a nucleus that contain the standard parameter sets for that nucleus userlib Contains user con
41. string gmapshim lt files mapname quit gt Start gradient autoshimming newshm Interactively create shim method readhw parl par2 lt varl var2 gt Read acquisition hardware values rts file lt status gt Retrieve shim coil settings sethw Set acquisition hardware values shim related shim Submit an Autoshim experiment stdshm Interactively create a shim method Svs file lt status gt Save shim coil settings acgqix lt par disconnect exit standby gt lt ret gt sethw lt wait nowait gt parl vall lt par2 val2 Parameters gmap_findtof n y Find tof before start of gradient shimming gmap_z1z4 n y Gradient shim z1 z4 then higher order shims hdwshim n y p Hardware shimming if available hdwshimlist z1 z1lz2xlyl List of shims for hardware shimming load n y Load status of displayed shims method file in shimmethods Autoshim method shimset 1 2 3 14 Type of shim set shimspath absolute path Path to user s shims directory wshim n e s g EE Conditions when to shim zl yl Plj icas Shim gradients X1 Y1 Z1 z0 2048 to 2047 32768 to 32767 ZO field position Using the Inout Window 1 For each of the shim values you want to change enter the shim gradient parameter with the new value e g z1 247 2 To load the new values enter load y su Saving and Retrieving Shim Values Previous shim values can be retrieved an
42. the Permanent menu or enter the smal 1 command e To alternately uncover and conceal the dg program when it is covered by the graphics window click on the Flip button in the Permanent menu or enter the 1ip command If VNMR is busy executing a command the mouse pointer becomes a miniature clock or hourglass when positioned over the graphics window dg Program At the bottom of the screen is the dg program which is used to display parameter lists line lists help files and other alphanumeric information For example entering the dg command in the input window produces a display of acquisition and processing parameters and their values in the dg program similar to Figure 12 ACQUISITION SAMPLE PROCESSING sfrq 500 618 date March 8 1b 50 00 tn H41 1995 sb not used i n at 2 305 solvent cdcl3 gf not used y np 29952 file exp awc not used nn su 6497 7 DECOUPLING lsfid not used SPECIAL fb 3600 dn H1 phfid not used temp not used bs not used dof 74 7 wtfile 0 dm nnn proc ft 23 0 dmm c fn used dmf 200 math f dlp 20 werr react wexp procplot wbs wnt wft Figure 12 Typical Parameter Display in dg Program Tcl Version of dg Window The Tcl Tool Command Language version of the dg program resides in the tcl bin directory of the VNMR system directory A Tcl script can be sent to the Tcl version of the dg window that makes the entries in the display interactive and allows customization of the layout The dg program is strictly
43. 1B 01 999083 00 A1298 Chapter 6 Preparing for an Experiment Sections in this chapter e 6 1 Preparing the Sample this page e 6 2 Ejecting and Inserting the Sample page 103 e 6 3 Retrieving Parameter Sets page 106 e 6 4 Removing and Inserting the Probe page 112 e 6 6 Tuning the Probe page 113 e 6 7 Spinning the Sample page 127 e 6 8 Optimizing Lock page 130 e 6 9 Adjusting Shims page 135 e 6 10 Using the Acquisition Window page 148 e 6 11 Shimming Using the Ultraenmr Shim System page 164 e 6 12 Gradient Autoshimming page 168 These sections are in the same order as typically performed by most users 6 1 Preparing the Sample Reliable and fast accumulation of data from multiple samples depends greatly on the way samples are prepared and positioned in the turbines and the autoshimming methods and lock power used Variations in bulk magnetic susceptibility at air to glass glass to solvent and solvent to air contact points can contribute a dominant portion of the variation of field homogeneity from sample to sample whether in an automation run or in manual operation The time spent shimming or even the need to shim is largely dependent on the care in controlling the effects of these contact points Solvent Selection Samples can be run as neat liquids or in solutions In most cases you will probably be running compounds in solution The solution should be chosen to be iner
44. 247 absolute location 272 absolute pathname 37 absolute intensity mode 232 245 absolute value 2D experiments 222 absolute value mode 72 74 79 80 225 absorption spectrum 224 Acetone button 68 acqbin directory 34 acqfil directory 208 Acqi button 66 acqi command 40 148 154 207 acqi par command 156 159 Acqproc command UNIX 208 Acqstat command UNIX 207 208 acqstat macro 40 acqstatus parameter 208 Acquire button 66 67 148 198 Acquire menu 70 acquiring data 183 acquisition 198 209 aborting 203 activity log 208 automated 98 automatic lock initiation 133 codes 208 data station restrictions 148 done code 208 error 204 error code 208 information 208 initiating 198 log 278 multiple users 207 processes 24 queueing 30 200 remote control 207 resume after stopping 202 stopping 202 stopping early 202 time 140 time estimate 189 time too short 227 windows 49 acquisition commands directory 34 acquisition computer 24 203 Acquisition Controller board 24 acquisition log file 37 Acquisition Status window 28 40 41 44 49 Acquisition window 28 31 40 41 42 44 49 148 149 acrobat directory 34 adaptive acquisition 33 ADC bits displayed 155 ADC overflow 215 add button 83 Add Spectrum button 82 add spectrum into add subtract experiment 82 Add Sub button 81 86 Add Subtract menu 82 addi command 83 Getting Started VNMR6 1B 299 Index additive wei
45. 999083 00 A1298 4 7 Setup Menus Button Description BINOM Set up a Binomial Water Suppression pulse sequence this sequence not supplied with the MERCURY VX MERCURY or GEMINI 2000 S2PUL Set up a S2PUL pulse sequence for the standard two pulse experiment More 1D Display the 1D Pulse Sequence Setup Secondary menu below 2D Display the 2D Pulse Sequence Setup menu page 69 Return Display the Setup menu page 67 1D Pulse Sequence Setup Secondary Menu The 1D Pulse Sequence Setup Secondary menu provides setups for three more 1D experiments This menu is activated by clicking on the More 1D button in the 1D Pulse Sequence Setup menu or by entering menu psgset1 Button D2PUL SSECHO XPOLAR More 1D 2D Return Description Set up a standard decoupler pulse sequence Set up a solid state echo pulse sequence only applicable on systems with the solid state NMR accessory installed Set up a cross polarization pulse sequence for solids only applicable on systems with the solid state NMR accessory installed Display the 1D Pulse Sequence Setup menu above Display the 2D Pulse Sequence Setup menu page 69 Display the Setup menu page 67 2D Pulse Sequence Setup Menu The 2D Pulse Sequence Setup menu provides setups for five 2D experiments and access to menus for 1D and additional 2D experiments This menu is activated by clicking on the 2D button in the 1D Pulse Sequence Setup menu or by entering
46. A1298 Getting Started VNMR 6 1B 121 Chapter 6 Preparing for an Experiment 122 The current Q value and resonant frequency appears at the top of the Tune Display window and a horizontal cursor appears on the plot In the Tune Display window use the middle mouse button to place the horizontal cursor on the base line reflected power level outside of the resonance line The Q calculation appears at the top of the Tune Display window The Q that is shown is determined as follows The software finds the lowest point on the display and designates this as the resonance The frequency displayed is at best only as accurate as the frequency difference between points You must take this into account when quoting Q measurements This lowest point is used as Vmin The software takes the level of the horizontal cursor as the baseline or V max V nax IS assumed to be a frequency where all the rf energy is reflected by the probe The two frequencies that have the signal level of Equation are and y V max Eq 1 J5 Q is calculated from Equation 2 where is the resonant frequency Q 0 Eq 2 0 The software checks that the low point the bottom of the dip is at least 15 dB below the baseline If this is not true the calculated Q value is not accurate and is therefore not reported the string appears in the Q value field The resonance frequency however is still given Calibrating the Tune Sys
47. All data processed in VNMR is processed using the method of Fourier transformation but there are three variations that are governed by the proc parameter e Most NMR data including all data acquired on MERCURY VX MERCURY UNITYINOVA UNITYplus GEMINI 2000 UNITY VXR and Gemini spectrometers is acquired using simultaneously sampled true quadrature detection This means that two orthogonal real and imaginary or x and y as you prefer data points are sampled at the same time and form a single complex data point in the FID Such data are processed using a normal complex Fourier transformation using proc ft e Some spectrometers notably those from Bruker Instruments acquire pseudo quadrature data by sampling two orthogonal data points sequentially rather than simultaneously Such data must be processed using a real Fourier transformation with proc rft Use convertbru to convert Bruker data see Chapter 10 Storing Retrieving and Moving Data for details e For simultaneously sampled data only it is possible to include as part of the Fourier transform process a linear prediction described in the next section proc 1p is used to trigger this operation Linear Prediction Raw time domain data acquired during a pulsed NMR experiment can have two flaws e Early points in the FID may be distorted due to a host of hardware characteristics such as preamplifier saturation probe ringing and filter non linear
48. B Band CM port at the rear of the magnet console interface Connect this cable to the PROBE J5321 port on the TUNE INTERFACE panel UNITYINOVA and UNITYplus 500 600 or 750 systems Disconnect the cable from the PROBE J5311 port on the broadband preamplifier or the 1H 9F J5301 port on the preamplifier Connect this cable to the PROBE J5321 port on the TUNE INTERFACE panel Then disconnect the cable from the OUTPUT port J5312 or J5302 and connect it to the TUNE OUTPUT J5323 port Two methods are available to set the tune frequency Until you set up the tune frequencies with one of the methods su or tune the TUNE INTERFACE panel will not work after powering on or after resetting the acquisition console e The first method is to enter go or su Each time go or an su executes the console receives a frequency for each channel defined for the experiment This frequency also becomes the one used during tune The table below shows the relationships between the channel selected and the associated parameters Channel 1 tn sfrq tof Channel 2 dn dfrg dof Channel 3 dn2 dfrq2 dof2 Channel 4 dn3 dfrq3 dof3 For descriptions of these parameters refer to the VVMR Command and Parameter Reference The second method is to enter tune Refer to description of tune in the VWMR Command and Parameter Reference for details The settings remain in effect until the next go or su command executes The t une command is available on UNITYINOVA and UNITY plus sy
49. Designer was used Do the following procedure to load a template file 1 Click on File in the main menu then Templates to open the Plot Templates window 2 Highlight select a template by either DOUBLE CLICKING on a file in the list in the upper region of the window or by entering the file name in the Template field Getting Started VNMR 6 1B 01 999083 00 A1298 9 8 Plot Designer Table 42 Plot Designer Tools Line Drawing Draws a line Box Draws a box Arrows Draws an arrow places the arrowhead at the point in which you START to draw the arrow Draws an arrow places the arrowhead at the point in which you END drawing the arrow Item Preferences Sets the color and size of lines and fonts To edit an 2 LL Io Lh a object highlight it by double clicking on it For a description of its properties see page 267 You can also open this tool by clicking on Region Preferences Fext Text Input Allows you to add text into your design Several options allow you to control the size and appearance of the text To use this tool see Adding Text on page 269 Erasers The ALL eraser removes all objects You can also remove selected objects by using the Region Delete All option described on page 267 The second eraser removes only selected objects You can also remove selected objects by using the Region Delete option described on page 267 hh Print Prints a file If you want the file to be the default template
50. EEEE 203 Acquisition Status Window ooo eeeeceeeeeeeeeeceeeeecaeesaecaecaecaeceaeeeeeeeeereeeeees 204 Receiver Gain ss ccsiisseeiteitaihec teste heed EEEE Ea eee ele aed 205 FIOM OSPOth iroso aaee cwotensapecised A E E Sk 206 File Protection 26 w diieseecsiitiin ese e E ES 206 Remote Acquisti oi 5 5 fe cesses osceccsssendeseesizscocgcnsbacondcsdesseetsussedesedivsssecdvemecaesTescotes 207 Acquisition Information oo ieeeceecceceeeeeereeeeecseeseecaeesaecaecesececeseeeeeeeeeeeeetees 208 Acquisition Status Codes oe ceceeeceecsesseeeeseeeeecseessecseesaecaecsseceseseeseseseeeeeeeeee 208 VNMR Error Messages sccisccsscsssesccesiecssesssaves er e e E ee EE EE 209 Noise Level Analysis cis cicicescscticescs cites er osen erT E AEEA ER E E E 209 Lao Applying Digital Filtering scrret et rerescnere oir eoni EEEE REEERE E a 209 Types of Digital Filtering ceine etorren strine eses er EE UE EURE EEE EEE EENES NEE 210 Conttolok DA E E ET 210 Tine DSP sesenta eea a eaaa eee eA 211 Real Time DSP sssscussget se sscetessacticeeuitscos ae cess sv EEE E R RE 213 Postacquisition DSP iienaa e E rE E REESE 217 Removing Quadrature Artifacts Using DSP sseseeseseseesesresrsresesresrrreerrrresrersee 218 To Apply Frequency Shifted Quadrature Detection s eseeseeereeeeeeereererererese 218 Chapter 8 Data Processing axzccisiictcsecti dence sccencctecas che vicceuiveesneteeneecdiciceercce 221 8l Weightins FUNCOM aggscesscsscescagecisscosscavs sgecsanececa
51. F19 P31 Other Return 2 Click on the nuclei desired or if the nucleus you want is not listed click on Other to enter a different nuclei The Solvent Selection menu appears with a choice of lock solvent CDC13 D20 Benzene DMS0 Acetone Other Return 3 Click on the solvent desired or if the solvent you want is not listed click on Other to enter a different solvent Using the Input Window Only e Enter the command setup nucleus solvent where nucleus is chosen from among the nuclei for the files in the directory vnmr stdpar typically H1 C13 P31 and N15 and solvent is chosen from among the solvents listed in the files in the directory vnmr solvents typically CDC13 C6D6 D20 DMSO Acetone CD2C12 and CD30D For example to set up parameters to do a carbon experiment with DMSO d as the solvent enter setup C13 DMSO To Create Selected Parameters For certain types of experiments the addpar macro creates selected parameters to add to the current experiment Using the Input Window e Enter the appropriate command to add parameters a nae addpar 3d ee addpar 4d addpar downsamp addpar fid addpar image A addpar lp addpar lp 1 eee 01 999083 00 A1298 For a 2D experiment For a 3D experiment For a 3rd rf channel For a 4D experiment For downsampling data For a FID display For imaging For 2D line listing For linear prediction acquisition
52. FID shimming The Style 1 FID shimming window is shown in Figure 41 and the Style 2 FID shimming windows are shown in Figure 42 Clicking on the Style 1 or Style 2 button near the top of the display Grid OFF Phase Cycle OFF gt Fid level 12 Hode ojx 1 best first coarse z toggles between the two AL fe a PS Pete Pe Ee styles 22 E 2 1 4 16 64 Style 2 FID shimming is 2i 3 _ 1 ESE EE not available on VXR S 220 E 4 i 4 16 64 or UNITY systems that have an output board with a 63 step FIFO It is also not available on GEMINI 2000 MERCURY or MERCURY VX systems 16 64 Figure 41 Opening Style 1 FID Spectrum Display Window acqi Program Before selecting the FID Spectrum display an experiment must be set up within VNMR Any experiment type can be used In an arrayed or multidimensional experiment the first element is used Entering the macro gf then submits the experiment for display by the acqi program but does not initiate data acquisition from the experiment Using gf prevents certain acquisition events from occurring such as spin control and temperature change The command go acqi canbe used instead of gf but is not recommended In using gf to control the acquisition of data the parameters alock and wshim are disabled loadis set to n The value of nt is not relevant the experiment continues indefinitely until y
53. Gradient shimming uses the current parameters after the pulse sequence is loaded seqfil gmapz Standard parameters can be loaded before making a shimmap by entering gmapz or by using the Gradient Nucleus menu button Parameters and files can also be explicitly loaded and distributed as described in the following subsections Loading a Shimmap To change shimmaps as a system administrator do the following 1 Enter gmapsys 2 Click on Shim Maps gt Shimmap Files gt Cd to Userdir 3 Selecta file 4 Click on Load Shimmap loads the shimmap files gshim list andgshim bas from gshimlib shimmaps mapname fidinto gshimlib data but does not load the parameters or click on Load Shimmap amp Params loads shimmap files and parameters The general user can also change shimmaps by entering gnapshim files from any experiment to display the Gradient Autoshimming Files menu and then clicking on either the Load Shimmap or Load Shimmap amp Params buttons Distributing a Shimmap The system administrator can copy a shimmap file from vnmrsys gshimlib shimmaps into the directory vnmr gshimlib shimmaps so that the file is accessible to all users To copy files do the following steps 1 Enter gmapsys 2 Click on Shim Maps gt Shimmap Files gt Cd to Userdir 3 Select a file 4 Click on Copy to Systemdir You must be vnmr1 for this button to appear Automated Shimming The shims must be mapped before gradient autoshimming is
54. MHz at 1 145 500 MHz at 1 479 and 600 MHz at 153 845 lock synthesizer As the field decays this number must be set downward to lower the lock frequency Under normal day to day operation you will not need to change this value The rfband parameter on all systems except MERCURY VX MERCURY and GEMINI 2000 indicates the rf band in use for each channel h indicates the high rf band for a channel 1 indicates the low rf band and c for calculated indicates that the system calculates the correct amplifier band based on the selected frequency The value of rfband is written as a string e g rfband hlc with the first channel determined by the first character the second channel by the second character etc The parameter rfchannel1 is available to give override capability over the selection of rf channels Refer to the description of rf channel in the VWMR Command and Parameter Reference for details Transmitter and Decoupler Positioning The movetof lt frequency gt macro moves the transmitter offset parameter tof so that the current cursor position defined by cr becomes the center of the spectrum If Getting Started VNMR 6 1B 01 999083 00 A1298 7 2 Setting Pulse Sequence Related Parameters referencing was used movetof maintains the referencing If you wish to specify the transmitter frequency directly rather than using the cursor position enter a value for the frequency argument This provides a convenient method o
55. Main Menu sssessssssscisseressessssuseesssssssroeeorsseressasiaresressstosssss 91 Conf puration Menu sis cisssi sccesias cidehaes stces ji scesuevsshiet ovsceseevoea wacsseumpevscnacensoubenocbeee 92 Chapter 5 Using the Command Mode sss secccsseeeeeeeseeeeeessseeeeeesseeeeees 93 Sal Commands oii sc csecsavesn cesisscaenscastvecastsacesoaavescecspacencevegs EEE EEE ESTEET EE ERER EE E ERS REE 93 Command ENUY i as sises casei sacesdtescahesats ter e Eneas eo a E EEE RENTEA EEE EEEE 94 Command Argument 00 0 ee eee ecceeeeeceseeesecaeeceecseesaecsaesaececeseceeeeseeeeeeseeeeaeeeaes 94 Siz Parameters lt sissiveeessdecises E E E a ckgadicevleaeei sdeeleas eE ENS 94 Parameter ENUY secciecdescsagevssscessescicsecsssedocescsdeuoddesdesiecticeuss cangevsesecdaseuocsscsasaseedeots 95 Parameter Dis play sincconisneiocsenieniaes aana ai itii iasi 96 Parameter Value Limitations seseseeeeseeresseeesesrestrersrrsreseeresreresrererreserrreererssret 96 Parameter Entry Limitations sssesseseeeesesreseseesesresesrrsrrrsseeresrreesreesreeerrssreresee 96 5 3 Command Line Editing and Reentry seeseseseeseseesresesreeerreerrsesreresrreresreresreeresreresesreseres 96 5 4 Macro Automation cccccccccccesssssceeceessaeeeceeeseesececeseseecececesssaecceceessaesesceeseatseeeeenenaes 98 Chapter 6 Preparing for an Experiment eccssseeeeeeseeeeeeesseneeeenseees 101 6 1 Preparing the Sample serseri esei alesis EEE E E ae 1
56. Processing Menu The 2D Data Processing menu is activated by selecting the Process button in the Main menu when a 2D experiment is active or by selecting the Reprocess button in the 2D Display menu It can also be entered through the command menu process_2D Button Description Select Params Display the 2D Processing Parameter Setup menu below Adj Weighting Display the Interactive Weighting menu page 72 Phase F2 Perform a 1D FT of first FID to allow phasing along f2 dimension only active in phase sensitive mode Transform F2 Perform a full set of transforms of the FIDs along the t2 axis and display the Interactive 2D Color Map Display Main menu page 74 Any currently active weighting functions are used Full Transform Perform a full set of transforms first along t2 then along tj using any currently active weighting functions At the end of processing display the Interactive 2D Color Map Display Main menu page 74 2D Processing Parameter Setup Menu Parameters can be set up to the standard values with one of the buttons on the 2D Processing Parameter Setup menu or they can be typed in and observed e g type fn 512 After parameter selection return to the 2D Data Processing menu with the Return button 01 999083 00 A1298 Getting Started VNMR 6 1B 73 Chapter 4 Using the VNMR Menu System 74 The 2D Processing Parameter Setup menu is activated by selecting the Select Params button in the 2D Data Pro
57. Selection File Name field 2 Click on the Load button Changing or Renaming A Color File To change the colors in a file 1 Load the file 2 Enter new color assignments 3 Save the file To change the name of a color file 1 Load the file 2 Save the file with a new name 3 Delete the file with the old name 260 Getting Started VNMR 6 18 01 999083 00 A1298 9 7 Plotting Removing A Color File To remove a color file from the list 1 Click on the file name 2 Click on the Delete button The deleted file is removed from the bottom list box 3 When you are prompted choose OK to delete the file or Cancel to keep the file Assigning Colors to A Plotter To assign colors to a plotter 1 Click on the Plot button 2 Choose the type of plotter that you have Use the previously listed procedures to save load change rename and remove files To use normal plotting commands 1 Exit the Color Selection window 2 Enter setcolor onacommand line Closing the Color Selection Window When you have finished using the program click on Exit to close the window Color Table Loader The macro Lloadcolors lt color_file gt loads the color table for the graphics window and plotters loadcolors is generated by the colors program and includes a series of set color commands On bootup the bootup macro calls loadcolors to set the graphics window and plotter colors Plotting Parameter Lists and Text Files A number
58. Show Fit 01 999083 00 A1298 Perform line listing on the current spectrum observed or calculated whichever was displayed last and use the listing as a starting point for a deconvolution s 1w is set to the measured width of the tallest line in the displayed spectrum Use file mark1d out created by the mark option while interactively displaying a spectrum as the starting point for a deconvolution If mark done with a single cursor the information is used to initialize the frequencies and intensities only with s1w set to the measured width of the tallest line in the displayed spectrum If mark was done with two cursors the average frequency of the cursors is the peak frequency and the difference is the line width thus allowing different starting line widths for different lines in the spectrum Fit the current spectrum using the current starting parameters usually set with or 2 The original spectrum is first saved in exp5 for possible later use in add subtract operations Display the numeric results of the last fit Display the simulated spectrum Getting Started VNMR 6 1B 85 Chapter 4 Using the VNMR Menu System 86 Button Description Plot Plot the original spectrum the simulated spectrum the individual components and the numeric results Add Sub Change to the Interactive Add Subtract menu page 83 and display the original and simulated spectra Regression 1 Menu The Regression 1 menu is the
59. Simulation Second Definition menu below Return Display the Spin Simulation Main menu above Spin Simulation Second Definition Menu The Spin Simulation Second Definition menu is activated by selecting the Other button in the Spin Simulation First Definition menu or by entering menu spins1_2 Button Description ABCDE Select five spin system ABCDE A2BCD Select five spin system A2BCD A3BC Select five spin system A3BC A2B2C Select five spin system A2B2C A3B2 Select five spin system A3B2 A3B2C Select six spin system A3B2C Other Display Spin Simulation Third Definition menu below Return Display the Spin Simulation Main menu page 83 Spin Simulation Third Definition Menu The Spin Simulation Third Definition menu is activated by selecting the Other button in the Spin Simulation Second Definition menu or by entering menu spins1_3 Button Description AX Select spin system AX AXY Select spin system AXY AX2 Select spin system AX2 AXYZ Select spin system AX YZ AX2Y Select spin system AX2Y AX3 Select spin system AX3 Other Show prompt Spin System and set system to that value Return Display the Spin Simulation Main menu page 83 Spin Simulation Secondary Menu The Spin Simulation Secondary menu is activated by selecting the Next button in the Spin Simulation Main menu or by entering menu spins2 Button Description list Display listing of last spin simulation Getting Starte
60. UNITY systems and any system with a type 2 or 3 interface board apinterface 2 or apinterface 3 homo does not control any signal routing the position of the relevant relays is controlled by whether homonuclear decoupling tn equals dn or heteronuclear decoupling tn not equal to dn is in effect On systems with the type 1 interface board apinterface 1 homo y also causes the decoupler signal to be combined with the observe signal before being sent to the probe On UNTYINOVA and UNITYplus systems only the parameter homo2 for the second decoupler homo3 for the third decoupler and homo 4 for the deuterium decoupler channel 192 Getting Started VNMR 6 1B 01 999083 00 A1298 7 2 Setting Pulse Sequence Related Parameters as the fourth decoupler are equivalent to the parameter homo homo2 works in conjunction with the parameters dm2 dmm2 homo3 works with parameters dm3 and dmm3 and homo4 works with dm4 and dmm4 On MERCURY VX MERCURY and GEMINI 2000 homo has no meaning Gated homo decoupling is used if the transmitter nucleus tn is H or R and the decoupler mode dm is set to y CAUTION Decoupler power greater than 2 watts in a switchable probe will damage the probe Always carefully calibrate high power decoupling to avoid exceeding 2 watts of power The maximum value for dpwr on a 200 300 or 400 MHz system with a linear amplifier on the decoupler channel has been set to 49 corresponding to approximately 2 watts of pow
61. VNMR you should click on Main menu then click on More and finally click on Exit VNMR As a shorthand notation to describe this action in VNMR manuals we will write Main Menu gt More gt Exit VNMR Chapter 4 Using the VNMR Menu System describes all of the buttons in the standard menus The label and action for all buttons in the VNMR menu system can be customized for local use The procedure is described in the manual VVMR User Programming Graphics Window Below the menu buttons is the main VNMR graphics window In this window are displayed FIDs spectra contour plots and other types of NMR data The graphics window also displays files when the File button in the Main menu is selected Specific commands that display information in this window are explained throughout this manual with instructions as to how to interact with the displayed information The graphics window can be either small in which the graphics window and the dg program can be viewed at the same time or large in which the graphics window covers the full screen You can change sizes through the menu system or by entering a command in the input window Getting Started VNMR 6 1B 01 999083 00 A1298 2 2 Working with VNMR on the Host Computer e To enlarge the graphics window to fill the screen select the Resize button in the Permanent menu or enter the Large command e To reduce the size of the graphics window to the small size select the Resize button in
62. a file containing the shim coil settings to be retrieved file can be a name only e g rts H11shp in which case the system searches for it or it can be an absolute path e g rts export home vnmrl vnmrsys shims H1lshp Refer to the description of rts in the VWMR Command and Parameter Reference for details on how the system searches for the file if you use only the file name The rts command copies the shim settings in the file to the parameter set of the current experiment and sets load y to facilitate subsequent loading of shims with the su command or other related commands Enter su The su command sets up the system hardware to match the current parameters including the shim settings you just retrieved but does not initiate data acquisition Now if you make a change in a shim setting through the Acquisition window that setting is retained until you change it by shimming again using acqi by entering another shim setting like z1 200 followed by load y su by using one of the autoshim methods or by again retrieving a file of shim settings Make sure the probe has a sample that it is spinning at the correct speed and that the system is locked onto the deuterium resonance from the lock solvent Getting Started VNMR 6 1B 01 999083 00 A1298 6 10 Using the Acquisition Window 4 Check that the lock signal is not saturated in the LOCK display window The signal is saturated if you change the lock power by 6 u
63. a minimum reading Turn the C coil matching rod for a minimum meter reading Adjust the TUNE knob if needed Switch back and forth between the 7C coil tuning rod and the BC coil matching rod until you achieve an absolute minimum meter reading Once a minimum is obtained enter tuneoff If the tuning is far off it may be better to turn each rod past the minimum meter reading before turning the other rod 10 Return the two cables to their original positions and turn the meter switch to SPIN Tunning Probes on UNITY and VXR S Systems For UNITY and VXR S systems refer to the manuals that accompanied the system or the probe for the information you need Getting Started VNMR 6 1B 01 999083 00 A1298 6 7 Spinning the Sample 6 7 Spinning the Sample On the UN TYINOVA MERCURY VX UNITYplus UNITY and VXR S systems and on MERCURY and GEMINI 2000 with spinner control when a sample is inserted the last entered spin rate is used to regulate sample spinning The actual spin rate is indicated three ways e In the LOCK display of the fir 1400 ACQUISITION Acquisition window acqi CLOSE FID SHIM LARGE program the actual spin rate is SPIN off LOCK off SAMPLE insert on on eject shown below the lock signal in green type if regulated in yellow if not regulated or in red if off see Figure 33 e In the Acquisition Status window acqstat program the actual rate is given as well as a spin regula
64. above From terminals or non Sun computers access to the experiment status is provided with the showst at command This command gives the same information as the Acgqstat window but in a non graphical manner Other options include entering the command explog Or you can enter the somewhat equivalent but possibly preferable command shell cat curexpt acgqfil log to show the complete file or shell tail curexp acqfil log to show the tail or end of the log file Either of the last two commands display in the text window the contents of the experiment log file which shows when the experiment was submitted when it was started and if done when it is done During the course of the acquisition block size complete messages and FID complete messages and error messages if present will be reported The value of ct also will be updated at the normal times For all experiments the parameters wbs wnt and wexp and associated commands wbs wnt and wexp are active just as they are if acquisition is run locally The issue of multiple users arises If an acquisition was initiated on the spectrometer by a user say vnmr 1 someone logging in remotely must also be vnmr1 in order to stop that acquisition If no acquisition is in progress any user can initiate an acquisition remotely No remote lockout is provided With a single user the second issue that arises is shared use of an experiment If you are in say ex
65. acquisition is not in progress In the Acquisition window the mouse can be used to eject and insert samples if the hardware is available turn the spinner on and off adjust the lock channel and adjust the various shim gradients Use of this window is described in Chapter 3 Both acquisition windows open automatically when you enter VNMR if your system is configured for acquisition not a data station To otherwise open and close these windows see Entering and Exiting VNMR on page 39 GLIDE Interactive Acquisition and Processing Window The GLIDE interactive data acquisition and processing window shown in Table 14 is activated by clicking on the GLIDE button in the Permanent menu or by entering the glide command in the input window Figure 14 GLIDE User Interface Window Refer to Chapter 3 Using GLIDE for a detailed description of the GLIDE window Workspace Menu Many windows for programs are accessible from the pop up Workspace menu shown in Figure 15 To open the Workspace menu and make a selection 1 Move the mouse arrow over any part of the workspace area of the screen where no windows appear Press and hold down the right mouse button until the Workspace menu appears Continue to hold down the right mouse button and drag the cursor to the item you want If the item you want has no small triangle to the right of it simply release the mouse button to select that item After s
66. active and the Custom Setup window appears 10 To use default values click on Go in the GLIDE interface to acquire a spectrum The system will autolock autoshim acquire process and plot the data using the default parameters enter Program GLIDE experiments can also be accessed from the ent er program The experiment file created by enter is now saved in a directory of the same name For example the command enter abc creates a directory named abc A file named abc and another directory named abc macdir will be in that directory abc has the experiment information and abc macdir has GLIDE related information for the automation run Customizing a 1D Experiment In addition to the previously outlined scenario GLIDE permits you to customize experiments to obtain for example a spectrum with a greater number of scans than the default As an example assume that the default number of scans for carbon 1D on the system is 1024 Your sample however is quite concentrated and you need only 16 scans You can set up the carbon 1D experiment and modify the number of scans using GLIDE 1 Follow steps 1 through 9 in the Running a Standard Experiment on page 54 but instead of choosing Proton 1D choose Carbon 1D in step 4 The Custom Setup window appears This window has four buttons that each open an associated setup window with parameters that can be changed These windows permit the user to perform in two different modes of operati
67. also be used to retrieve data However use this method to retrieve only data on parameters and FIDs Perform the following steps to retrieve data with GLIDE 1 Activate GLIDE by clicking GLIDE button in the Permanent menu 2 Click on Recall 3 Inthe Recall Setup window type the full path of the FID file that you want 4 Click on Retrieve The data file is recalled If the data was acquired with GLIDE the def files are also recalled into GLIDE Using CDE File Manager to Retrieve Data The CDE File Manager can be used to retrieve data on parameters FIDs or shim files To use this method the 1istenon macro must be or must have been executed If file retrieval is a regular mode of operation consider putting 1istenon in your local login macro Do the following steps to retrieve data with CDE 1 Start the CDE File Manager from the CDE toolbar 2 Goto the desired directory and double click the desired parameter FID or shim file After you have selected the desired FID file it is processed and displayed def files files acquired with GLIDE are retrieved into GLIDE Correcting Saved Parameter Sets The updatepars macro corrects saved parameter sets With the release of VNMR version 4 2 all the parameters upper limit lower limit and step sizes were tightened Further additions were made in VNMR 4 3 and VNMR 5 3 updatepars searches a directory for parameter and FID files and corrects the procpar files found It is
68. an optional argument for axis that is used instead of the current value of the parameter axis The optional argument vertical_start defines the vertical position where the scale is drawn the default is 5 mm below the current value of the parameter vp The second optional argument plot_start is interpreted as a modified start of plot The pen option defines the pen number to be used The ppf command plots peak frequencies in units specified by the axis parameter above the peaks selecting only those peaks greater than th high ppf nol1 plots peak frequencies using the last previous line listing while ppf pos plots positive peaks only Other arguments for noise suppression noise_mul1t and label positioning work the same as the dpf command described above The p11 command produces a columnar line list on a plotter similar to what would appear on a printer The output is automatically formatted into multiple columns depending on the number of lines The syntax is p11 lt x y minimum_y gt The arguments x and y are the x and y position of the upper left of the line list and minimum_y is the minimum y at which to reset back to the top The p1h command plots a proton spectrum based on parameters pl tmod and intmod e pltmod off sets no plotting e pltmod fixed takes sp and wp as is e pltmod full adjusts sp and wp to plot the full spectrum e pltmod standard uses a macro that adapts output for a variety of spectra e pltmod
69. and Mode A changing the value of that slide control affects all pulses simultaneously For further information on IPA statements see VNMR User Programming Shimming on the FID The strategy for shimming on the FID is somewhat different from that of shimming on the lock In general the adjustments are made on the basis of the shape of the FID not on its amplitude The best single criterion is that one is attempting to increase the signal strength of the FID across the FID display Best results can be initially obtained by Figure 45 Spectrum Display Window selecting parameters so that with nt with IPA acqi Program set to 1 and the dl at at approximately 1 0 an off resonance FID with good signal to noise at the beginning and pure noise at the end is observed in the df display This may require adjustment of pw Once this is obtained enter gf and go to the interactive FID display Select Style 1 or Style 2 FID shimming Shimming on the Spectrum As most shimming is done in order to obtain a correct spectrum the strategy for shimming on the spectrum is somewhat obvious For a first time it is recommended that a well shimmed sample with a singlet be used You can then make an intentional misadjustment in a shim and observe the effect on the spectrum A suggested procedure for shimming is the following 1 Set phfid 0 2 Enter go to acquire a spectrum Process it and expand the display to focus on the p
70. and flipflop This incompatibility is taken care of automatically by the software which turns off DSP and sets oversamp n if you attempt to acquire data using an incompatible pulse sequence If you want to obtain the benefits of DSP in such experiments use inline or postacquisition DSP Preserving the full potential dynamic range benefit of DSP for dp y real time DSP contains an inherent gain of 16 or the equivalent of 20 bits of data A consequence of this gain is that if you look at the output of a single transient the largest possible signal is no longer 32768 216 but instead 524288 27 In other words the system behaves as if it has a 20 bit digitizer instead of a 16 bit digitizer For dp n the gain of 16 mentioned above is disabled and therefore the main data value 1s 32767 Another consequence of the gain with dp y is that if the ADC is filled on a single transient and the signals add coherently on successive transients as they do in most experiments but not in say an indirect detection experiment after a minimum of 4096 transients 23 21220 the accumulating signal can overflow the available memory the largest signal becomes greater than 2 and cannot be stored in memory The hardware does not prevent this overflow and it is possible to obtain data that is useless in such a case If you need to run more than 4096 transients use inline or postacquisition DSP One subtle point involves ADC overf
71. are higher than the reference line tmsref tries avoiding those by taking the line furthest to the right in that area as long as it is at least 10 of the main Si CH3 signal Large signals within 0 6 ppm for H or 6 ppm for 13C to the right of TMS may lead to misreferencing The set ref macro adjusts the referencing so that the solvent frequency is correct Even when no reference substance is present in the sample set ref uses absolute resonance frequencies calculated for a proton frequency of 100 0000000 MHz as defined in the file vnmr nuctables nuctabref which contains about 25 of the most common nuclei set ref can easily be expanded to cover any other nucleus as well a recipe on how to expand set ref is given in the header of the file vnmr nuctables nuctabref The setref macro assumes that the system is locked and that the lock solvent is defined in vnmr solvents If you are working without lock and still want to use set ref you must ensure that the field offset has been previously adjusted so that the lock frequency is on resonance with a sample of similar susceptibility To ensure that the field offset is adjusted do the following procedure 1 Insert a sample with deuterated solvent 2 Adjust z0 or Lkof in acqi so that the lock frequency is on resonance 3 Switch off the lock 4 Insert the nondeuterated sample On UN TYINOVA systems set ref first calculates the lock frequency in MHz as lock_frequency lockfreq lk
72. around on the dg window and create or remove new items For more information about configuring the dg window see Customizing the Interactive dg Window in chapter 6 of the User Programming manual CONSOLE and VNMR Shell Windows If OpenWindows is running in the upper right hand corner of a typical VNMR screen display are two icons for shell windows CONSOLE and VNMR as shown in Figure 13 Under CDE these CONSOLE icons are not needed The CONSOLE shell window is Figure 13 CONSOLE and VNMR automatically created when OpenWindows Shell Windows is started at login time do not confuse this window with the NMR console This window is used by the UNIX operating system to display diagnostic messages such as su command succeeded for user A or starting Acaqproc To see these messages double click the CONSOLE icon with the left mouse button Do not quit the CONSOLE shell window otherwise system messages are written to the background or workspace causing the window graphics to scroll off the screen However if you are using CDE you can quit this window The VNMR shell window icon is also automatically created when OpenWindows is started Because every UNIX command must be started from a shell window the Vnmr command to start VNMR is entered in this window Certain diagnostic messages from Vnmr are displayed in the VNMR window Again do not quit this window However if you are using CDE you can quit this window F
73. automatic teller machine ATM cards and similar plastic cards Many wrist and pocket watches are also susceptible to damage from intense magnetism A table on the back of the 5 Gauss Warning Sign shows the typical 5 gauss stray field for various magnet systems 01 999083 00 A1298 Getting Started VNMR 6 1B 19 SAFETY PRECAUTIONS Caution Notices continued CAUTION Check helium and nitrogen gas flowmeters daily Record the readings to establish the operating level The readings will vary somewhat because of changes in barometric pressure from weather fronts If the readings for either gas should change abruptly contact qualified maintenance personnel Failure to correct the cause of abnormal readings could result in extensive equipment damage CAUTION Never operate solids high power amplifiers with liquids probes On systems with solids high power amplifiers never operate the amplifiers with a liquids probe The high power available from these amplifiers will destroy liquids probes Use the appropriate high power probe with the high power amplifier CAUTION Take electrostatic discharge ESD precautions to avoid damage to sensitive electronic components Wear grounded antistatic wristband or equivalent before touching any parts inside the doors and covers of the spectrometer system Also take ESD precautions when working near the exposed cable connectors on the back of the console Radio Frequency Emission Regulations
74. been previously placed into the add subtract experiment as the second input Non interactive addition of the current spectrum into the add subtract experiment Non interactive subtraction of the current spectrum into the add subtract experiment Non interactive combination of the minimum of the current spectrum and the spectrum in the add subtract experiment Getting Started VNMR 6 1B 01 999083 00 A1298 4 11 Analyze Menus Interactive Add Subtract Menu addi Program The Interactive Add Subtract menu part of the addi program is typically entered by clicking on the Interactive Mode button in the Add Subtract menu by selecting the Add Sub button in the Deconvolution menu or by entering the command addi Button Description Box OR If labeled Box go to the box mode with two cursors Cursor If labeled Cursor go to the cursor mode with one cursor Select Select the current add sub or result spectrum as active Expand OR If labeled Expand expand area between cursors box mode Full If labeled Full display full area cursor mode sp wp Adjust the start and width of the active spectrum sub If labeled sub select the result spectrum to be the difference between the OR current and the add sub spectra min If labeled min select the result spectrum to be a minimum intensity of OR either the current or the add sub spectra add If labeled add select the result spectrum to be a sum of the current and the add
75. by Figure 43 Autoshim Method Editor Panel selecting the desired shim buttons with acqi Program the left mouse button A selected coil can be deselected by selecting it again with the mouse The buttons at the bottom of the window allow the user to specify an estimate of the starting shim quality and a specification of how tight to make the convergence criterion The buttons at the upper left of the window allow the user to load save and delete shim methods A method must be saved before it can be used 158 Getting Started VNMR 6 1B 01 999083 00 A1298 6 10 Using the Acquisition Window Spectrum Display r Tia ACQUISITION 5 CLOSE LOCK SHIM LARGE Style 2 Figure 44 shows the FID Spectrum x172 FID Spectrun PANEL Shin IPA display window with a typical spectrum up Single Grid OFF Trace GH down peak max 165 display Style1 The spectrum display can also be viewed in Style 2 The menus and buttons in the window are the same as for the FID display except that vertical scaling is represented as a multiplier shown near the top left corner e g x4 means the data is multiplied by 4 Multipliers available SHIM TJcoarse z x best First include x1 x2 x4 x8 x16 and x32 Z1 182 1 4 16 64 The up and down buttons select the Dezel eer z4 Sier Seas vertical scaling multiplier ae e ta CEE CEE IBT S Saas The spectrum display is controlled by gad bien a Se ee Se t
76. can use np N final desired np because the final np is usually much larger than dscoef 2 2 After a data set has been acquired enter the macro pards to create additional parameters downsamp dscoef dslsfrq dsfb and filt file used by downsampling 3 Setting up of the parameters can be made easier if an initial Fourier transform spectrum exists already In this case the macro movedssw can be used to set the parameters by using cursors in the ds spectral display Position the vertical cursors around the region of interest and enter moveds sw Otherwise set the parameters as follows e downsamp specifies the downsampling factor applied after digital filtering For example starting with a spectral width of 100 kHz and downsamp set to 20 downsampling reduces the final spectral width to 5 kHz The spectral width sw of the data set after digital filtering and downsampling is acquired sw downsamp Setting downsamp to allows digital filtering with a filter bandwidth specified by ds fb without downsampling Setting downsamp to n allows normal data processing in VNMR without digital filtering dscoef specifies the number of coefficients used for filter computation The default of 61 is usually a good choice A larger number of coefficients gives a filter with sharper cutoffs and a smaller number of coefficients gives a filter with more gradual cutoffs Larger values in the range of 199 to 399 coefficients may have to be used to prevent a
77. change of a sample using the automatic sample changer e For shims on the FID enter f or fn n is an integer where f indicates automatic shimming is done prior to the data collection of each new array member in a multi FID experiment not available on MERCURY VX MERCURY and GEMINI 2000 fn where n is an integer indicates shimming is done prior to data collection of every nth FID For example wshim f 16 will shim prior to acquiring FIDs 1 17 33 etc This method is only relevant to arrayed or 2D experiments not implemented on MERCURY VX MERCURY and GEMINI 2000 Using GLIDE 1 Ifthe GLIDE interactive window is not open open it entering glide in the input window or by clicking on the GLIDE button in the Main Menu Click on Setup Choose an experiment and solvent In the AutoSHIM field click on YES Click on Setup gt Custom gt Acquire Click on Do gt Close Dn Fwy Getting Started VNMR 6 1B 01 999083 00 A1298 6 9 Adjusting Shims Background Autoshim Background Autoshim is controlled by the parameter met hod and the command shim This is a complete background Autoshim method that provides no interaction with the operator whatsoever The type of automatic shimming to be done during routine sample changes depends on the level of homogeneity required on any particular sample the change in sample height and the maximum time desired for shimming e For average homogeneity needs with samples which a
78. choices available 3 Continue to hold down the right mouse button As the mouse cursor arrow is dragged up or down the menu each selection in turn is highlighted When the choice you desire is highlighted release the right button Your choice is selected and the pop up menu disappears Changing Parameter Values If changes are made to lock shim gain and spin parameters in the LOCK FID Spectrum and SHIM displays the new values are returned to VNMR only by clicking the CLOSE button If the current experiment has the parameter load set to y the shim values are not returned to that experiment However if changes in Llockpower and lockgain are made in VNMR e g entering lockpower lockpower 10 the Acquisition window does not learn of the change if it is disconnected but not exited To get the new values in to the Acquisition window you must type su or and click on the Acqi button to restart If changes to Lockpower and lockgain are made only within Acquisition window there is no problem When the Connect button is clicked the acqi program reads all shims and lock parameters from the acquisition computer so that entering Lockpower 10 su then clicking the Connect button sets Llockpower to 10 within acqi This is independent of the load parameter When changes to a display are made in rapid succession especially in FID when long delays are used the mouse may seem inoperative This becomes apparent when the left mouse button no
79. contain Varian s time corrected zero phase digital filters These filters allow very flat baselines to be obtained with no frequency dependent phase shift across the spectra Getting these flat baselines does require some changes in setup and acquisition parameters from those used for analog filters Many users working with spectra of proteins are accustomed to using the hoult and calfa macros to adjust the acquisition conditions such that spectra are obtained with a frequency dependent phase shift 1p of zero and with minimal distortions of the second and subsequent data points with analog filters These conditions are typically satisfied with negative values of alfa The same acquisition conditions do not result in the flattest possible baselines when using real time DSP The following procedure is recommended to set alfa and rof2 1 Start by using normal positive values of alfa and rof2 e g alfa 6 rof2 2 in fact the software automatically sets these values the first time you activate DSP 2 Obtain a spectrum and phase it properly 3 Enter crof2 to recalculate rof2 so that 1p will be zero 4 Reacquire the spectrum to verify that 1p is now zero After the last step the baseline should be reasonably good To improve it even further you can make fine adjustments to alfa and rof2 keeping the sum of the two constant e g enter alfa alfa 0 5 rof2 rof2 0 5 ga Once good values are obtained you should find them relativel
80. containing indicators and displays that show status and temperature or the variable temperature unit lock level acquisition and other information about each active rf channel Top level directory of a UNIX file system Also login name of the UNIX system administrator Set of coils inside the magnet that induce changes in the shape of the magnetic field Sun Microsystems operating environment Includes SunOS Optional software available from Varian that simulates single pulse experiments on solids under magic angle spinning MAS or VAS conditions Sun Microsystems operating system Part of the Solaris Type of Varian NMR spectrometer system Type of Varian NMR spectrometer system Type of Varian NMR spectrometer system UNITYINOVA UNITYplus and UNITY spectrometer systems User contributed files placed in the userlib directory Name of Varian s NMR application software package Login name of the NMR system administrator Version of VNMR for IBM workstations Version of VNMR for SGI workstations Type of Varian NMR spectrometer system Gemini VXR 4000 and XL spectrometer systems VNMR display screen background where no windows appear 297 Getting Started VNMR 6 1B Glossary 298 Getting Started VNMR 6 1B 01 999083 00 A1298 Symbols button 42 single quotation marks notation 95 Abort Acq button 207 bru files 290 def files 278 fid files 279 282 login file 48 macdir for
81. correction 77 242 252 baseline flatness 188 baseline performance 214 Bayes software package 33 BC button 77 be command 252 bearing air 105 beginning acquisition 70 01 999083 00 A1298 Benzene button 68 best button acqi 156 beta parameter 187 bin directory 34 BINOM button 69 binomial water suppression 69 blanked amplifiers 188 block size storage 203 borders showing and hiding 263 Both button 75 Box button 71 73 74 75 76 83 234 239 243 box command 273 bpa macro 261 Brickwall filter 214 broadband switchable probe 23 Broaden button 72 Bruker data processing 227 Bruker data autophasing 225 Bruker tape 290 bs parameter 156 158 203 btune macro 124 125 buttons on menus 59 By Date button 89 By Size button 89 C C13 button 68 c13 parameter set 145 C13 CDC13 button 67 calcdim command 200 calculate contour plot 80 synthetic spectrum 85 calculating field maps 170 calfa macro 216 calibration automated 98 Cancel button 75 Cancel Cmd button 65 cancel correction 252 cancel currently active command 65 cancel integral reset points 253 carbon connectivities 33 carbon spectrum plot 250 carbon carbon connectivity 2D 70 cat command 277 cautions defined 17 cd command UNIX 37 cd command VNMR 275 cdc command 252 CDCl as solvent 67 CDCI3 button 68 CDE menu 50 CD ROM drive 24 celem parameter 200 Center button 78 79 center butto
82. d2 at 4 Once all the parameters are set click on Automake Shimmap step 8 The parameters are saved when the shimmap is done and are used the next time gradient autoshimming is run To use homospoil deuterium gradient shimming with different solvents set the parameter gmap_findtof y This should be done before making the shimmap or may be set in the corresponding parameter set in gshimlib shimmaps Gradient shimming will then perform a calibration to find tof before autoshimming starts This takes an extra iteration in the shimming procedure but is essential for homospoil deuterium gradient shimming to function correctly in automation Full Deuterium Gradient Shimming Procedure for Lineshape The automated deuterium gradient shimming module must be installed to use this procedure 1 Insert the appropriate lineshape sample chloroform in acetone d6 and find lock Turn off spinning and disable sample changer control Adjust lock power lock gain and lock phase as necessary Do quick shimming on z1 z2 x1 yl use zlc z2c if present 2 Find the 90 pulse on 7H as follows Enter s2pul tn 1k tpwr 42 pw 200 b Enter ga and wait for acquisition to finish You should see only a single line Place the cursor on resonance and enternl movetof c Enterarray pw 20 100 100 Enter ga and wait for acquisition to complete d Set pw90 to the first maximum 3 Set up gradient shim parameters Enter gnapsys and click on Set Para
83. date Jul2996 dirq 400 075 solvent CDC dn H file expor Vhome dpwr 30 vrimr1 009 Tid ion dof o didtid dm nnn STANDARD 1H OBSERVE Pulse Sequence s2pul Figure 74 Window with Data and Without Borders and a Grid Using Templates You can create your own templates After you have created a design do the following procedure to save your design as a template 1 Click File Templates to open the Plot Templates window 2 Enter a name in the Template field If you want the file to be the default template click the box next to Use this template as default After you select a file as a template the next time that you start Plot Designer it will automatically open with the template 3 Click Save to store the template in Svnmruser template plot directory If you try to save a template with the same name as an already existing template a warning notifying you that the file will be overwritten appears If you do not want the file replaced click Cancel 4 Quit the Plot Templates window by clicking on Close Loading a Template After you have created templates you can run Plot Designer with a specific template by typing the jplot command and the template name For example entering jplot t1 starts Plot Designer with the tl template automatically loaded If you opened Plot Designer with the jdesign macro the workspace will either be empty or contain the design that was being worked on the previous time Plot
84. digital filtering e In the first called Ifs low frequency suppression a low pass digital filter is applied to the acquired FID This filter severely attenuates all signals that lie outside the passband of the filter leaving only the on resonance solvent signal and other low frequency signals that fall within the filter bandwidth This filtered FID is then subtracted from the original FID to remove the solvent peak contribution The Fourier transform of this FID gives the solvent subtracted spectrum e In the second called zfs zero frequency suppression the acquired FID is also low pass filtered but then the filtered FID is fit with a polynomial specified by the parameter ssorder and the polynomial is subtracted from the original FID This has the effect of removing from the FID only the signal that is exactly on resonance The Fourier transform of this FID produces the solvent subtracted spectrum The solvent subtraction parameters ssfilter sslsfrq ssntaps and ssorder control processing If these parameters do not exist in the current experiment they can be created by entering addpar ss The parameters ssfilter and ssorder select the processing option as follows e The zfs zero frequency suppression option is selected if both ssfilter and ssorder are set to a value other than Not Used e The lfs low frequency suppression option is selected if ssfilter is set to a value other than Not Used and ssorder is se
85. digital filtering and downsampling to the acquired data prior to storage to disk on the host computer Only the downsampled data set is stored using this method DSP prior to data storage to disk has a time constraint the digital filtering and downsampling must be completed within the time between transfer of successive data blocks or increments of a 2D experiment to the host computer disk Additional processing done during acquisition such as wnt also adds to the time constraints This processing can limit the speed of rapid arrayed experiments and depends on the type of Sun host computer and the parameters used Inline DSP is activated by setting the global parameter dsp to i If dsp is not present or is set to n DSP is disabled If dsp i setting the oversamp parameter to a value greater than 1 in a particular experiment causes the next experiment run to be oversampled digitally filtered and downsampled back to the selected sw prior to saving it to disk 01 999083 00 A1298 Getting Started VYNMR 6 18 211 Chapter 7 Acquiring Data On the UN TYINOVA inline DSP is completely compatible with interleaving and with stopping and restarting on acquisition with sa and ra On systems other than UN YINOVA inline DSP is not possible if interleaving is active i1 y Also the command sa can be used to stop acquisition but ra cannot be used to resume it To Apply Inline DSP 1 Enter dsp i This turns on inline digital filtering and
86. dimension For linear prediction 1st implicit dimension For linear prediction 2nd implicit dimension Getting Started VNMR 6 1B 111 Chapter 6 Preparing for an Experiment addpar oversamp For oversampling data addpar ss For solvent suppression With no argument specified addpar displays instructions for its use Refer to the description of addpar in the VVMR Command and Parameter Reference for a list of the parameters created with each addpar argument To List Parameter Groups You can display various groups of parameters in the text window using the dg command or one of the macros dg1 dg2 dgs and dglp The string parameters dg dg1 dg2 and dgs control which parameters are displayed by the macro with the same name as the parameter e g parameter dg controls the parameter group displayed by macro dg Text editors paramvi parameter or paramedit parameter are available for modifying the string parameters Refer to the manual VVMR User Programming for details on how to modify the parameters Using the Inout Window e Enter the appropriate command or macro dg Display group of acquisition and 1D 2D processing parameters dg1 Display group of display parameters dg2 Display group of third and fourth rf channels parameters typically for the second and third decouplers respectively and 2D processing of 3D data sets parameters dgs Display group of shims and automation parameters dglp Display group of linear predict
87. done and you can move on to the next task Another important example of queuing on the system occurs with data acquisition Just like plotting you need not be concerned whether an acquisition is in progress when you set up an experiment and issue the command to start the acquisition If no acquisition is in progress at that time any acquisition you request starts immediately If an acquisition is in progress your acquisition request waits until the current acquisition is finished and starts at that time Because a particular acquisition can take many hours the system even enhances the queuing feature by informing you of the projected completion time of the current acquisition so you will know when the next one begins Note that queuing is fully automatic and requires no special commands or other operations Multitasking Unlike queuing which occurs sequentially the multitasking feature of the system allows simultaneous activities to occur The data system includes a number of computers and microprocessors all of which can be active at the same time On N YJNOVA systems the acquisition computer s operating system is multitasking which allows data acquisition data transfer and status checking simultaneously In addition the UNIX operating system used on the host computer allows multiple tasks such as printing plotting data processing and communication with other computers to all proceed at the same time even with a single pr
88. example if you select the More button the following extension of the Main menu called the Secondary Main menu replaces the Main menu Write Pulse Sequence Configure UNIX Exit VNMR Return By clicking on the Return button or pressing F5 in the Secondary Main menu the Main menu now replaces the Secondary Main menu you are back where you started Similarly you can display dozens of menus each with buttons capable of certain actions affecting system operation For reference Table 3 outlines the default version of the VNMR menu system see Customizing the menu System below Menu buttons that call another menu are underlined in the list If your prefer you can also call up a particular menu by typing menu menu_name where menu_name is the name of the menu e g menu workspace calls up the Workspace menu Some menus have a separate command for example entering the command files displays the Files Main menu For the names of menu files look in the vnmr menulib directory Note that selecting a particular button may produce more than one action depending on the current value of certain parameters the nature of the data or any other identifiable factor For example in the case of the Main menu the Process and Display buttons both first look to see whether the experiment holds 1D or 2D data and then display a 1D or 2D menu appropriate to the experiment Interactive Programs with Menus The VNMR software contains
89. filel lt file2 lt gt gt gt cptmp lt file gt 19p getld lt experiment gt get2d lt experiment gt hip hregions integrate isadj lt height lt neg_height gt gt isadj2 lt height lt neg_height gt gt sf p3lp procld proc2d procarray process procplot rttmp file stack mode svtmp lt file gt Parameters pkpick string stackmode stackmode horizontal vertical diagonal 01 999083 00 A1298 Automatic stacking for processing and plotting arrays Processing of 1D carbon spectra Remove old files and directories from an experiment Copy experiment data into experiment subfile Process 1D fluorine spectra Select a 1D experiment for processing Select a 2D experiment for processing Process 1D proton spectra Select integral regions in proton spectrum Automatically integrate 1D spectrum Automatic integral scale adjustment Automatic integral scale adjustment by powers of two Process 1D phosphorus spectra Process simple non arrayed 1D spectra Process 2D spectra Process arrayed 1D spectra Generic automatic processing Automatically process FIDs Retrieve experiment data from experiment subfile Fix stacking mode for processing and plotting spectra Move experiment data into experiment subfile Peak pick Stacking control for processing arrayed 1D spectra Getting Started VNMR 6 1B 99 Chapter 5 Using the Command Mode 100 Getting Started VNMR 6
90. first of three menus for performing regression analysis To display the Regression 1 menu with a display of data in the regression inp file click the Analyze button in the Main menu then click on the Regrs button This menu can also be activated by entering menu regressionl1 Button Description x linear Show the displayed data points against a linear x axis scale X square Show the displayed data points against a squared x axis scale x log Show the displayed data points against a logarithmic x axis scale dp linear Fit a straight line to the data points and display dp quad Fit a quadratic curve to the data points and display dp exp Fit a exponential curve to the data points and display Next Display the Regression 2 menu below Rt Display the Analyze menu page 81 Regression 2 Menu The Regression 2 menu is activated by selecting the Next button in the Regression 1 menu or by entering menu regression2 Button Description y linear Show the displayed data points against a linear y axis scale y square Show the displayed data points against a squared y axis scale y log Show the displayed data points against a logarithmic y axis scale dp linear Fit a straight line to the data points and display dp quad Fit a quadratic curve to the data points and display dp exp Fit a exponential curve to the data points and display Next Display the Regression 3 menu below Rt Display the Regression 1 menu above Regress
91. gt M M gt M M gt T and T gt T B and E are inaccessible The starting criterion should never affect the final result only the time in which that result is produced If the starting criterion is specified as T for example and the optimum shim is far off this shim will eventually be found The search will however take longer than if a starting criterion of L had been specified Shim Methods for Autoshim A shim method consists of a text string contained in a file within the VNMR system s or a user s Shimmethods directory That text string will be interpreted as a series of instructions describing the shimming method Commands in elements include e Turn on and off the spinner e Set maximum shim time per element Getting Started VNMR 6 1B 01 999083 00 A1298 6 9 Adjusting Shims e Set the delay between lock level samplings e Specify the gradients to be shimmed and the criterion used for shimming A complete method consists of one or more elements separated by commas and terminated with a semicolon e g f ry t600 szq cmm The element setting which specific gradient or gradients to be shimmed has the syntax sxx cyz where s identifies the shim part of the form xx is a two character code for a specific shim gradient or gradient combination c identifies the criterion part of the form y is the starting criterion and z is the desired ending criterion Table 18 lists standard two character codes for shim gradi
92. in a multiprocessing multiuser environment A plotter can be shared between several users and or processes that generate plots at the same time A plotter can even be shared between multiple VNMR instruments and workstations as long as they are connected to each other via Ethernet On the other hand one system can support multiple plotters which permits use of the optimal device for each task Table 40 lists commands and parameters associated with plotting Table 40 Plotting Commands and Parameters Commands ap lt template gt Print out all parameters bpa sc2_minimum Plot boxed parameters hpa Plot parameters on special preprinted chart paper killplot Stop plot job and remove from plot queue page lt num_pages lt clear file gt gt Submit plot and change plotter page pap lt lt template gt x lt y gt lt size gt gt Plot out all parameters pltext Plot text file ppax x lt y gt gt Plot parameter list in English setpen lt maxpen max_num_pen gt Set maximum number of HP pens setplotdev lt plotter_type gt Return characteristics of a named plotter showplotq Display plot jobs in plot queue showplotter Display currently defined plotters and printers vnmrplot lt file gt Plot files UNIX pltext lt lt file gt lt x lt y lt width gt gt gt gt lt Sx_next Sy_next Sy_increment gt Parameters ap string All parameters display control maxpen 1 to number of pens Maximu
93. in some cases by first setting gzsize 4 and clicking on Autoshim on Z to shim on z1 z4 and then shimming the low order transverse shims and then increasing gzsize and shimming again This may also be done using gmap_z1z4 y Ona short sample it also can be useful to remap the shims Some shim systems may need additional time when running the shim mapping experiment to allow the shims to settle The added time is especially noticeable on some systems for ZA To account for added time lengthen the d1 delay or add dummy scans in between each array element e g ss 2 Decreasing the amount a shim is offset also allows the shim to settle more quickly Enter gmapsys vi to edit the values in the Offset column and then enter gnapsys shimmap manual to map the shims with user defined offsets A new mapname may also be set using gmapsys vi Coarse shims are used on systems on which they are available To use fine shims on these systems enter gmapsys vi to edit the entries in the shim column e g change z1c to z1 and then enter gnapsys shimmap manual to map the shims For samples in H 0 the water protons provide sufficient signal for shimming For samples other than water deuterium gradient shimming is strongly recommended if there is sufficient deuterium signal Proton gradient shimming can be made to work in samples other than water if there is sufficient proton signal and the signal is well resolved does not overl
94. is even possible to start another copy of VNMR running in a noninteractive background mode If you had an extremely long operation to perform such as an 8K X 8K 2D Fourier transform this operation could be performed in this background mode leaving your Getting Started VNMR 6 1B 01 999083 00 A1298 1 3 Advanced Features interactive copy of VNMR free to start the next acquisition or do some spectral display and plotting etc More information on the background mode of VNMR is found in the manual VNMR User Programming Within the NMR software package there is also an important part of the software that is separate from the basic VNMR program and that is the Acquisition window This window permits locking and shimming FID display and interactive parameter adjustment IPA Because this activity runs in a separate window it is a permissible multitasking activity Thus even while a long transform is occurring you can insert the next sample and start performing locking and shimming Experiments NMR scientists like all scientists are accustomed to performing experiments For this reason the data system organizes its data along the same lines In VNMR an experiment is a directory on a disk in which parameters and data are stored The values of the parameters represent the conditions under which the data in the file was collected or will be collected Each experiment has a number shown by Exp on the first line of the status window
95. is internally calculated to a power of 2 therefore fn 1 6k actually sets the Fourier number to 2 or 16384 These definitions of p d and k are made in the boot up macro with the command unit Additional suffixes can be defined and p d and k can be redefined with the unit command Mathematical expressions can contain numbers with these suffixes so you can enter for example sw 10pt tof 2k A string parameter takes a variable length alphanumeric string as a value The strings are always enclosed within single quotation marks For example the value of dmm decoupler modulation mode might be c while the value of dm decoupler mode might be nyy Many alphabetic parameters have values of y for yes and n for no By setting a parameter to the n value certain numeric parameters are capable of being turned off The parameter temp for probe temperature is an example To select a temperature of 60 C type temp 60 to turn off the temperature regulation type temp n A parameter that is deactivated by setting its value to n can be reset to its last numeric value by entering a value of y For example if the current value of line broadening is 1 5 i e 10 1 5 you can deactivate line broadening with lb n A subsequent 1b y will restore the value of 1b to 1 5 Parameter Entry All parameters are entered the same way type the name of the parameter an equals sign the value and then press the Ret
96. longer inverts the panel buttons or when the right button brings up the Frame menu instead of inverting the Panel button When this happens wait for the next update of the graphics window then proceed Getting Started VNMR 6 1B 01 999083 00 A1298 6 10 Using the Acquisition Window LOCK Display The LOCK display appears when the LOCK button is clicked from any Acquisition window Figure 39 shows a typical LOCK display B troi ACQUISITION B CLOSE FID SHIM LARGE SPIN off LOCK off SAMPLE insert SPINNER liquids on on eject solids mas lock level Cee C 320 zo Silk 4 16 64 E 31 lockpower r 4 16 64 E 42 lockgain Sis 4 16 64 E 166 m lockphase le 4 16 64 E 20 E spin 1 4 16 64 Figure 39 LOCK Display Window acqi Program At the top of the LOCK display is a row of buttons labeled CLOSE FID SHIM and LARGE these buttons were described above Below these buttons are the SPIN LOCK and optionally SAMPLE menus e SPIN sets sample spinning off and on e LOCK sets lock to off on or auto auto is available only on UNITY and VXR S systems Selecting auto chooses hardware simple Autolock which is described on page 132 e SAMPLE controls inserting and ejecting samples if spin control hardware is installed This menu was described above The central part of the window shows the lock signal and below that the current status f
97. menu psgset2 Button COSY COSYPS HETCOR NOESY ROESY 1D More 2D Return Description Set up a homonuclear correlation pulse sequence absolute value Set up a phase sensitive pure absorption COSY pulse sequence Set up a heteronuclear correlation pulse sequence Set up a NOE 2D correlation pulse sequence Set up a rotating frame NOE 2D correlation pulse sequence Display the 1D Pulse Sequence Setup menu page 68 Display the 2D Pulse Sequence Setup Secondary menu below Display the Setup menu page 67 01 999083 00 A1298 Getting Started VNMR 6 1B 69 Chapter 4 Using the VNMR Menu System 2D Pulse Sequence Setup Secondary Menu The 2D Pulse Sequence Setup Secondary menu provides setups for five more 2D experiments and access to menus for 1D and additional 2D experiments This menu is activated by clicking on the More 2D button in the 2D Pulse Sequence Setup menu or by entering menu psgset3 Button Description DQCOSY Set up a COSY with double quantum filtered pulse sequence HET2DJ Set up a heteronuclear J resolved 2D pulse sequence INADQT Set up a carbon carbon connectivity 2D 2D INADEQUATE pulse sequence this sequence not supplied with the GEMINI 2000 HOM2DJ Set up a homonuclear J resolved 2D pulse sequence TOCSY Set up a total correlation 2D pulse sequence this sequence not supplied with the GEMINI 2000 1D Display the 1D Pulse Sequence Setup menu page 68 More 2D Display the
98. mode 257 high speed line control 24 ho parameter 237 HOM2DJ button 70 Home button 88 home directory 34 36 37 88 homo parameter 191 194 homo2 parameter 192 homo3 parameter 192 homo4 parameter 192 homogeneity adjustments 135 139 homogeneity quality 139 homonuclear correlation 69 homonuclear decoupling 194 195 homonuclear decoupling control 191 homonuclear J resolved 2D 70 homonuclear operation 185 homospoil gradient shimming 174 homospoil process 206 homospoil status 190 horizontal axis selection 80 host computer 25 203 Host Acquisition Link HAL 24 hosts file 282 285 hoult macro 188 216 HP 7475A plotter 255 HP 7550A plotter 255 HP Params button 78 hpa command 262 HPGL graphics language 255 Hproj max button 75 Hproj sum button 75 hs parameter 206 hst parameter 206 htune macro 124 126 Hz to plotter units 273 hzmm parameter 250 hztomm command 273 Getting Started VWMR6 18 307 Index I I2 field 284 IBM RS 6000 computer 290 IBM workstations 25 icon for closed window 28 50 idelay statement 159 ilfid command 229 Image button 79 80 Imaginary button 71 234 imaginary channel 224 234 Imaging button 70 imaging probe tuning 116 Improving Results suggestions 176 in parameter 128 134 in vivo spectra phasing 225 INADEQUATE pulse sequence 70 INADQT button 70 increment FID interferogram index 72 223 indefinite acquisition 188 INE
99. not available on MERCURY VX MERCURY and GEMINI 2000 systems e Controlling the eject air to insert and eject the sample only if the spin control hardware is present Table 20 lists the commands and parameters associated with this window Table 20 Interactive Acquisition Commands and Parameters Commands acqi lt S ret gt Open the Acquisition window acqi par Send selected parameters to acqi acqi disconnect Disconnect from acqi program acqi exit Exit acqi program acqi standby Start acqi program and put in standby mode gf Set parameters for FID spectrum display go Submit experiment to acquisition su Submit a setup experiment to acquisition go lt lt acqi gt lt nocheck gt lt nosafe gt lt next gt lt sync gt lt wait gt gt Parameters dmgf av Absolute value display of FID data or spectrum in acqi phfid 360 to 360 deg n Zero order phasing constant for the np FID 148 Opening the Window The Acqi button is automatically available in the Main Menu when VNMR is started Otherwise to open an Acquisition window enter the acqi command in the input window To successfully use the acqi command your system must be configured for acquisition you cannot use acqi on a data station Entering acqi on a data station causes the message Cannot run acqi acquisition communication not active In macros acqi can be given a return value to determine its success or failure of
100. numbers and a set of special keys such as Control Delete Backspace and Return These special keys are particularly useful for editing commands in the input window Command Line Editing and Reentry on page 96 covers this use of the keyboard Getting Started VNMR 6 1B 01 999083 00 A1298 2 2 Working with VNMR on the Host Computer There are also a series of function keys labeled F1 through F9 on the top row of the keyboard These functions keys can be used as an alternative to the mouse in selecting buttons in the VNMR menu system This topic is discussed further below The two columns of keys on the left side of the keyboard L1 to L10 on some keyboards and the function keys F10 to F12 are not used in VNMR but can be helpful for working in the OpenWindows or UNIX environment For example positioning the cursor over a window and then pressing the Open L7 key changes the window into an icon To do the opposite open an icon position the cursor over the icon and press Open L7 Or to move a window to the front of other windows move the cursor over any part of the window and press the Front L5 key Remote Status Module The optional remote status module is a small enclosure with indicators and displays usually placed next to the host computer display Although considered here as part of the user interface the remote status module actually connects directly to the NMR console not to the host computer like the rest of the u
101. of commands and macros are available for plotting lists and text files e ppa lt x lt y gt gt prints the most important parameters in an English language format with full explanation of each parameter If the x and y coordinates are given as arguments the plot can be positioned as desired The coordinates control the x and y offset in mm from the lower left of the plot to the starting position at the upper left e bpa plots a box around the entire chart assuming blank paper and then plots chemist style parameters in boxes along the lower edge of the chart bpa is the same as ppa but with a different layout Both ppa and bpa behave somewhat naively if the pulse sequence is more complex but they were designed primarily for chemists not for spectroscopists e pap lt lt template gt x y lt character_size gt gt also plots parameters but it uses a mnemonic format listing only the two or three character names and values of all the parameters The ap parameter controls display of pap Use the command paramedit ap to modify the string value of ap See the VVMR User Programming Manual for information on the template argument The x and y arguments are the same as ppa above For pap only a character size can be specified as a multiplier the default is 0 7 e ap lt template gt prints out all parameters in the parameter list The ap parameter controls display of the ap command Use paramedit ap to m
102. of either Gaussian apodization with gfs n which leads to Gaussian line shapes or line broadening with 1b greater than 0 which leads to Lorentzian lineshapes is especially critical for deconvolution Other line shapes cannot be handled by the deconvolution program but may be appropriate for 1D resolution enhancement or in absolute value 2D experiments In any case weighting affects the integrals of different lines in different ways and should be used with great care if quantitative results are requested The command resolv lt a b gt sets defaults of a equal to 0 1 and b equal to 0 3 into the formulas Lb 0 318 a sw and gf b sw thereby calculating reasonable values for the resolution enhancement parameters 1b and gf The arguments a and b can also be selected by the user Several macros exist that set weighting parameters to give certain window functions These include gaussian pi3ssbsq pi4ssbsq sqcosin and sqsinebell The parameter wt file is available for handling user written weighting functions see the manual VNMR User Programming for details Getting Started VNMR 6 1B 01 999083 00 A1298 8 2 Interactive Weighting 8 2 Interactive Weighting The wt i command allows interactive setting of weighting parameters 1b gf gfs sb sbs and awc If wti is called with an index number as an argument e g wti 3 the desired FID number in a multi FID experiment is selected otherwise the current index is
103. of the NMR data such as peak heights integrals and frequencies e NMR parameters treated as variables in a computer program Unlike MAGICAL the predecessor to MAGICAL ID which operated relatively slowly using an interpreted mode MAGICAL II macros are parsed so that their execution is extremely rapid Indeed many of the standard commands in the VNMR software are written in MAGICAL II and yet they run essentially at the same speed they would have run if they had been written in a more traditional language such as C Besides allowing creation of customized NMR algorithms for data acquisition or analysis MAGICAL II also allows data acquisition and analysis to be linked for adaptive acquisition a critical capability for applications such as the LC NMR One of the interesting attributes of MAGICAL II is that all of its features can be directly executed from the keyboard without actually creating a macro Do you want to double the vertical scale Just enter VS VS 2 Do you want to display the central 50 of the spectrum Simply enter f wp 0 5 sw sp sptwp 2 You can even write a simple computer program directly from the keyboard Would you like to compute 27 Try entering the following and see if you get the right answer rl 1 r2 1 repeat rl 2 r1i r2 r2 1 until r2 gt 7 r1 MAGICAL II is discussed in detail in the manual VNMR User Programming Users who wish to modify the existing software or add their own macros are strongly encourage
104. ones are blanked out in regions in which they are behind the earlier FIDs Other than the difference in displays dfww and dfs function the same and use the same arguments The pfww command plots whitewashed FIDs This command functions the same as df ww except that pfww plots FIDs and does not use the color argument 9 4 Interactive Spectrum Display After data is transformed a spectrum becomes available for display and plotting The normal spectrum display program is ds which enables interactive manipulation of a single 1D spectrum ds is entered by the command ds lt index gt or from the menu system by selecting one of the buttons Transform or Weight Transform in the 1D Data Processing Menu Table 36 lists commands and parameters associated with the interactive spectra display 01 999083 00 A1298 Getting Started VWMR6 1B 237 Chapter 9 Display Plotting and Printing Table 36 Interactive Spectrum Display Commands and Parameters Commands cz lt freql freq2 gt Clear integral reset points ds lt index gt ds lt options gt Display a spectrum inset Display an inset spectrum Parameters cr number Current cursor position delta number in Hz Difference of two frequency cursors intmod off full partial Integral display mode io 0 to 200 in mm Integral offset is 1 to le9 Integral scale 1p 3600 to 3600 in deg First order phase on directly detected dimension lv1 number Zero order bas
105. or less description of the file More complete documentation for each file is found in the relevant directory in a file by the same name as the file but with README appended The README file tells you who submitted the file gives you a general overview of its purpose and identifies its limitations e g the file only works on a three rf channel system or requires linear amplifiers Finally files that provide new functionality to VNMR some just modify or improve existing macros pulse sequences etc have an associated file in the user1lib manual directory with complete instructions on how to use this pulse sequence macro etc Complete instructions for using the material in the user library and for submitting material to the library are found in the user1ib README file Users are encouraged to add to the value of the user library concept by contributing material to it subject only to the requirement about providing online documentation to accompany the submitted material The CD ROM containing VNMR also contains a current copy of the Varian NMR user library Refer to the manual VNMR and Solaris Software Installation for installation User Library Terms and Conditions Material submitted to the user library is distributed by Varian as a service to its users All rights to the material submitted are retained by the submitter unless explicitly surrendered in the accompanying README document You
106. oval surrounding the digital readout Z gt ro _ oO zmiant gt Figure 22 TUNE INTERFACE Panel 114 Getting Started VNMR 6 1B 01 999083 00 A1298 6 6 Tuning the Probe e Below the display are two single digit readouts labeled CHAN and ATTEN The CHAN readout can be set to 0 for OFF or to the channel being tuned 1 2 3 etc and the ATTEN readout is the amount of attenuation analogous to the TUNE LEVEL knob on older systems The attenuation is selected in units of 10 dB The maximum attenuation is 79 dB which is selected by a setting of 8 Above and below each readout are buttons for setting the value of the readout At the lower right of the panel is a red indicator light and a BNC probe port labeled PROBE J5321 Tuning a probe on a YN YINOVA or UNITYplus system using the TUNE INTERFACE panel takes the following steps 1 3 Set up the spectrometer to observe the nucleus of interest Often the system is already set to the correct nucleus if not proceed as if you were setting up an experiment see Chapter 7 Acquiring Data for information Using the appropriate procedure given below for your system change the rf cable attached to the probe channel you plan to tune No filters should be in line during the tuning procedures e UNITYTNOVA and UNITY plus 200 300 or 400 systems Disconnect the cable from the H Band CM or the
107. page 286 To Display Remote Nodes Available The dnode command displays all remote nodes available to limNET dnode is entered without arguments and can be used from either VNMR or the UNIX shell To Transfer a File From a Remote Node The eread command transfers the contents of a file associated with a remote node to the local destination The syntax is the following From UNIX eread local_file remote_node remote_fil From VNMR eread local_file remote_node remote_file All three arguments are required The names of the remote computers or nodes available to the limNET protocol are held in the vnmr nodes file The dnode command displays a list of available nodes which each user needs to know Getting Started VNMR 6 1B 01 999083 00 A1298 10 4 Transferring Data Using Ethernet and limNET For example to transfer the contents of the file dsk1 osv700 which resides in the remote node called v 400 to the local destination file called osv700 enter From UNIX eread osv7 00 v400 dskl osv700 From VNMR eread osv700 v400 dskl osv700 To Transfer a File To a Remote Node The ewrite command transfers the contents of a local file from a UNIX system to the remote destination file associated with the remote node The syntax is the following From UNIX ewrite local_file remote_node remote_fil From VNMR ewrite local_file remote_node remote_file The arguments are defined the same as for the eread command To List th
108. probe and system Commands for Setting Parameters Given a desired flip angle in degrees pw flip_angle lt 90_pulse_width gt calculates the flip time in us and then enters the value into pw e g pw 45 enters a pw pulse of 45 If the parameter pw90 exists and no second argument is entered pw90 is taken as the 90 pulse An entered second argument resets pw90 Similarly the command pl flip_angle lt 90_pulse_width gt allows entry of the parameter p1 in degrees The command ernst tl_estimate lt 90_pulse_width gt uses an estimate of the T time for a peak of interest and a 90 pulse width determined by the parameter pw90 to calculate the optimum Ernst pulse width The new pw is entered in the parameter table If the parameter pw90 exists and no second argument is entered pw90 is taken as the 90 pulse Entering a value for the second argument resets pw90 The Ernst pw gives optimal sensitivity for the recycle time set by the user as determined by d1 at at More information about ernst can be found in R R Ernst and W A Anderson Rev Sci Inst 37 93 102 1966 The setting of parameters alfa and rof2 the times that follow the final pulse can be important where the flatness of the baseline is of concern The hoult macro sets these values as described in D I Hoult J Magn Reson 51 110 1983 Getting Started VNMR 6 1B 01 999083 00 A1298 7 2 Setting Pulse Sequence Related Parameters The t ime mac
109. regions are displayed as dotted lines To clear the integral reset points before beginning the command cz must be used no menu choice is provided for this action Interactive Zero and First Order Base Correction Mode The Lvl Tit button activates interactive zero and first order baseline correction mode The zero order correction is represented by the 1v1 parameter the first order correction is represented by the tlt parameter If no integral is displayed when the lv tlt button is activated the integral is automatically displayed Position the mouse arrow on an integral region of interest about halfway vertically up the screen and click the left mouse button A horizontal cursor will intersect at the mouse arrow Two vertical cursors will be placed on either side of the mouse arrow Now moving the mouse arrow above or below the horizontal cursor but within the two vertical cursors and clicking the left or right button will adjust the zero order baseline correction parameter 1v1 Clicking the mouse above the horizontal cursor will increase 1v1 while clicking below the horizontal cursor will decrease 1v1 Placing the mouse arrow right on the horizontal cursor and clicking the mouse button will restore the initial baseline correction value Now move the mouse arrow to another region of the spectrum outside the vertical cursors and click the left mouse button again A new horizontal cursor will be displayed at the mouse arrow two new verti
110. second level menu After the data has been processed you are left in the appropriate interactive display 1D or 2D where you can adjust the expansion vertical scale or threshold before making the plot Refer to the User Guide Liquids for details of the interactive 2D display When the display has been adjusted to your satisfaction click on Autoplot in the second level menu to plot the currently displayed portion of the spectrum If high resolution 1D spectra are available in the current data directory they will be plotted along the edges of the 2D spectrum to aid in interpretation Walkup NMR Refer to the Walkup NMR Using GLIDE manual for detailed instructions on how to perform walkup NMR experiments and system calibrations using the GLIDE interface 58 Getting Started VNMR 6 1B 01 999083 00 A1298 Chapter 4 Using the VNMR Menu System Sections in this chapter e 4 1 Working With Menus page 60 e 4 2 Customizing the Menu System page 64 e 4 3 Menu System Step by Step page 64 e 4 4 Permanent Menu page 65 e 4 5 Main Menu page 66 e 4 6 Workspace Menu page 67 e 4 7 Setup Menus page 67 e 4 8 Acquire Menu page 70 e 4 10 Display Menus page 77 e 4 11 Analyze Menus page 81 e 4 12 File Menus page 87 e 4 13 Secondary Main Menu page 91 Like most software the VNMR software package can be operated by using a keyboard to type in commands and parameters thus c
111. shimming hardware Hardware shimming is automatically suspended during software autoshimming MERCURY UNITY plus and GEMINI 2000 Systems Hardware autoshimming is not available Using the Input Window e Enterhdwshim y su On N TYINOVA hardware shimming starts at the next acquisition during the first delay and stops when acquisition is complete On UNITY and VXR S this command turns on hardware Z1 shimming e Enterhdwshim p su On TYINOVA hardware shimming starts at the next acquisition during the first presaturation pulse and stops when acquisition is complete On UNITY and VXR S this command does not activate shimming e To turn off shimming enter hdwshim n su Gradient Autoshim First confirm that gradient shimming is installed on your system and that the shims are mapped with gradient shimming If the gradient shimming is not installed see Gradient Autoshimming on page 168 Gradient autoshimming can be initiated by any of the following ways e Using the Menu Buttons In the Main Menu click on Setup gt Shim gt Gradient Autoshim on Z Current parameters and data are saved and gradient shimming is started in the current experiment Parameters and data are retrieved when gradient shimming is finished To stop gradient shimming before shimming is completed in the Main Menu click on Setup gt Shim gt Quit Gradient Shim Quitting aborts the experiment and retrieves the previous parameter set a
112. spin parameter The spin command also sets rf frequency decoupler status and temperature The value of the spin parameter is changed when a sample is inserted or one of the commands spin go ga au or sample is entered Thus the value of spin is not necessarily the current experiment The dgs macro displays the group of shim and automation parameters including spin The spin 01 999083 00 A1298 Getting Started VNMR 6 1B 127 Chapter 6 Preparing for an Experiment Table 14 Sample Spinning Commands and Parameters Commands acqi Open the Acquisition window acqmeter lt host gt Open the Acqmeter window dgs Display group of shim and automation parameters spin Submit a spin setup experiment spinner Open the Spinner Control window acgqix lt par disconnect exit standby gt lt ret gt Parameters in ntt p y Lock and spin interlock spin 0 5 to 39 n Sample spin rate speed can also be made a part of the standard parameter set for a given nucleus this is covered later Applies to all systems if the Spinner Control for manuals optional spin control hardware Spin Speed Control is installed w Turn spinner off A Turn spinner on at 15 Hz e Enter spin spin 5 where is the desired spin E rate For example entering 0 10 20 30 40 50 spin 15 spin adjusts Experiment Control the spin rate to 15 Allow spin control in an experiment with go If spin is set to a x particular va
113. strong resonance which includes the majority of solvents of interest for routine NMR use Proton gradient autoshimming with PFG is available on all systems configured with a PFG accessory Deuterium gradient shimming is only available on UN YINOVA UNITY plus MERCURY VX and MERCURY systems and not on GEMINI 2000 UNITY and VXR S systems because lock sample and hold capability is required to perform deuterium gradient shimming A hardware upgrade is also required to perform deuterium gradient shimming System configuration requirements are summarized in Table 21 Table 21 Gradient Shim Availability System Gradient Shim Availability UNITY NOVA UNITY plus H or 7H with PFG or Homospoil MERCURY VX MERCURY IH or 7H with PFG or Homospoil UNITY VXR S GEMINI 2000 IH with PFG only a Automated deuterium gradient shimming module required for deuterium gradient shimming with PFG or homospoil b Automated liquids solids spinner controller and automated deuterium gradient shimming module required for deuterium gradient shimming 168 Getting Started VNMR 6 1B 01 999083 00 A1298 6 12 Gradient Autoshimming Gradient Shimming Method The gradient shimming method uses a pair of gradient profile type experiments to calculate the Bo field and make appropriate corrections to the shims The pulse sequence and calculation are described in detail in the chapter on PFG modules experiments in the manual User Guide Liquids NMR The full
114. subtraction filtering 228 solvent suppression pulse sequences 228 solvent volumes 102 solvents directory 111 solvents file 248 solvents selection 110 solvinfo command 248 sort directory entries 89 source code files 36 sovent frequency 248 sp parameter 232 250 Getting Started VWMR6 1B 315 Index sp wp button 73 83 239 240 243 spefrq command 247 spectra phasing 224 spectra positioning 262 spectral display 159 225 231 243 intensity 223 intensity control 239 line frequencies and amplitudes 78 phase parameters 77 plotting 243 referencing 247 starting frequency 240 vertical spectral display position 232 width 187 width adjustment 240 window size 185 windowing mode 239 240 spectrometer frequency reference 247 spectrometer system units 23 Spectrum button acqi 155 spin command 127 spin menu 151 161 spin parameter 127 152 spin rate adjustment 127 128 spin simulation analysis menus 83 Spin Simulation First Definition menu 83 Spin Simulation Line Assignment menu 85 Spin Simulation Main menu 83 Spin Simulation Second Definition menu 84 Spin Simulation Secondary menu 84 Spin Simulation Third Definition menu 84 spin speed interlock 134 spin status 151 Spin System button 83 spinner command 127 129 spinner control 127 142 Spinner Control window 127 129 spinning regulation 128 Spinsight data retrieval 280 spline fit baseline correction 251 split macro 250 sqcosin
115. such it takes the major share of the attention in this manual e NMR system console The main unit of the spectrometer system Housed in one two three or four cabinets depending on the model and configuration of the spectrometer the system console contains digital and rf radio frequency circuit boards amplifiers frequency synthesizers power supplies and other assemblies With the exception of an occasional special experiment that requires reconfiguring some of the acquisition hardware you will rarely need to even open a console door e Superconducting magnet The magnet holds the probe and provides a stable magnetic field Units enclosed or attached to the magnet leg or standing on the floor beside the magnet contain rf control circuitry and amplifiers as well as air control systems for spinning cooling and lifting the sample e Probe The probe transmits rf power to the sample and detects minute voltages in return Many sizes and types of probes are available including broadband and switchable probes that allow observing most nuclei of relevance without changing the probe Routine sample to sample probe tuning is covered in Chapter 6 Preparing for an Experiment while changing probes and tuning the probe to other nuclei is discussed in the installation manual for the probe Host Computer The host computer based on a Sun Microsystems workstation controls the spectrometer The primary user interaction with the
116. system configurations supported The system administrator must make a shimmap on deuterium before deuterium gradient shimming can be used Follow the procedure Mapping the Shims on page 169 using the deuterium signal for all steps use tn 1k for step 4 and select Pfg H2 at step 6 The transmitter power t pwr should be kept low to avoid probe arcing with a 90 pulse greater than about 200 us Deuterium gradient shimming is recommended for shimming in automation with different solvents The system administrator should also uncomment the Table 23 Typical 2H Gradient Shimming Parameters for Common Solvents section in the gmapz macro which sets Solvent n wee parameters based on solvent similar to the deuteroacetone 4 6 12 section of the set 1k macro The gmapz DO 4 3 macro may be customized for particular deuterobenz ne A 3 applications Table 23 summarizes the recommended parameters for some anne nn ce common deuterated solvents deuterochloroform 64 3 The deuterium parameters are saved for future use when the shimmap is saved and are used the next time gradient autoshimming is run Homospoil Gradient Shimming for H or 2H It is also possible to use the Z1 room temperature shim as a homospoil gradient instead of using a pulsed field gradient or PFG Use of this option is recommended only if a PFG amplifier or probe is not available For details on how to configure a homospoil gradient see the section Homosp
117. text editor and change the number preset at the factory to 1 at the end of the VNMR errorLines entry To set the scrollable window to a single line window change the VNMR errorLines entry to 1 by preceding the line with the character If the scroll bar is not there the err log command will display the last ten error messages in the dg program the global parameter errloglen controls the number of lines displayed ten lines is the default Note that the status window only provides information about the experiment in progress and does not reflect user input Input Window Below the status window enclosed in a box is the input window This window is the only place to type VNMR commands and it must be active before you can type input On most systems you activate the window by moving the mouse pointer into one of the VNMR windows and pressing the left mouse button The cursor a small box becomes solid to indicate that the computer is ready for input from the keyboard 01 999083 00 A1298 Getting Started VNMR 6 1B 45 Chapter 2 VNMR Basics 46 As you type input the cursor moves to the right indicating the current input position Pressing the Return key terminates the end of one line of input Commands can be strung together across the input block with spaces separating them They can also be entered separately with Return pressed after each command After Return is pressed the computer checks the line you typed for correct s
118. that segment 01 999083 00 A1298 st Timing QPower Pt Mode M Label M Value O More Property Exp Time 00 00 56 Scan il Figure 55 Display Properties Panel dps Program Getting Started VNMR 6 1B 189 Chapter 7 Acquiring Data 190 The Property button opens a second window shown in Figure 56 that allows you to set configuration options The Status Concept Every pulse sequence can be divided logically into periods of time The standard two pulse sequence for example can be divided as shown in Figure 57 This sequence has three logical periods referred to in the diagram as A B and C These periods are used in controlling the decoupler status as well as the homospoil status discussed later in this chapter For example say we want the decoupler to be on during period A on during period B and off during period C Using the letter n to signify no or an off status and y to signify yes Figure 56 Property Button Window or an on status we could then dps Program describe the desired decoupler status as yyn Setting dm yyn will select this experiment which in the heteronuclear case might produce a coupled spectrum with NOE or in the homonuclear case might be used for solvent presaturation experiments dm nny would give us an experiment with the decoupler only on during period C the acquisition time which in the heteronuclear case would b
119. the larger numbers alone will cause compress or gzip to be much less efficient gzip isa public domain program available from the user library And the bit pattern from floating point data is much less compressible than integer data because the floating point format contains fewer repetitive bit patterns It is possible that the size of the file actually increases after applying the compression program If compress and gzip both do not work the only compression option is the VNMR command compress fid which forces a data set into single precision dp n format A disadvantage of compressfidcompared to compress and gzip is that the original data cannot be reconstructed after the compress fid compression even though the information losses may be marginal in most cases Compressing Double Precision VNMR FID Data The command compressfid compresses double precision VNMR FID data to single precision and updates the parameter dp in procpar This results in a major decrease of almost 50 percent in the required disk space to store the data and a slight decrease in the resolution of the stored data compressfid can be run through a macro interface in VNMR or directly at the UNIX level For details refer to the description of compressfidin the VNMR Command and Parameter Reference 01 999083 00 A1298 Getting Started VNVR6 1B 293 Chapter 10 Storing Retrieving and Moving Data 294 Getting Started VNMR 6 1B 01 999083 00 A1298 Glossary acquis
120. the bottom of the tray may flex and when released the tube make rock slightly within the hole If so back out the tube a fraction of a millimeter to seat the turbine firmly without rocking Location zero is fitted with a more rigid bottom and better resists flexing Sample Tubes Finally it is helpful to buy the best quality NMR sample tubes and to clean the outside of each tube with a solvent such as isopropyl alcohol followed by a careful wiping with a wiper tissue before placing the tube in the probe 6 2 Ejecting and Inserting the Sample On MERCURY VX MERCURY GEMINI 2000 YN INOVA UNITYplus UNITY and VXR S spectrometers with automatic insert eject the spectrometer is equipped with hardware and software to provide computer control of sample ejection insertion spinning locking and shimming This section covers computer controlled sample ejection and insertion Table 10 lists the commands and parameters related to sample changing Manual control of ejection and insertion is also provided on each of these systems to enable you to withdraw samples if necessary but it is strongly recommended that you rely on computer control for maximum reproducibility and safety On MERCURY and GEMINI 01 999083 00 A1298 Getting Started VNMR 6 1B 103 Chapter 6 Preparing for an Experiment 104 Table 10 Sample Changing Commands and Parameters Commands acqi Interactive acquisition display change Submit change sample experiment t
121. the file in the user s shims directory If that directory does not exist it saves it to directory named by the shimspath parameter If shimspath does not exist it saves the file in the system shims directory provided the proper permission mode is set The macro diffshims shimfilel shimfile2 compares the values for the room temperature shims stored in two separate files written using svs Using the Input Window to Retrieve Saved Shim Coil Settings 1 Enter rts file where file is the name of a file containing shim coil settings to be retrieved e g rts acetone If file is an absolute path rts uses it to find the file to retrieve Otherwise it checks for the file in the user s shims directory If that directory does not exist it checks for the file in the directory named by the shimspath parameter If shimspath does not exist it retrieves the file in the system shims directory After the file is retrieved rts sets load y to facilitate loading of the shims The rts command also extracts the shim parameter values from a parameter or data sets saved with macros svf or svp and sets Lload y to facilitate subsequent loading of shims The commands su shim go ga and au reset load n to prevent a subsequent inadvertent loading of the shims Thus if a sample is to be rerun on the same probe and under the same conditions for which an earlier experiment has already been performed and stored settings for the repeat r
122. the help screen for the currently active menu Flip Alternately uncover and conceal the text window Used when the graphics 01 999083 00 A1298 window covers the text window Getting Started VNMR 6 1B 65 Chapter 4 Using the VNMR Menu System Button Description Resize Changes the size of the graphics window If the graphics window is small the graphics window and the text window can be viewed at the same time clicking on Resize enlarges the graphics window to cover most of the screen Alternatively if the graphics screen is large clicking on Resize reduces it back to the default size When the graphics window covers the text output window the Flip button above is then used to alternately uncover and conceal the text window Acqi Opens an acquisition window If your system is not configured for acquisition you will not see this button 4 5 Main Menu 66 Of all of the menus the most important is the Main menu because it serves as a focal point from which all other menus can be reached If you think of the menu system as a tree the Main menu is the trunk from which all the other menus grow Since the Main menu can be reached at all times by using the Main Menu button in the Permanent menu you can very quickly get from any place in the menu system to any place else The choices in the Main menu enable you to display ten second level menus including the Secondary Main menu which is an extension of the Main menu M
123. the left button and 20 for the right button Therefore consider the left button the coarse adjust and the right button the fine adjust During the entire phasing process only the update region centered between the vertical cursors is redisplayed to reflect the new phase parameter The width of this update region Getting Started VNMR 6 1B 01 999083 00 A1298 9 2 Interactive FID Display is controlled by the global parameter phasing which sets the percentage of the screen display to be updated e phasing 20 causes only the region between the vertical cursors to be updated e phasing 70 causes 70 of the screen to be updated The value of phasing can vary between 10 and 100 Continue this process until the FID in the update region is properly phased The middle button adjusts the vertical scale of the FID It can also cause the latest phase correction to be applied to the entire FID To apply this phase correction position the mouse arrow at a point on the FID that is on scale and click the center button This will leave the vertical scale unaffected but will recalculate the phase of the entire FID Clicking the center button above or below the FID will raise or lower the vertical scale Note that the real display shows the real FID channel A when phfid n or 0 If phfid 90 the real display shows the imaginary FID channel B Interactive FID Windowing The sf wf button activates the interactive FID wind
124. the original eread command If a file is found limNET on the UNIX system will transfer it to your local VXR style system If no file is found limNET checks if any files have the original name with the suffix added If exactly one such file is found it is transferred to your local VXR style system In either situation the type of entry on the local VXR style system is based on the suffix of the file on the remote system If the remote file has no suffix or the suffix is ambiguous the entry type defaults to a data file No upper case characters can appear in either the directory or the file name on the UNIX system If any are used the transfer fails with a report indicating the file does not exist or cannot be found The limNET software converts any upper case letters to lowercase when accessing the file system of UNIX File security on the UNIX computer is maintained several ways The limNET server insists that the world have permission to complete the requested transfer Thus a file can be read only if the world has read access to that file Read and execute access is also required for the parent directory and each level above it all the way back to the root For example File to be read Required access export home vnmrl vxr example rwxr xr Parent directories Required access export home vnmr1 vxr rwxr xr x export home vnmr1 rwxr xr x export home rwxr xr x Getting Started VNMR 6 1B 01 999083 00 A1298 10 4 Transferring Data Usi
125. the real dc offset e r2 returns the imaginary dc offset e r3 returns the real rms noise e r4 returns the imaginary rms noise e x5 returns the average rms noise e r6 returns the percentage channel imbalance 7 5 Applying Digital Filtering The digital signal processing DSP capability of VNMR provides many benefits such as constant noise level across the spectrum improved integral accuracy increased dynamic range and flatter baselines DSP usually involves the following three steps all of which are automatically performed by the DSP software e The first step is to oversample the data Oversampling means acquiring data with larger spectral width using a larger number of data points For example instead of collecting an 8 Kword data point set with a 5 kHz spectral width a 160 Kword data set is acquired at 100 kHz In DSP terms this represents 20 times oversampling An advantage of oversampling is that noise is reduced in situations where the noise in the time domain FID is predominantly from round off errors digitization errors in the analog to digital converter ADC This happens at low spectrometer gain settings where the real noise being sampled by the ADC is small perhaps less than 3 bits Another advantage is that digital filters should cause less distortion of the FID leading to many of the benefits of DSP mentioned in the introductory paragraph of this section e After the oversampled data is acquired the ne
126. the sample in the location specified by loc and inserts it into the probe The sample macro performs the combined operations change spin lock and shim convenient for setting up a new sample on a system with a sample changer Using GLIDE 1 Ifthe GLIDE interactive window is not open open it entering glide in the input window or by clicking on the GLIDE button in the Main Menu 2 Click on Experiment amp Solvent 3 Inthe space after Location enter the location where you want the sample placed 4 Click on Close The system recalls parameters and performs the actions described for the change command above 6 3 Retrieving Parameter Sets At any given time you are joined to an experiment with a particular set of parameters These parameters remain active until they are changed Thus to repeat an experiment you have just performed no parameter setup is necessary yjust start the acquisition 106 Getting Started VNMR 6 1B 01 999083 00 A1298 6 3 Retrieving Parameter Sets If you just need to change one or two parameters from the previous experiment in order to set up the next experiment that can be done by entering those parameters in the input window e g pw 6 nt 16 Refer to Setting Frequency Related Parameters on page 183 and Setting Pulse Sequence Related Parameters on page 185 for a description of these parameters If many parameters have to be changed you could enter the parameters one by one but a m
127. the sp wp mode the left button adjusts the starting frequency in the display e The center mouse button changes the vertical scale of the spectrum or integral so that it goes through the current mouse position If the mouse cursor is positioned at the left edge of the spectrum the horizontal position of the spectrum or integral is adjusted e The right mouse button positions the second cursor relative to the first cursor In the sc wc mode the right button adjusts the width of the display on the screen In the sp wp mode the right button adjusts the width of frequencies displayed 9 5 Spectral Display and Plotting Table 37 lists spectral display commands and parameters and Table 38 lists commands primarily associated with plotting of spectra The two tables work together The tools in Table 37 are used to set up the spectra on the screen for plotting using the tools in Table 38 Display Parameters Parameters intended mostly for spectral display include vs sp wp vp cutoff th axis rfp and rfl The s fr and r macros allow working with the display parameters as a set e The s macro saves a copy of the current values of all display parameters as a display parameter set Up to nine sets can be saved with the labels set 1 set 2 etc The s command is entered as s where is the number from 1 to 9 of the display parameter set e g entering s3 saves set 3 e The fr macro entered as fr where ranges from 1 to 9 e g f
128. the width of the base of the water Z and Z2 may need to be tweaked if Z5 changes by more than 100 to 200 coarse units About 80 to 90 percent of the odd order axial gradient induced water width is probably dominated by Z5 with Z7 and perhaps some Z3 providing the rest The even order axial shims Z2 Z4 Z6 and Z8 affect the asymmetry of the residual water line using presaturation All four of these even order axial shims can affect the final water linewidth with Z2 and Z4 being at about the 5 mM solute level and above Z6 being at about the 1 mM solute level and Z8 being at about the 0 3 mM solute level The even order axial shims will perform as you would expect unless the sample is less than 40 mm in length in which case the shims still control the water linewidth but much less responsively Beware of the use of Z4 to narrow an asymmetric residual water line of a sample shorter than about 40 mm One is probably destroying the base of the standard lineshape faster than the residual water signal is being narrowed This is because the residual water resonance width is affected more by magnetic susceptibility interfaces as the sample gets shorter For samples under 40 mm the iterative use of Z5 Z7 with Z6 Z8 Z4 Z2 can narrow the residual water line but the results obtained may be hard to reproduce on subsequent samples due to an increased sensitivity to slight changes in sample geometry Shimming Different Sample Geometries Some suggesti
129. themselves organized into directories The UNIX file system is traditionally depicted in a tree structure with all files and directories are hierarchically organized into a top level directory whose symbol is a slash and name is root The root directory ultimately contains all other directories and files VNMR Directories and Files Figure 7 is a diagram of the part of the UNIX file system that is important in using VNMR software In the diagram the directories vnmr home and usr are shown as subdirectories of root To identify these directories as first level subdirectories of root a slash is placed in front of the directory name vnmr export home and usr Knowing the location and contents of system directories and files used by VNMR is helpful when trying to understand the UNIX file system vnmr export home usr Contains all VNMR software on Solaris vnmr is actually a link to export home vnmr so vnmr is also in the directory home Contains the default location for users home directories Contains UNIX libraries and online reference materials The vnmr directory contains numerous subdirectories including acqbin acrobat bin fidlib glide help kermit lib maclib manual menulib nuctables Getting Started VNMR 6 1B Contains commands related to the data acquisition process Contains files and reader software for VNMR Online Contains commands used for VNMR but executed from
130. throughout t60 szq cmm t240 sza cmm means shim Z1C Z2C for 60 seconds maximum then shim all Z gradients for a maximum of 4 minutes Use medium to medium criterion throughout f ry t600 szq cmm means turn on spinner and FID shim Z1C Z2C with medium to medium criterion for 10 minutes maximum not available on GEMINI 2000 t60 sza cmm gq t30 sz1 cmm with wshim f 20 means initially shim on all Z gradients for 60 seconds then shim Z1 After every 20 FIDs shim Z1 for 30 seconds sza cmm q t30 szq cmm with wshim f10 means initially shim on all Z gradients with no time out and then perform a Z1 Z2 shim for 60 seconds every 10 FIDs Interactive Autoshim To enter the interactive Autoshim mode from the Acquisition window do the following 1 2 Open the SHIM display Use the mouse to make a series of choices for computer shimming perhaps the Z1 and Z2 gradients and select a criterion such as L gt M Click on the auto button in the SHIM display to initiate Autoshim 01 999083 00 A1298 Getting Started VNMR 6 1B 143 Chapter 6 Preparing for an Experiment 144 After completion of that shim operation you can select a different combination of gradients and begin another autoshim process or you can terminate the entire process at that point For further information refer to SHIM Display on page 161 If desired interactive Autoshim and manual emulation modes can also be interspersed The interac
131. to another experiment Set parameters for digital filtering and downsampling Set parameters for digital filtering and oversampling Create digital filtering and downsampling parameters Create oversampling and digital filtering parameters Acquisition time Default value of osfilt Downsampling factor applied after digital filtering Digital filter coefficients for downsampling Digital filter bandwidth for downsampling Bandpass filter offset for downsampling Type of DSP for data acquisition File of FIR digital filter coefficients Frequency shifted quadrature detection Number of data points Digital filter coefficients for oversampling Oversampling filter for real time DSP Digital filter bandwidth for oversampling Bandpass filter offset for oversampling Oversampling factor for acquisition Spectral width in directly detected dimension or np in the normal manner the software and hardware automatically oversamples at the maximum rate and then digitally filters and downsamples the data according to the selected sw and np parameters If the user wishes to disable DSP for a particular experiment the oversamp parameter can be set to n and oversampling and DSP are not be used Or if desired the oversamp parameter can be set by direct numeric entry to a value less than the maximum e g oversamp 4 Be warned however that oversamp is reset to its maximum value the next time sw is entered in that experiment Inline DSP Inline DSP applies
132. to the bottom of the display is set by the vp parameter The cut of f parameter defines the distance above and below the current vertical position at which the spectrum is truncated For example cutoff 50 will truncate data at vo 50 mm and vp 50 mm Vertical Scale Adjustment Two vertical scaling modes are available normalized and absolute intensity e The nm command selects the normalized display mode in which spectra are scaled so that the largest peak in the spectrum is vs mm high e The ai command selects the absolute intensity mode in which the scale is kept constant from spectrum to spectrum This allows comparison of peak heights from one spectrum to another The modes are mutually exclusive the system is always either in normalized or absolute intensity display mode The aig parameter contains the result of the ai or nm command It can be queried aig to determine which display mode is active The vsadj macro automatically sets the vertical scale adjustment vs in the ai mode so that the largest peak is 0 9 wc2max vp sc2 mm tall The syntax is vsadj lt height gt Include height as an argument to specify the desired height in mm of the largest signal in the displayed portion of the spectrum The macros vsadjh and vsad jc function the same as vsad Jj except that the solvent and TMS signals are disregarded from their respective proton or carbon spectra for the vertical scale adjustment vsad jh also has the do_not_igno
133. to the right of the Grid switch When the Signal Avg switch is turned on the pulse sequence runs blocksize bs transients before returning data to the interactive program When Signal Avg is turned off it runs one transient To change the number of Signal Avg transients change the bs parameter and run gf to update the acodes When the Phase Cycle switch is turned on the default phase cycling will be turned on cp y and will cycle the phase over bs transients even if Signal Avg is off When the Phase Cycle is off the default phase cycling will be turned off cp n Further to the right are labels for Trace and Mode which control the display of the FID in the window Trace has these choices e Clicking on the slashed circle sets the trace to off the default e Clicking on the recycle symbol shows the current trace in blue and the previous trace in yellow so the traces can be compared e Clicking on the pin makes current FID stay the same color in blue and updates the previous FID in yellow To select a new current FID click on the pin again Mode has the following choices e Clicking on the dot puts the FID display into a dot mode mostly useful for solid state NMR The dot display mode only works if it can be displayed that is the value of np is small enough so the data points can be separated e Clicking on the single curve sets the standard FID display mode the default e Clicking on the double curves sets an
134. user executes a user macro named userplh e pltmod variable adjusts sp and wp to plot only the region of interest e intmod off gives no integral e intmod partial gives a series of integrals over each region 01 999083 00 A1298 Getting Started VNMR6 1B 249 Chapter 9 Display Plotting and Printing e intmod full gives a single integral over the entire spectrum Similarly p1c plots a carbon spectrum and p1p plots a phosphorus spectrum based on the parameters pltmod and intmod as described above For both macros the user macro is userplc if pltmod user Given a spectrum divided into regions by the region command or by the cursors in the ds program the macro aexppl lt expansion_factor gt plots automatically each region at the horizontal scale requested in Hz mm The default scale is 2 Hz mm Several generic plotting macros such as plot and plot1d are available that call specialized plotting macros depending on the user definition or other wise on the type of data in the experiment For details see the VNMR Command and Parameter Reference Display Limits Because of the use of different plotters with different dimensions the parameters sc wc sc2 and wc2 need to be set differently to position plots and displays in the same relative position on the page The full center left and right commands do nothing more than modify sc wc sc2 and wc2 to place the display and plot in the desired portion of t
135. when Gradient Shimming System menu was Old Shims New Shims Min Shims Return entered Set shims from before first iteration of gradient shimming Set shims from last iteration of gradient shimming Set shims from minimum rms err in last set of gradient shimming iterations Return to the Gradient Shimming System menu Gradient Shimming Display Menu The Gradient Shimming Display menu is used for displaying items associated with gradient shimming To open this menu click on Display in the Gradient Shimming System menu Button dgs List Shims Display Shimmap Display Fit Show Record Plot Return Description Display shim parameters Display current mapname and last shim changes Display current shimmap used by gradient shimming Display shim fit from last iteration of gradient shimming Display record of shim adjustments from last gradient shimming run Enter Gradient Shimming Plot menu Return to the Gradient Shimming System menu Gradient Shimming Plot Menu The Gradient Shimming Plot menu is used for printing and plotting shim parameters and files To open this menu click on Plot in the Gradient Shimming Display menu Button Description Print dgs Print shim parameters Print Shims Print current mapname and last shim changes Plot Shimmap Plot current shimmap Plot Fit Plot last iteration shim fit Plot bO Plot bO shim plot Return Return to the Gradient Shimming Display menu Gett
136. window appears shown in Figure 35 that begins showing the lock level Clicking with the right mouse button inside the window opens a popup menu that allows you to display VT and spin information or open a properties window that allows you to alter the display also in Figure 35 Figure 35 Acqmeter Lock Displays The entire lock optimization process can be acqmeter Program skipped if optimum lock parameters are already known for a particular solvent and probe combination Values for these parameters can be entered as part of a macro or using normal parameter entry e g by entering Llockgain 30 lockpower 24 These parameters do not take effect until an su go or equivalent command is given If automatic shimming is to be used it is important to obtain an optimal lock signal Manual adjustment often is done to achieve the maximum lock amplitude This can result in a partly saturating condition and a true non saturating power is usually 6 to 10 dB lower The response of the lock level is governed by the T of the deuterated lock solvent as well as the magnet determined or chemical exchange determined 7 of the solvent This T can vary widely from about 6 seconds for acetone d to about 1 5 seconds for CDCI and lower for more viscous solvents To allow a reliable repeatable selection of lock power automatic optimization may be used This section describes the lock parameters Lockpower lockphase and lockgain an
137. with the right mouse button adds the value shown on the button clicking with the left mouse button subtracts the value shown on the button Getting Started VNMR 6 1B 01 999083 00 A1298 6 10 Using the Acquisition Window Generally there are one two or three panels of Z spinning shims between two and five panels of non spinning shims and one panel of lock parameters Each of the shims should be adjusted to give maximum homogeneity and spin top area of window and lock parameters adjusted appropriately The bottom row of buttons adjust the lock receiver gain Note that when in the FID display window these buttons adjust the observe receiver gain The macro gf provides a convenient way to set up an interactive acquisition session gf temporarily disables autogain spin regulation and receiver phase alternation sets wshim n and alock n and then runs acgi par andgo acqi Note that if the Acquisition window closes when the FID button is closed it is usually because no gf or go acqi was executed Typical actions in using acqi for a FID display are the following 1 Make sure you have good parameters by acquiring a spectrum with ga 2 When is spectrum is acceptable enter gf 3 Click on the Connect button followed by the FID button FID Shimming Windows Style 2 Style 2 FID shimming is not available on VXR S or UNITY systems that have an output board with a 63 step FIFO It is also not available on GEMINI 2000 o
138. xyz 288 where xyz is the name of the directory you wish to create and 288 is the number of entries that were found in the Gemini or VXR directory 288 would correspond to a disk backup The device can be something other than rmt 1 such as rmt 0 For Silicon Graphics systems the following commands are appropriate mt rewind mt fsf 1 dd if dev nrtape of xyz 288 ibs 512000 conv swab mt rewind In these commands xyz is the name of the directory you wish to create and 288 is the number of entries that were found in the Gemini or VXR directory 288 would correspond to a disk backup For either system the directory that results xyz 288 in this example must next be decomposed by entering e g decomp xyz 288 The decomp command creates a new directory xyz and the individual files found in that directory can be read into VNMR using the convert command Reading Bruker Data Files from 9 Track Tape The UNIX shell script readbrutape reads one file from a Bruker tape into a UNIX file The syntax used is readbrutape file lt number_skipped gt where file is the name of the file read into UNIX For identification the bru extension is added to the file name The optional argument number_skipped is the number of files skipped and includes the header file which is assumed to the first file on the tape The default is the script reads the first file after the header file If number_skipped is set to 0 there is no rewinding and the first fi
139. you walk up to the workstation you just sit down and start using the system In other cases however you may wish to take advantage of the login and logout features of UNIX so you need to know how to enter and exit VNMR The system administrator must understand this process of course Table 1 lists the commands and menu buttons associated with entering and exiting VNMR Table 1 Entering and Exiting VNMR Command acqi Open the Acquisition window acqstat lt remote_system gt Open the Acquisition Status window login username Log into UNIX with user name given UNIX logout Log out of UNIX UNIX exit Call the vnmrexit command vnmrexit Exit from VNMR system Menu System Main Menu More Exit VNMR Exit from VNMR system Exit button on CDE toolbar Exit from VNMR system To Start VNMR Before logging into the system you must have a user name shown by username in the following procedure assigned by your system administrator The standard software is installed so that vnmr1 is always configured as a user but your system administrator probably defined others as well 01 999083 00 A1298 Getting Started VNMR 6 1B 39 Chapter 2 VNMR Basics 1 Ifusing the CDE interface enter your user name in the login window Otherwise if a login prompt is displayed enter your VNMR user name remember to terminate your input by pressing the Return key login username If another prompt is displayed instead of the Login prompt ente
140. 0 left half of the screen page 78 79 left phase 224 left arrow key 97 left shifting a FID 226 length of 90 degree pulse 188 If command 108 276 lfs low frequency suppression 228 liamp parameter 253 lib directory 34 libraries of software 34 Library button 67 lifrq parameter 253 limNET protocol 281 limNET server shutdown 286 limnetd process 286 line broadening 221 line broadening parameters 72 line broadening weighting 72 223 line listing on the current spectrum 85 linear amplifier power control 190 linear baseline correction 252 linear modulators 193 linear prediction algorithm 228 data processing method 227 linear pulse amplifier 24 linear x axis scale 86 linear y axis scale 86 line drawing capability 272 Lines button 78 liquid column length 101 list button 84 list files 276 listenon macro 109 138 280 Ikof parameter 152 ll button 85 llamp parameter 246 llfrq parameter 246 load parameter set into current experiment 87 parameters and data 90 shims 90 streaming tape to current directory 89 Varian data to current experiment 87 Load button 87 90 load parameter 136 137 154 Load Params button 90 Load Shims button 90 loc parameter 106 local oscillator 191 lock 129 135 effect of solvent 130 frequency 24 184 gain 131 01 999083 00 A1298 Index lock transmitter 184 mode 206 parameters 130 132 152 power 131 power and gain optimization 133 power when shi
141. 01 SOlVENt SCCM ves se cicssissshsosesseansevseacanschvacs dendsbad cbesacssabivedsioassgunestdansean sdapsetaaes 101 01 999083 00 A1298 Getting Started VNMR 6 1B 7 Table of Contents S mple Height cenon oinor eE rE EEEE SELEENA EREE sheuecbuanades 101 Sample POSIMOM s 2 se5eicesissshcosnssienseesiecayestiacssontsuadaseiaebyassseastsunsevsgeadanseaadscdosenazcs 102 S mple LUBSS enretenar ee dasci a aE a EESE Ei ERE eiT 103 6 2 Ejecting and Inserting the Sample ssessessesessssssessesrsersreesesresesrssesresesrrsreereseeresreresre 103 To Eject a Sample Without a Sample Changer sssseeeeseeeeseeresesreersreerrrreseersee 104 To Insert a Sample Without a Sample Changer seseesesseseseeresesresrsreerreresreree 105 To Change a Sample With a Sample Changer oo eee ee ceseeeeeeseeeeeeeeees 106 6 3 Retrieving Parameter Sets ci iccicd iscsi bescestistisesiastees dies adveab bane e i o Tiv dees desea 106 Location of Parameter Sets csiccsian duis dese eosian adie ueeaeeteis 107 To List Parameter Sets aa scasccescesclesisssassheslsasaduecietetssdevsotsvosaatests pvenseesvacbsessnesbet 108 To Recall Any Parameter Set sssesssesssorsesessceseeeseesoeeseesseesseensesrenssenssees 109 To Recall Standard Parameter Sets 0 0 eee cseeeceeceeeceeceseeseceseeeeeeeeeereeeeees 110 To Create Selected Parameters cece ecesesecseesseceecesececeseeseeeseeeeeeeeeeeeeeeees 111 To List Parameter Groups 000 0 eee ceceecce
142. 01 999083 00 A1298 9 8 Plot Designer Adding Text To add text into your design do the following procedure 1 Click on the text input tool 7e to open the text input window 2 Type text in the field at the top of the window You can customize your text by clicking on the desired options and entering a font size in the indicated field 3 Click on Put and drag the cursor into the workspace then click once to paste in the text To copy text that is already on the workspace and paste it in different font styles do the following procedure 1 Highlight the text 2 Open the Text Input window shown in Figure 78 by clicking the text input tool freal Font family SansSerif gt Serif Monospaced Font style nol Bold 6 Italic oe Plain Font size 16 Put Cancel Clear Close Figure 78 Text Input Window 3 Select a Font family and Font style and enter a Font size 4 Click Put to paste the text in the workspace Changing Font Color To change the color of fonts repeat the procedure for Changing Line Color Adjusting and Restoring Plot Parameters When you draw a region the scaling parameters of the plotting area wcmax and wcmax2 are adjusted by the macro jplotscale The scaling parameters of a plot that is imported into a region io is vs wc and wc2 are automatically adjusted according to wcmax and wcmax2 If you want to use the adjusted parameters enter the following command string which
143. 083 00 A1298 Chapter 9 Display Plotting and Printing Sections in this chapter 9 1 Interactive FID and Spectrum Display this page 9 2 Interactive FID Display page 233 9 3 Stacked and Whitewashed FID Display and Plotting page 236 9 4 Interactive Spectrum Display page 237 9 5 Spectral Display and Plotting page 243 9 6 Integration page 250 9 7 Plotting page 254 9 8 Plot Designer page 262 9 9 Printing page 271 9 10 User Controllable Line Drawing page 272 Display plotting and printing of data are highly individualized activities Each user has their own ideas about proper formats necessary expansions etc For this reason this chapter more than any other should probably be read from beginning to end 9 1 Interactive FID and Spectrum Display The interactive display programs covered in this chapter are the df program for FID display and the ds program for spectrum display In the displays of these programs you can interact with the FID or spectrum in three different ways Each mouse button can be labeled with the name and value of some display parameter different parameters are present depending upon the nature of the display These labels are highlighted in the lower right comer of the display screen Clicking a mouse button produces a change in the corresponding parameter Parameter values can be entered by hand For example typing vs 500 will change the ver
144. 1e9 Vertical scale of FID vo number in mm Vertical offset vpf number in mm Current vertical position of FID vpfi number in mm Current vertical position of imaginary FID we 5 to wcmax in mm Width of chart wf 0 to at in sec Width of FID plot Stacked FIDs The dfs command displays one or more FIDs as a stacked display in which each FID is offset horizontally and vertically from the previous FID The position of the first FID is governed by the parameters wc sc and vpf Each subsequent FID is positioned relative 236 Getting Started VNMR 6 1B 01 999083 00 A1298 9 4 Interactive Spectrum Display to the preceding FID by the offset parameters vo and ho For a left to right presentation ho is usually negative for a bottom to top presentation vo is positive The syntax for dfs is the following dfs lt lt start gt lt finish gt lt step gt lt all imag gt lt color gt gt For arrayed 1D or 2D data sets a particular FID can be viewed by supplying the index number as an argument Multiple FIDs can be displayed by supplying the indices of the first and last FIDs The optional st ep argument is the increment for the FID index the default is 1 If imag is supplied as a keyword argument only the imaginary FID channel is displayed the default is al1 to display all FIDs A color red green blue etc can be supplied as an argument as well The following commands are variations of dfs an
145. 2 228 dgs macro 112 127 136 dgs parameter 112 dhp parameter 193 diagnostic messages 48 diffshims macro 138 diffusion software 33 digfilt macro 218 01 999083 00 A1298 Index Digital Acquisition Controller board 24 digital filter 209 digital filtering 228 digital integral amplitudes 254 digital quadrature detection 218 digital resolution 140 247 digital signal processing DSP 209 digitization errors 209 dimension of an experiment 200 dir command 276 directories 34 change 88 create new directory 276 delete 87 file suffix on Ethernet 284 make copies 276 remove 276 rename 276 size of entries 89 sort entries 89 transfer over Ethernet 282 user 36 working 37 Directory button 89 Directory menu 88 Directory Secondary menu 88 dispersion spectrum 224 display 1D spectrum and scale 77 2D contour display 79 2D interferogram as contour map 74 ADC bits 155 arrayed parameter value 96 box drawing 273 data stacked and whitewashed 80 Ethernet nodes available 282 Ethernet remote nodes 282 experiment log file 207 experimental spectrum 83 FID 154 231 FID last acquired 155 FIDs horizontally 237 file contents 277 files 46 90 fit a line to data points 86 full spectrum 250 gray scale image 79 grid lines 155 inset of spectrum 242 integral intensities 78 integral reset points 253 integrals 250 iterative optimization spectrum 85 last fit results 85 library of experiment fi
146. 2 quality 139 01 999083 00 A1298 Index routine basis 147 shimming mode 161 user defined shim methods 142 shims controls 156 shims directory 36 138 278 shimset parameter 132 136 141 shimspath parameter 138 278 279 ShNum button 76 Show Fit button 85 Show Output Devices button 92 271 Show Params button 83 Show Shims button 90 Show Time button 70 showplotq macro 255 showplotter macro 257 Silicon Graphics SGI workstation 25 290 simple Autolock 132 151 simple locking 153 Simulate button 83 Simulation button 81 simultaneous access to files 206 simultaneously sampled data 227 sine transform 224 Sinebell button 74 sinebell constant 72 221 223 sinebell shift constant 72 221 223 sinebell weighting 74 Single button acqi 155 single quote notation 95 single pulse experiments 114 six spin system 84 Size button 77 79 size of directory entries 89 Sizes button 89 slide control 152 slw parameter 85 SMALL button acqi 149 small command 47 small graphics window 46 snap spacing controlling 263 software libraries 34 software simple Autolock 132 Solaris computing environment 33 solids high power amplifiers caution 20 solid state echo pulse sequence 69 Solvent button 54 solvent parameter 249 solvent peak suppression 228 solvent presaturation experiments 190 solvent selection 101 Solvent Selection Menu 110 Solvent Selection menu 68 Solvent Subtraction 226 solvent
147. 2 Set nucleus for 7H C13 Set nucleus for 1 C N15 Set nucleus for PN F19 Set nucleus for F P31 Set nucleus for 2 P Other Shows prompt Enter Nucleus of Interest and sets nucleus to that value Return Display the Setup menu page 67 Solvent Selection Menu The Solvent Selection menu sets the solvent to the value requested by the user then returns the user to the Setup menu This menu is typically activated by a selection of a nucleus on the Nucleus Selection menu or by entering menu solvent Button Description CDCI3 Set solvent for CDCl D20 Set solvent for D20 Benzene Set solvent for benzene DMSO Set solvent for DMSO Acetone Set solvent for acetone Other Shows prompt Enter Solvent and sets solvent to that value Return Display the Setup menu page 67 1D Pulse Sequence Setup Menu The 1D Pulse Sequence Setup menu provides setups for five 1D experiments and access to menus for 2D and additional 1D experiments This menu is activated by clicking on the Sequence button in the Setup menu or by menu psgset Button Description APT Set up an Attached Proton Test pulse sequence for CH multiplet selection DEPT Set up a DEPT pulse sequence for CH multiplet selection spectrum editing and signal enhancement INEPT Set up an INEPT pulse sequence for CH multiplet selection and signal enhancement this sequence not supplied with the GEMINI 2000 Getting Started VNMR 6 1B 01
148. 20 The covers on the instrument form a barrier to radio frequency rf energy Removing any of the covers or modifying the instrument may lead to increased susceptibility to rf interference within the instrument and may increase the rf energy transmitted by the instrument in violation of regulations covering rf emissions It is the operator s responsibility to maintain the instrument in a condition that does not violate rf emission requirements Getting Started VNMR 6 1B 01 999083 00 A1298 Introduction This manual is designed to acquaint you with the basics of operating a Varian high resolution NMR spectrometer system running VNMR 6 1B VNMR is Varian s NMR application software package The manual contains the following chapters Chapter 1 Overview of Varian NMR introduces you to the Varian NMR system its user interface advanced features and how VNMR and UNIX files are organized Chapter 2 VNMR Basics covers entering and exiting VNMR and working with VNMR on the host computer Chapter 3 Using GLIDE explains the basics of GLIDE a user interface designed for walk up NMR operation Chapter 4 Using the VNMR Menu System covers using the buttons in the VNMR menu system another user interface that simplifies NMR operation Chapter 5 Using the Command Mode covers the basics of using the command mode to enter commands macros and parameter settings Chapter 6 Preparing for an Experiment de
149. 200 completed FIDs 200 dimension 200 files 67 lock mode 206 lock system 206 locked 207 log file 207 number 45 stop acquisition 202 text files 197 Experiment button 54 experiment time 189 experiments accessing GLIDE 55 customizing using GLIDE 55 data collection 277 data storage 31 defined 31 277 display experiment list 31 files 277 01 999083 00 A1298 Index introduction of computed data 281 multiFID 31 multiple 32 number 31 path to experiment 277 repeating 106 run unlocked 132 running standard 54 explib command 31 32 explicit acquisition compatibility 215 explog command 207 exponential analysis plot 81 Exponential button 81 exponential least squares analysis 81 exponential weighting 72 221 223 export directory 34 36 exptime command 189 extract files from VXR library 287 extract shim parameter values 138 F f command 250 F1 Mode button 80 F1 Transform button 74 F19 button 68 F1 F9 keys 43 F2 Mode button 80 fb parameter 187 fdformat command UNIX 291 292 FID display 154 231 236 display parameters 232 files 37 library 34 phase rotation 233 plotting 236 raw data file 37 shimming on the 142 start of plot 232 storage 31 37 updating 234 vertical display position 232 vertical scale adjustment 234 viewing a particular FID 233 windowing mode 234 235 FID button acqi 149 154 155 FID Display Menu 234 fid file 37 278
150. 2D Pulse Sequence Setup menu above Return Display the Setup menu page 67 Applications Mode Menu Different applications modes give access to extra or different macros and menus if they have been installed The Applications Mode menu is entered by selecting App Mode in the Setup menu or by entering the command menu appmode Button Description Standard Set parameter appmode to standard and set system lookup paths for maclib menulib and help to the standard directories vnmr maclib vnmr menulib and vnmr help Imaging Set parameter appmode to imaging and set system lookup paths for maclib menulib and help to look in the imaging directories defined by the parameters systemmenulibpath and syshelppath before looking in the standard system directories Return Display the Setup menu page 67 4 8 Acquire Menu 70 Data acquisition in a variety of modes can be initiated with the Acquire menu This menu is typically entered by selecting the Acquire button in the Main menu by selecting the Acquire button in the Setup menu or by entering the command menu acquire Button Description Show Time Display time that current experiment takes if acquisition is started with existing parameters Go Begin an acquisition with no subsequent data processing Go Wft Begin an acquisition and weight and Fourier transform the FID automatically when acquisition is complete Getting Started VNMR 6 1B 01 999083 00 A1298
151. 3 Chapter 6 Preparing for an Experiment seccssseeeeesseeeeeeeesneeeeeeseees 101 Chapter 7 Acquiring Data accctiss ciceccccess ecaiens caceensnsaescsnsedcwteadseccetensaidezcsacane 183 Chapter 8 Data Processing siscvicssiasnseccssnticccienasccsnsansdensennssdecetestuccecestuneencannee 221 Chapter 9 Display Plotting and Printing cccssseccseseeeeeeesseneeeeeesees 231 Chapter 10 Storing Retrieving and Moving Data ss seccesssseereeeees 275 E 2 1 ee ne E Ee Tne re nr meen eee nen ener renee 295 aLI gaan eee eee eer 299 01 999083 00 A1298 Getting Started VNMR 6 1B 3 Getting Started VNMR 6 1B 01 999083 00 A1298 Table of Contents SAFETY PRECAUTIONS ge eee 17 NVEROGUICUION ssc dacsitestasns T A 21 Chapter 1 Overview of Varian NMR _ q ccccsssseecesseneeeenseeeeeeenssneeeeenseeeeees 23 1 1 Varian NMR Spectrometer System 00 eee cee cese cee ceseeeeceseeeeceeeeeeeeseeeaecaeeesecsaesaeenaes 23 HOSU Computer sss cossesvesicssescsscassaustasnceuscscepsondecesedsbibicey cesbiarepusdanseebiasnesta TESS 23 NMR System Console is ciccsessetdcascheis tcessaieh cactistevscientoesesnesocaseeuisteanbonesaspeceantens 24 Superconducting Magnet and Probe 000 ee eeeeececseeeceeeeeeeeeeeeeecaeeseecaeeaecneeeaees 25 Bee User Inte nace secs ties esane nE Eea sabe eds Us AEA EA Sessa eos aR ES 25 VINMIR Soft Wate essees na uenee ieena poaae add tad oh pegesnseseeedeusbeiss Guanes 25 Mouse Key
152. 40 8 220 140 8 DraftMaster_B 370 225 8 370 225 8 DraftMaster_C 520 350 8 520 350 8 DraftMaster_D 800 480 8 800 480 8 DraftMaster_E 1000 780 8 1000 780 8 ThinkJet_192 200 115 1 200 240 1 ThinkJet_96 200 115 1 200 240 1 QuietJet_192 330 230 1 330 240 1 QuietJet_96 330 230 1 330 240 1 LaserJet_150 200 105 1 200 150 1 LaserJet_150R 200 105 1 250 180 1 LaserJet_300 200 105 1 200 240 1 a LaserJet_300R 200 105 1 250 180 1 a LJ_B300R 400 210 1 400 210 1 LJ_A3_300R 380 235 1 380 235 1 LaserJet_600 200 105 1 200 140 1 LaserJet_600R 200 105 1 250 180 1 PS4079_HPGL 400 205 1 400 205 1 PS_A 180 140 1 180 140 1 PS_AR 250 155 1 250 155 1 a The standard LaserJet Plus in its high resolution mode plotter code LaserJet_300 can only support wcmax wc2max lt 200 105 If wc2max is increased above 105 wcmax has to be reduced accordingly This restriction does not apply if the 2 Mbyte memory expansion has been installed in the LaserJet Plus Plotter Resolution and Speed Pen plotters operate at a fixed resolution For raster graphics printers ThinkJet LaserJet etc a high resolution and a medium resolution mode is provided 256 Getting Started VNMR 6 1B 01 999083 00 A1298 9 7 Plotting e The high resolution mode the plotter code with the larger number appended e g LaserJet_300 should be used for high quality 1D NMR spectra and grayscale images The medium resolution mode e g LaserJet _150 should be acceptable for 2D contour m
153. 64113 Li6 44 156355 Li 116 603793 Be9 42 164581 B10 32 241720 Bll 96 265604 C13 75 454856 N14 21 672340 N15 30 416302 017 40 675777 F19 282 298612 Ne21 23 683721 Na G Figure 29 Pull Down Menu for Marker 1 You can change the vertical scale of the Tune Display window by selecting whether the data is scaled in a linear or logarithmic manner see Figure 30 1 Inthe Scale field the Tune Control panel provides two scaling modes e Select dB to provide a logarithmic scale in units of dB e Select Linear to a linear scale with arbitrary units Scale dB Linear Max 0 00 _ GB Step 5 00 dB div CE Figure 30 Scale Controls The dB scale shows a deeper dip for more accurate match adjustment 2 Inthe Max field type a value you want for the top line in the Tune Display Setting a Max value beyond system limits generates a beep and an error message 3 Inthe Step field type a value you want for the number of units per division mark of the current scale dB or linear on the y axis of the Tune Display Step helps by making the height of a probe resonance appear larger or smaller Setting a Scale value beyond system limits generates a beep and an error message Q Calculation Probe Q factor determines sensitivity Q is defined as the frequency of the resonant circuit divided by the half power bandwidth 1 Near the bottom of the Tune Control Panel select Q calculation On 01 999083 00
154. 75 2D Peak Picking Display Menu ll2d Program The 2D Peak Picking Display menu part of the 112d program is activated by selecting the Display button in the Interactive 2D Peak Picking Main menu Button Sh Pk OR Hd Pk Sh Num OR Hd Num Sh Box OR Hd Box Getting Started VNMR 6 1B Description If labeled Sh Pk show a at the location of each peak If labeled Hd Pk hide do not show a at each peak If labeled Sh Num show a peak number next to each peak If labeled Hd Num hide do not show peak numbers If labeled Sh Box show a box with the area integrated to get the volume of the peak If labeled Hd Pk hide this box 01 999083 00 A1298 4 10 Display Menus Button Description Sh LbI OR If labeled Sh Lbl show a peak label next to each peak Hd Lbl If labeled Hd Lbl hide do not show peak labels Sh All Show number box and label for all peaks Hd All Hide do not show number box and label for all peaks Return Display the Interactive 2D Peak Picking Main menu page 75 4 10 Display Menus Two different menus for display of data are provided The menu displayed depends on whether a 1D or 2D experiment is active 1D Data Display Menu The 1D Data Display menu is activated by selecting the Display button in the Main menu while a 1D experiment is active or by entering the command menu display_1D Button Description View Display norm
155. 8 unlocked experiments 132 Unmark button 76 up button 155 up arrow key 97 update old parameter characteristics 109 updatepars macro 280 upper barrel warning 18 use fitspec button 85 Use Line List button 85 use Il button 85 Use Mark button 85 user directories 36 user group library 38 user library 38 user name assignment 39 user contributed files 36 userfixpar macro 110 usergo macro 198 userlib directory 36 38 userplc macro 250 userplh macro 249 user selected shim methods 142 user written weighting functions 222 usr directory 34 V variable temperature VT accessory 195 196 variable temperature status 43 Varian NMR software program 25 VAX computer 281 Getting Started VYNMR 6 18 317 Index version of parameter set 280 vertical scale 42 vertical scale adjustment 77 vertical scale of display 232 vertical scaling modes 245 vertical scaling multiplies 159 vf parameter 223 232 234 View button 77 VNMR display screen 27 entering 39 exiting 40 51 menu system 59 software 25 system directory 88 systems 281 user directory 88 vnmr directory 34 36 VNMR Online hypertext manual 34 50 VNMR shell window 48 vnmrl directory 36 vnmrl user 36 vnmreditor variable 197 VnmrI 25 290 vnmrplot command 255 vnmrprint command 271 VnmrsSGI 25 290 vnmrsys directory 36 37 vnmrtext variable UNIX 48 Vnmrx 25 vo parameter 237 volmgt program 291 Volume button 75 vp par
156. Alternatively you can move the cursor within the window you want to close and then press the Open key L7 on some keyboards on the keyboard Getting Started VNMR 6 1B 01 999083 00 A1298 2 2 Working with VNMR on the Host Computer Figure 17 Icons for Closed VNMR Windows To open any of these icons move the mouse arrow over the desired icon and either double click the left mouse key or press the Open key L7 on the keyboard CAUTION You could exit the VNMR application from the closed icons but do not exit this way The VNMR program keeps data and parameters in internal buffers If you exit from a closed icon the buffers will not be written to the hard disk and data will be corrupted or lost The correct way to exit from VNMR is to reopen the combined status and input window the icon containing the word Master four times and then follow the procedure in Entering and Exiting VNMR on page 39 01 999083 00 A1298 Getting Started VNMR 6 1B 51 Chapter 2 VNMR Basics 52 Getting Started VNMR 6 1B 01 999083 00 A1298 Chapter 3 Using GLIDE Sections in this chapter e 3 1 Activating GLIDE this page e 3 2 Using GLIDE page 54 e 3 3 Customizing Combination Experiments page 56 GLIDE is a user interface designed for walk up NMR use It facilitates setup acquisition processing and plotting tasks To customize GLIDE refer to the manual Walkup NMR Using GLIDE which contains a more detailed description
157. Automake Shimmap Find gzwin and then run shimmap experiment Make Shimmap Run shimmap experiment Shimmap Files Enter Gradient Shimming Files menu Current Mapname Show current mapname used for gradient shimming Save As Save current parameter set and shimmap files Enter mapname when prompted Return Return to the Gradient Shimming System menu Gradient Shimming Files Menu The Gradient Shimming Files menu is used for loading and copying shimmaps To open this menu click on Shimmap Files in the Gradient Shimming Map menu Button Description cd to Userdir Change directory to userdir shimmap or cd to Systemdir Change directory to systemdir shimmap Copy to Userdir Copy selected shimmap into user shimmap directory or Copy to Systemdir Copy selected shimmap into system shimmap directory 01 999083 00 A1298 Getting Started VNMR 6 1B 179 Chapter 6 Preparing for an Experiment 180 Button Make Systemdir Load Shimmap Load Shimmap amp Params Rename Return Description Make system shimmaps directory if user is vnmr1 Load files for selected shimmap Load files and parameters for selected shimmap Rename selected shimmap under a new mapname Return to the Gradient Shimming Map menu Gradient Shim Setting Menu The Gradient Shim Setting menu sets shim values To open this menu click on Set Shims in the Gradient Shimming System menu Button Starting Shims Description Set shims from
158. Designer 271 R r macro 243 ra command 202 radio frequency emission regulations 20 raw data storage 31 01 999083 00 A1298 Index rcp command 282 Read All button 89 Read button 76 Read Text button 76 readallshims macro 136 readbrutape shell script 290 readhw command 132 README file 38 readultra macro 167 real channel 224 real time DSP 210 213 recalling command line entries 97 display parameters 243 receiver gain 206 receiver gating 191 receiver gating times 188 receiver overload 205 Redisplay button 82 Redraw button 74 reduce size of graphics window 47 Reference button 79 80 reference frequency 247 reference in both dimensions 80 reference line 247 reference position 247 reffrq parameter 247 248 reflected power 25 refpos parameter 247 Region button 77 region command 250 253 Regression 1 menu 86 Regression 2 menu 86 regression analysis 86 regression inp file 86 Regrs button 81 relative path 38 relief valves warning 19 remote acquisition 207 remote file copy 282 remote host busy 286 remote host name 282 remote interactive shimming 207 remote node 282 remote status module 27 43 remote tape 291 removable quench tubes warning 19 removing directories 276 files 276 floppy disk from drive 291 lock 208 Rename button 91 rename command 276 renaming directories 276 files 91 Reprocess button 74 77 79 Reset button 75 reset integral to zero 253 Re
159. E ENGAGED To revert to the manual mode push the Mode button and then the Blank button on the interface box Turning the System Off and On The system is typically left on continuously except for maintenance To Turn Off the System Use the following procedure to power down the Ultraenmr Shims system 1 Save the current shim values into one of the 62 available shim files 2 Load in file 0 3 Turn off the orange lighted rocker switch on the power strip in the lower back of the shim power supply To Turn On the System Use the following procedure to turn the shim system back on 1 Press the rocker switch on the power strip The orange light in the switch should turn on and the interlock board in the bottom left front of the shim power supply should 01 999083 00 A1298 Getting Started VNMR 6 1B 167 Chapter 6 Preparing for an Experiment display two red lights and one green light The bootup of the computer in the shim power supply takes approximately one minute During the bootup all eight indicators situated above the eight buttons on the interface box are usually lighted green Note that the system will not boot unless a readable floppy disk is in the system floppy drive When the bootup is complete the interface box displays several status messages indicating how many PROM based default files were used during bootup 2 When the final question is displayed on the interface box you must answer yes before the high power inte
160. FID output from real time DSP 216 fidlib directory 34 fidpar macro 236 FIDs acquisition time too short 227 completed in experiment 200 composite displays 237 compressing FID data files 292 compute FID file 281 convert multiple FID into single FID 229 dc level 223 distortion from hardware 227 extend direction 227 296 intensity 223 left shifting 226 Getting Started VNMR6 1B 305 Index noise level 209 phase rotation 226 retrieve FIDs in FID file 279 saving 277 stopping spike at start of FID 188 weighting function 221 write FID data text file 278 field homogeneity quality 139 field offset 136 field offset control 184 fifth rf channel parameters 110 File button 46 66 75 File Info button 87 file parameter 109 files compressing 292 creation 276 delete 87 276 display contents 277 Ethernet filename suffixes 283 experiments 67 make copies 276 overview of structure 35 rename 276 security maintenance 284 sharing using a floppy 291 transfer over Ethernet 282 files command 90 Files Data menu 90 Secondary menu 90 Files Information menu 89 Files Main menu 87 Files Secondary menu 90 files system 34 Files Tape menu 89 filter cutoff 210 filter non linearities 227 filtering algorithm 209 filtfile parameter 213 218 filtlib directory 213 218 Find Correlations button 82 fine attenuator 193 fine power control 191 fine shim gradients 136 finite impulse response FIR file
161. Figure 38 Figure 38 Abbreviated Acquisition Window appears On all systems when acqi has already been started by another user you will be unable to open the Acquisition window by clicking on the Acqi button If acqi is successfully started the Acqi button in the Main Menu vanishes There is now a CLOSE button in each Acquisition window Clicking this button causes the acqi window to disappear and the Acqi button to reappear in the permanent VNMR menu panel Connecting to the Acquisition System After you click the Acqi button or enter the acqi command the Acquisition window shown in Figure 37 is displayed on the right side of the main VNMR display The initial window has five buttons that are selected by clicking with the left mouse button CLOSE Causes the Acqi button in the Permanent VNMR menu to reappear The VNMR command acqi disconnect is equivalent to clicking the CLOSE button If go or su is typed in the input window acqi disconnects and returns the parameters and then the command is started within VNMR LOCK Opens the LOCK display described on page 151 FID Opens the FID display described on page 154 From the FID display you can select the Spectrum display described on page 159 SHIM Opens the SHIM display described on page 161 LARGE Generates a larger graphics window This might be useful to you for example when shimming on larger magnets or when tuning the probe and you need to observe the scr
162. GLIDE experiments 55 par files 278 279 slash symbol directory 34 gt AV button 72 74 gt PH button 72 74 question mark notation 96 backslash notation 94 197 Numerics 10 Gauss Warning Sign 18 1D Data Display menu 77 1D Data Display Secondary menu 78 1D Data Manipulation menu 77 1D Data Processing menu 71 1D Display Size Selection menu 78 1D experiment customizing 55 1D Plotting menu 78 1D Processing Parameter Setup menu 72 1D Pulse Sequence Setup menu 68 1D Pulse Sequence Setup Secondary menu 69 20 bit digitizer 215 2D button 69 2D Data Display menu 79 2D Data Display Secondary menu 80 2D Data Manipulation menu 79 2D Data Processing menu 73 2D Display Size Selection menu 79 2D Interferogram Processing menu 74 2D Line List button 82 2D Peak Picking Automatic menu 75 2D Peak Picking Edit menu 76 2D Peak Picking File menu 76 2D Plotting menu 80 2D Processing Parameter Setup menu 74 5 Gauss Warning Sign 17 19 60 dB fine attenuator 193 6 dB fine attenuator 193 90 degree pulse length 114 188 A A2B button 83 A2B2C button 84 A2BC button 84 A2BCD button 84 A3B button 84 A3B2 button 84 A3B2C button 84 A3BC button 84 aa command 203 207 AB button 83 ABC button 83 ABCD button 84 ABCDE button 84 01 999083 00 A1298 Index Abort Acq button 65 203 abort acquisition 203 abort experiment in progress 65 absolute cursor position
163. IX_file Do not use vxr_unix ona file other than a text file obtained from a VXR style based system The VNMR command vxr_unix only may omit UNIX_file in which case the output is sent to the text window Converting Data Files Data files also have a different format on the UNIX based systems than they do on the VXR style systems Data files transferred from a VXR style system therefore have to be converted to the format used in UNIX based systems From VNMR the command convert VXR_file loads the data from the file VXR_file into the current experiment and converts it to the new format the convert command must be used instead of rt when VXR style data is to be read A similar UNIX command cpos_cvt VXR_file also converts the data set but writes the converted data into a subdirectory of the current working directory using the original name of the data set Decomposing a Library The command decomp lt VXR_file gt takes a VXR library as loaded from a VXR style system and extracts each entry into a separate UNIX file The file can be obtained from a magnetic tape or over limNET A limit of 432 entries is imposed decomp creates a UNIX subdirectory in the current working directory and uses that to write each VXR entry as a UNIX file The name of the UNIX subdirectory is derived from the VXR library name The name of the original VXR file must have an extension in the form NNN where NNN is the number of entries in the original VXR l
164. NEUE B Line Width e std_er caltostd_er sys Scale dB Linear Markers ee Max 0 00 HEEE E To restore these system calibration files click the O OQaulation Restore Sys Backup button The program replaces Step 00 ee sale ay m Smoothi the new calibration files with the sys Smoothing Off 1 2 3 4 Sn ng calibration files created at system installation Line width 1 3 5 7 9 step Calibrate Q calculation Online Descriptions of the Tune Control Panel To get on line descriptions of the buttons and fields in the Tune Control Panel click the Help button with the right mouse button A pull down menu similar to that shown in Figure 32 appears Select the topic of interest from the menu Figure 32 Help Pull Down Menu Tuning Probes on MERCURY VX MERCURY GEMINI 2000 For GEMINI 2000 systems the btune ctune dtune htune and tuneoff macros turn rf on and off at the transmitter boards for tuning MERCURY VX and MERCURY use only btune and tuneoff None of these macros use arguments e On MERCURY VX MERCURY and GEMINI 2000 broadband systems bt une turns on the broadband transmitter directing about 0 5 watts of rf at frequency s frq tof to the probe Before using btune switch the cable on the magnet leg tuneof f turns off the transmitter On GEMINI 2000 H 3C systems ht une turns on the H transmitter directing about 0 5 watts of rf to the probe tuneof f turns off the transmitter Similarl
165. NMR i1t file should be set to the empty string i e two single quotes with no space between them 4 If oversamp is set to a value greater than 1 the next experiment is oversampled digitally filtered and downsampled to the sw selected prior to saving it to disk After acquiring a data set without digital filtering the moveossw macro can be used to set oslsfrqand sw to appropriate values for oversampling and digitally filtering for the region of the spectrum selected between the cursors in the ds display You must manually set oversamp to an appropriate value Real Time DSP Real time DSP available on certain systems such as the YINOVA applies digital filtering during data acquisition prior to storing the data in the memory of the acquisition computer Data sampling is performed at a maximum rate of 400 kHz with a maximum oversampling factor of 68 Thus a typical 7 kHz spectrum is oversampled at a factor of 57 a 25 kHz spectrum is oversampled at a factor of 16 Above sw 200000 oversampling and hence real time DSP is not possible and is automatically deactivated Oversampling lessens the effect of digitization noise on the spectrum more so the more oversampling is done At low gain this can produce a marked improvement in the obtainable signal to noise S N ratio Equivalently the use of oversampling and digital filtering will produce the same S N at lower receiver gain values To Apply Real Time DSP When real ti
166. Overview of Varian NMR For example if you enter cd export home vnmrl vnmrsys within VNMR the directory vnmrsys becomes the new working directory Since global is a file in the directory export home vnmrl vnmrsys you can now refer to it by just global e g cd global rather than by the export home vnmrl vnmrsys global absolute path global is a relative path because it is a name relative to your current working directory Notice that although the relative path is almost always shorter to use a relative path you must know the name of the related working directory User Library The Varian NMR user group library placed in the user1ib directory contains a series of files similar to those found in the directory vnmr maclib psglib menulib ete The purpose of the user library is to provide a mechanism for user contributions in the area of pulse sequences macros menus stand alone programs etc User contributions are briefly tested and checked for conformance to documentation standards but are not Varian software The contributions are supported by online documentation but not by Varian applications or service support personnel Contributors can include the contributor s phone number e mail FAX number or address if they are willing to answer questions but they are not obligated to do so The file userlib CONTENTS provides an alphabetical listing of all files in these directories together with a brief one sentence
167. PT button 68 INEPT pulse sequence 68 Info button 76 initiate acquisition 198 inline DSP 210 211 218 input window 44 45 ins parameter 252 253 insert button acqi 150 Insert button GLIDE 55 105 inserting a sample 105 inset command 242 inssref parameter 253 insufficient free disk space 198 integer arguments 94 integral blanking mode 254 integral intensities 78 integral offset 232 242 integral position with respect to spectrum 232 integral reset mode 239 241 integral reset points 77 253 integral scale 242 integral scale adjustment 77 integral value scaling 253 Integrals button 78 interactive adjust 1D spectrum 77 adjust 2D contour display 79 adjust gray scale image 79 adjust stacked and whitewashed data 80 Autoshim 139 Autoshim mode 144 commands 94 define shim methods 143 FID manipulation 233 FID windowing mode 234 235 files program 275 integral reset mode 239 241 lock display 151 parameter adjustment 159 phasing mode 234 235 240 probe tuning 116 spectra display 237 spectral windowing mode 239 240 spectrum display 225 308 Getting Started VNMR 6 1B weighting 223 zero and first order baseline correction mode 241 Interactive 1D Spectrum Display Menu 238 239 Interactive 1D Spectrum Display menu 73 Interactive 2D Color Map Display Main menu 74 Interactive 2D Display Projection menu 75 Interactive 2D Peak Picking Main menu 75 interactive acquisition window 148
168. Preference Controls eececessssecssesesseeseeeeeeceaesceeeceecneeseesecnecaeeeeaesaeeeeeeseaees 263 Tabled Plot Designer TOOLS o 23 cstecieondoeetisht an ane Ens Ea aANT EE Eeken EnEn iia 265 Table 43 Region Editor Buttons 5 i5cs0 c 0 c bcdeeiaeedbee ral eede abe ivedenteessbeeienteceberaeesiphoelbactvabes 267 Table 44 Printer Associated Commands and Parameters csessssesseseseeceeeeceseeeeeeceeenaeneeeees 271 Table 45 User Controllable Line Drawing Commands cc eceseeseseceeesseseeeeenecaeeeeeaecaeeeeeeeeaees 273 Table 46 Directory and File Handling Commands and Parameters scsssessseseeseceeeeeeeeesees 276 Table 47 Data Storage Commands and Parameters 0 cccesecssseceseceececeseeseeneceeeeteaesaeeeeeeeeaees 277 Table 48 Data Retrieval Commands and Parameters scssscsssesecseceeeseeaeceeeecaesaeeeseenaeneesees 279 Table 49 Ethernet and limNET Data Transfer Commands 0 ceeeeesseseeseceeeeceseeeeeeceeenaeseeeees 281 Table 50 Data Conversion Commands 0 ssssesecssssseeeeesecseescessesecaceecssesaeceseesaesaseeseeenaeseesees 287 Table 51 Magnetic Tape Operations Commands 0 ce eeesesseeceseeceeeceeceeseeseenecaeeeteaecaeeeeeeeeaees 289 16 Getting Started VNMR 6 1B 01 999083 00 A1298 SAFETY PRECAUTIONS The following warning and caution notices illustrate the style used in Varian manuals for safety precaution notices and explain when each type is used WARNING War
169. Reference for details including a caution about using mxconst Getting Started VNMR 6 1B 01 999083 00 A1298 7 4 Performing Acquisition If an acquisition is to be prematurely terminated because sufficient signal to noise has been obtained or because the experiment has proved useless the aa command to abort acquisition should be used or the Abort Acq button on the Permanent Menu If the experiment is active it is aborted immediately all data is discarded and the experiment is interpreted as an error Any data collected from an earlier block size transfer is retained If any werr processing is defined that processing occurs followed by any queued experiments The login name and the FID directory path in file are used as keys to find the proper experiment to abort At times it is convenient to abort an acquisition but have wexp processing occur instead of werr processing The halt command is provided for this purpose See the next section Automatic Processing for more details on wexp and werr processing Under some circumstances there is a delay between the time go is entered and the acquisition is started During this time instructions based on the selected pulse sequence are being generated This is signified by the letters P SG appearing in the upper left corner of the status window An aa or halt command issued under these circumstances reports that no acquisition is active but it instead stops the instruction gener
170. This gradient checking is active for Performa I II gradients and Performa XYZ gradients For every timed event during a pulse sequence the levels of each gradient are checked against predefined safety limits The criteria are that a gradient may not be on at full power for more than 10 ms There is also a 2 duty cycle limit Finally at the end of each FID accumulation the duty cycle cannot exceed 50 Getting Started VNMR 6 1B 01 999083 00 A1298 7 4 Performing Acquisition Table 27 Commands and Parameters for Acquiring Data Commands Abort acquisition with error acqdisp message Display string on the acquisition status line acqmeter lt host gt Open the Acqmeter window acqstat lt remote_system gt Open the Acquisition Status window Acqstat lt rem_sys gt lt f file gt lt amp gt Open the Acquisition Status window UNIX au Submit experiment to acquisition and process data autolist Set up and start chained acquisition calcdim Calculate dimension of experiment errlog Display recent VNMR error messages expactive lt exp_number gt lt ans gt Determine if experiment has active acquisition explog Display log file of experiment ga lt nocheck gt Submit experiment to acquisition and FT the result gmapshim_au Start acquisition with gradient shimming go Submit experiment to acquisition go_sequence Pulse sequence setup macro called by go ga and au halt Abort acquisition with no error jexpl jexp2 jexp9 Join exist
171. UISITION ST F dB On GEMINI 2000 systems Background Color Fij snow the highest receiver gain is gain 40 On YNTYJ OVA and Foreground Color black UNITYplus 500 600 and 750 Sennen label lotic MHz systems only the aon controllable usable range of Font Of Value 9x15 gain is 18 to 60 when using low band observe nuclei gain Item Name Setting increases in steps of 2 dB Se gain n activates Autogain Label Setting in which the gain is automatically adjusted at the start of acquisition for an optimum value After the Color Of Value black acquisition is finished setting gain y then allows the value Item Show Yes No of gain to be read by typing gain followed by a question mark i e gain Color Of Label black Apply Reset riley Close Figure 64 Acqstatus Setup Window Acqstatus Program Homospoil Homospoil is a process by which the homogeneity is temporarily made very bad spoiled to cause any transverse magnetizations present at that time to decay rapidly to zero The parameter hs turns on homospoil pulses at various times in some pulse sequences If homospoil is activated by the hs parameter e g hs yn the duration of the gradient pulse is controlled by the parameter hst GEMINI 2000 systems do not have homospoil so hs must be nn otherwise a warning message is displayed at a go ga or au command hst is ignored on the GEMINI 2000
172. UNIX Contains directories with FID data and parameter files that can be used to practice data processing if no spectrometer is available to generate real data Many of the examples used in this manual guide you through a step by step approach to one or another aspect of using the software based on the data in this directory Contains the files used by the GLIDE user interface Contains help files for the VNMR menu system Contains the public domain serial communications program kermit and the related help file kermit doc Contains software libraries each a collection of routines used by VNMR and PSG Contains numerous text files for system macros written in the MAGICAL II language The files can be modified by the system administrator described in NMR System Administrator and Other Users on page 36 if desired Contains text files providing help in using VNMR commands Contains numerous system menus written in the MAGICAL II language The system administrator can modify these menus Contains text files for looking up a nucleus and translating it into the appropriate transmitter and decoupler frequencies for the rf type and field strength in use 01 999083 00 A1298 export home vnmr root m vnmr 1 4 Introduction to UNIX and VNMR Files acqbin bin fidlib acrobat glide help kermit lib maclib manual KEY menulib nuctables parlib psglib seqlib shapelib shimmethods shims
173. XR style file the file represents If the UNIX file name contains no suffix or is ambiguous the limNET software assumes the file is a VXR style data file The limNET protocol can transfer VXR style directories program files and data files The VXR style commands DIR and DLIST use the mnemonics DR PR and DA respectively to identify such entries The VNMR suffix for each is the following e Directory files have the suffix see below e Program files have the prg suffix e Data files have the dat suffix The suffix for a directory file is the total number of entries allocated in the VXR style directory Therefore if F IDL1B has e g 36 entries it becomes fiblib 36 in VNMR For program files and data files a dot and prg or dat is added e g MNP PGM becomes mnppgm prg and VCOEFS becomes vcoefs dat Be aware that the information in the I2 field normally the date is lost when the file is transferred to VNMR The exception is of course a VXR style directory Initiating Transfers from a Remote Node The limNET software lets you start a transfer from a remote node on a VXR style system When you use the ewrite command to transfer a file to a UNIX system the name of the file on the UNIX system will have a suffix indicating what type of VXR style entry the original file was When you use the eread command to transfer a file from a UNIX system the limNET software on the UNIX system searches for the file as specified in
174. YINOVA systems MERCURY VX MERCURY and GEMINI 2000 systems have two channels The main features of additional channels on UNITYTNOVA include independently generated rf high speed line control of the rf transmitter board a dedicated linear pulse amplifier and channel independence each channel is separate A waveform accessory can be also be integrated into the UN YINOVA console with as many as four waveform generators This option is not available on the MERCURY VX MERCURY and GEMINI 2000 systems Varian features a wide range of gradient and shim systems in many sample sizes and for all applications liquids solids and imaging For pulsed field gradient PFG experiments your system may have one of the Performa PFG modules Varian shim systems range from 13 channels for the GEMINI 2000 and UNITY and VXRS systems to 40 channels for the Ultraenmr shim system II MERCURY VX and MERCURY are 14 channels Getting Started VNMR 6 1B 01 999083 00 A1298 1 2 User Interface Superconducting Magnet and Probe The superconducting magnet and probe although separate are closely related The types and configuration of these components and associated electronics differ between systems Figure shows two representative systems On systems without sample changers the user s primary interaction with the magnet and probe is to insert the sample into the hole at the top of the magnet Under some circumstances the probe needs to be tuned to elect
175. Z etc The field offset coil ZO zee zero alters the total magnetic field Each shim gradient is controlled by its own parameter for example the X1 shim gradient is controlled by a parameter named x1 For Z1 and Z2 gradients there are two parameters for each z1 and z2 which are the fine gradients and z1c and z2c which are the coarse gradients In addition the field offset is controlled by a parameter z0 The full set of shim gradient parameters is displayed by entering dgs which causes the group of shim parameters to be displayed Depending on the value of the shimset parameter shim values range from 2047 to 2047 or from 32767 to 32767 with a value of zero producing no current The limits for each shim gradient are listed in the VVMR Command and Parameter Reference The macro readallshims reads all shims from the hardware and sets the values into the shim parameters in the current parameter tree The shims used depend on the shimset configuration For the shim set on the Ultraenmr shim system readallshims is active only if hardware to software shim communication is enabled readallshims is not available on GEMINI 2000 systems The macro setallshims sets shims from the current parameter tree into hardware setallshims is equivalent to entering load y su but without setting all the hardware parameters normally set by su temperature decoupling transmitter initialization etc The shims used de
176. Z4 iteratively until the lock signal is maximized you may well find that your signal shape has degraded considerably Hence the following procedure is suggested for a second level of shimming 1 After Z1 and Z2 have been adjusted for maximum lock signal write down the lock level adjust Z3 in one direction say by 4 and then reoptimize Z1 and Z2 iteratively until the lock signal is at a maximum Note this level of the lock signal If the lock signal is higher than it was before when you first wrote it down continue changing Z3 in the same direction Every change in Z3 must be followed by optimization of Z1 and Z2 until the lock level is at a maximum 2 Repeat step with Z4 That is change Z4 in one direction then optimize Z1 and Z2 If the lock level does not go up change Z4 in the opposite direction and optimize Z1 and Z2 Continue until the highest possible lock level is obtained 3 Repeat steps 1 and 2 iteratively until the highest possible lock level is obtained 4 Turn the spinner off and go through the non spin shims one at a time maximizing the lock level for each one Then return and go through each again Continue through all until the lock level is as high as possible If lock is lost increase the lock gain 5 Turn the spinner on and optimize Z1 and Z2 as described above return to the non spins turn the spinner off and reoptimize these Continue until the highest lock level is obtained For an ultimate check
177. a colon The following two examples should suffice e Remote copy of an entire directory r option in the current directory named noesy fid data files always end in fid toa remote host VARIAN600 into the named file rcp r noesy fid VARIAN600 usr2 slp noesy fid e Remote copy of a newfid fid in the home directory of vnmr1 on the remote host VARIANS00 into the home directory of vnmr1 where it will be given the same name rcp r VARIAN500 vnmrl newfid fid vnmrl The names of the known remote hosts are contained in the file etc hosts or inthe NIS files enter yocat hosts ina UNIX shell and are established by the system administrator A user only needs to know the name of each computer system To test connectivity the rsh command is available e g rsh VARIAN500 ls Transferring Data Using limNET The user interface to the limNET software consists of the commands eread ewrite elist dnode and eaddr These commands are available from the VNMR program or from the UNIX shell In VNMR each argument is a string so typically each argument must be enclosed in single quotes although string variables can be used also From the UNIX shell each argument is separated by a space Examples of both are given below Throughout the section VXR style Gemini VXR 4000 or XL systems are usually referred to as a remote node Note that after data is transferred it must be converted This is covered in Converting Data Between Systems on
178. a number of interactive programs dconi df ds 112d etc with menus that operate the same as the main menu system Table 3 includes these programs and menus To run these programs enter the program name e g dconi Since these programs are integrated into the main menus system each can also be called from one or more of the buttons in the menus listed in Table 3 Getting Started VNMR 6 1B 01 999083 00 A1298 4 1 Working With Menus Table 3 VNMR Menu System Part of 4 Note Underlined button labels means that the button displays another menu Permanent Menu always present page 65 Abort Acq Cancel Cmd GLIDE Main Menu Help Flip Resize Acqi Main Menu from Main Menu button in Permanent menu page 66 Workspace Setup Acquire Process Display Analyze File More Workspace Menu from Workspace button in Main menu page 67 Library Exp2 Exp3 Exp4 Exp5 Exp6 Create New Delete Setup Menu from Setup button in Main menu page 67 H1 CDCI3 C13 CDCI3 Nucleus Solvent Sequence App Mode Acquire Nucleus Selection Menu page 68 H1 H2 C13 N15 F19 P31 Other Return Solvent Selection Menu page 68 CDCI3 D2O Benzene DMSO Acetone Other Return 1D Pulse Sequence Setup Menu page 68 APT DEPT INEPT BINOM S2PUL More ID 2D Return 1D Pulse Sequence Setup Secondary Menu page 69 D2PUL SSECHO XPOLAR More1D 2D Return 2D Pulse Sequence Setup Menu page 69 COSY COSYPS HETCOR NOESY ROESY 1D More 2D Return 2D Pulse Sequence Setu
179. aaed EE AE 193 Temperature Related Control cisiicscssiccascsssssseuscssssscssecseutesbancssscesvansupaveanscsvaescaaee 195 Temperature Related Parameters 0 eee eeeseecseessececeeeceeceaececeseeeeeeeeereeeeees 196 Pulsed Field Gradient Related Parameters cc eceeeeseeeeeseceeceseeeeeeseeereeeeees 196 01 999083 00 A1298 Getting Started VNMR 6 1B 9 Table of Contents 7 3 Creating and Editing Experiment Text Files oes ceeceseceeeeseeeeeeeeseeeeaeeees 197 Creating and Editing a Text File oo cece cseesaececeaecaeceseeeeeeeeereeeeees 197 Displaying and Handling a Text File oe eee ee ceeee cee ceseceeceseeeeeeseeeeeeeeees 197 LAP Performing ACQUISITION ce cos ccsepenssdecs cxsvsceecsspessdescesascteesssesensscsugecundevdgacessrenitesnssoeseessee 198 Initiating Acquisito Misono anae an siti i 198 Shimming During an Acquisition sesssseeeesseeeseseesrsrrerrresrerrsrreresreresreersrrereees 200 Queueing ACQUISITIONS ciaisensis aeaee e Eta er SE ra aeie ieS 200 Chained ACg iSitiOI srersisiircsnroseriorakrencre chin Miuecbcpcksseesonsvossaenstssvensteasscuneunedeles 201 Stopping and Resuming Acquisition 00 0 0 ee eeceeeceeceseeeeeeeeeeeeeseeeeeeaeeeaeeaee 202 Pausing Halting and Aborting Acquisition 00 0 eee eee eese cee ceseeeeeeseeeeeeeeees 202 Data Precision and Overtlow cssussecsesessspcess euassadertiensecpeeisrnstienstoeesesbtas cates 203 AULOMALIC Processing siirsi vices Hass em ewaci bet ca swestsvosncen E EE Ee NEE
180. abenssasiyelvvbesenst 253 Inte pral REGIONS isc ssc voeicchscceveasdenstesienanesesauseuss rR ESEE EEE E EE Re EEEE EEEa a 253 Integral Display and Plotting sacscssiercencrrisnciseeciiereirin iesi 253 YT Ploto sicci eoio ns E ERE EEE EE EEEE EE ea 254 Plotter Output cnrs nonnene E E aniaantien 254 Plotter Configuration sessseeseseesesesesiesesreeretsrsrtesstsrerststtrerstsisteesstsretsessrrrersrseee 255 Plotter Resolution and Speed sssesseseeeesseseseseesrsresrseesrerssreresrresreresreesrresrereet 256 Selecting a Plotter spinis ceni E E E E E 257 Color Printing scanio en E Sueded EE RES 257 Plotting Parameter Lists and Text Files oo eee cee ceeceseeeeceseeeeeeeeeeeeeeeees 261 OB Plot DeSISMEL ss cssccccs vice ccbssssaassrsattesbeeasasieskseuheccenscnseennsdebensneyscbvede sesusvanaauenudeassensceesaens 262 SYSTEM REGUIFEMIEM biisns svsckesak dee tiacesleks obsc satsscasvoodaeesbevensvessdvasts srebncests E REEERE 262 Starting Plot Designet ios sssscosesscassedsescensctvacedeabvbad sbesaensnsvscdsasuasessessdansnancscdoseduaes 262 Customizing a Plot sesinin beesvshs As eotes sist decker sus sdeueativonssin ses aE E E EEE eaten ease 263 Adjusting and Restoring Plot Parameters 00 0 0 cee sees ceeceseceeceseeeeeeeeeeeeneeees 269 Moving Objects and Changing Object Size oe ee eee eeee cee ceseeeeeeseeeeeeeeees 270 Changing the Shape of the Plot Designer Window 0 eeeceeseteeeetreeeeeteeeees 270 Changing the Size of the Plot Designer Win
181. additive weighting constant Return Return to last menu active before entering the wt i program 72 Getting Started VNMR 6 1B 01 999083 00 A1298 4 9 Processing Menus Interactive 1D Spectrum Display Menu ds Program The Interactive 1D Spectrum Display menu part of the ds program is typically entered by selecting the Transform button or the Weight Transform button in the 1D Data Processing menu or by entering the menu ds_1 or ds command Button Description Box OR If labeled Box select two cursors go to box mode Cursor If labeled Cursor select one cursor go to cursor mode No Integral OR If labeled No Integral hides integral display Full Integral OR If labeled Full Integral display all integral regions Part Integral If labeled Part Integral display every other region Expand OR If labeled Expand expand to area between cursors box mode Full If labeled Full display full area cursor mode sp wp Adjust the start and width of the displayed spectrum Mark Mark cursor position in cursor mode or region box mode Phase Enter the interactive phasing mode Th Interactively adjust the horizontal threshold Resets Interactively define or remove integral reset points Dscale Toggle on and off the display of a scale below the spectrum LvI Tlt Interactively adjust 1v1 and t1t parameters Set Int Set integral scaling Return Return to last menu active before entering the ds program 2D Data
182. adout 115 attenuator configurations 191 192 au command 138 198 200 201 audio filter 187 auto assign button 85 Auto button 75 auto button 140 161 300 Getting Started VNMR 6 1B autolist macro 201 Automake Shimmap button 170 automated acquisition 98 data acquisition 98 plotting 99 processing 99 shimming 172 Automated Shimming menu 178 181 automatic block size processing 204 phase calculation 77 phasing 225 selection of peak regions 77 shimming 36 130 139 142 144 145 161 Automatic button 71 198 Automatic COSY Analysis menu 82 Automatic DEPT Analysis menu 81 automatic gain 205 automatic lock full optimization 134 optimizing Autolock 133 simple Autolock 132 automatic phasing algorithms 225 automatic teller machine ATM cards caution 19 autoname command 278 Autophase button 77 AUTOSHIM menu 162 autoshim method 158 Autoshim on Z button 172 Autoshim see automatic shimming autostack macro 99 AV button 80 av command 225 awc button 72 223 awc parameter 221 AX button 84 AX2 button 84 AX2Y button 84 AX3 button 84 axes positioning 262 axis parameter 232 246 249 253 axisf parameter 232 234 AXY button 84 AXYZ button 84 B B shimming criterion 140 background Autoshim 139 145 background mode operation 30 Backup File button 76 bad shimming criterion 140 bandpass filter 212 217 bandwidth of digital filter 212 217 bar command UNIX 291 baseline
183. al 1D spectrum and scale No interactive adjustment is allowed Interactive Display normal 1D spectrum and allow for interactive adjustment Massage Display the 1D Data Manipulation menu next Size Display the 1D Display Size Selection menu page 78 Reprocess Display the 1D Data Processing menu page 71 Plot Display the 1D Plotting menu page 78 More Display the 1D Data Display Secondary menu page 78 1D Data Manipulation Menu The 1D Data Manipulation menu is activated by selecting the Massage button in the 1D Data Display menu or by entering the command menu massage_1D Button Description DC Drift correct and display the selected spectrum Region BC Autophase Adj VS Adj IS Adj WP Return Automatic selection of peak regions in the selected spectrum and display the result Perform a fifth order baseline correction using the current integral reset points to determine peak regions Display the resulting spectrum Perform automatic calculation of the spectral phase parameters then display the result Adjust vertical scale then display the spectrum Adjust integral scale then display the spectrum Adjust width of plot then display the spectrum Display the 1D Data Display menu page 77 01 999083 00 A1298 Getting Started VNMR 6 1B 77 Chapter 4 Using the VNMR Menu System 78 1D Display Size Selection Menu The 1D Display Size Selection menu is activated by selecting the Size
184. alfway vertically up the screen and click the left mouse button A horizontal cursor will intersect at the mouse arrow Two vertical cursors will be placed on either side of the mouse arrow A small region of the spectrum will be displayed in a different color if a color display is present and only this spectral region will be interactively updated Now moving the mouse above or below the horizontal cursor but within the two vertical cursors and clicking the left or right button will adjust the zero order or frequency independent phase parameter rp Clicking the mouse above the horizontal cursor will increase rp cause a clockwise rotation of the peaks while clicking below the horizontal cursor will decrease rp and cause a counter clockwise rotation Placing the mouse arrow right on the horizontal cursor and clicking the left button will restore the initial phase The left and right button of the mouse differ only in their sensitivity Full scale top to bottom of the screen corresponds to approximately 180 for the left button and 20 for the right button and hence you can consider the left button the coarse adjust and the right button the fine adjust During this entire process only the update region centered between the vertical cursors will be redisplayed to reflect the new phase parameter The width of this update region is controlled by the global parameter phasing which sets the percentage of the screen display to be u
185. am is activated by selecting the Peak button in the Interactive 2D Color Map Display Main menu Button Auto Edit File Display Return Description Display the 2D Peak Picking Automatic menu next Display the 2D Peak Picking Edit menu page 76 Display the 2D Peak Picking File menu page 76 Display the 2D Peak Picking Display menu page 76 Display the Interactive 2D Color Map Display Main menu page 74 2D Peak Picking Automatic Menu ll2d Program The 2D Peak Picking Automatic menu part of the 112d program is activated by selecting the Auto button in the Interactive 2D Peak Picking Main menu Button Box OR Cursor Peak Volume Expand OR Full Both Adjust Reset Return 01 999083 00 A1298 Description If labeled Box select two pairs of cursors box mode If labeled Cursor select one pair of cursors cursor mode Automatically pick peaks Automatically determine peak bounds and calculate volumes If labeled Expand expand to area between cursors box mode If labeled Full display full area cursor mode Pick peaks and calculate volumes Adjust peak bounds so that none overlap Delete all peaks in the peak table Display the Interactive 2D Peak Picking Main menu page 75 Getting Started VNMR 6 1B 75 Chapter 4 Using the VNMR Menu System 2D Peak Picking Edit Menu Il2d Program The 2D Peak Picking Edit menu part of the 112d program is activated by selecting the Ed
186. ameter 232 240 245 vpf parameter 232 234 236 vpfi parameter 234 Vproj max button 75 Vproj sum button 75 vs parameter 223 232 239 vsadj macro 245 vsadj2 command 245 vsadjc macro 245 vsadjh macro 245 VT experiment warning 18 VT status 152 vtc parameter 196 vttype parameter 151 205 VXR library file extraction 287 vxr_unix command 287 VXR 4000 systems 281 VXR S systems 281 VXR style systems 281 VXR style tape 290 Ww walkup NMR 58 Walkup NMR Using GLIDE manual 58 WALTZ 16 decoupling 193 194 195 warnings defined 17 water suppression 69 147 waveform generator accessory 24 waveform generator programmable decoupling 194 wbs command 204 318 Getting Started VNMR 6 1B wbs parameter 71 204 208 wc parameter 232 236 250 wc2 parameter 250 we2max parameter 255 256 257 wemax parameter 255 256 257 weight and Fourier transform 71 221 weight Fourier transform phase each FID 81 Weight Transform button 71 weighting function 221 223 user written 222 weighting parameters 72 werr command 203 weir parameter 203 204 208 wexp command 204 wexp parameter 71 203 204 208 wf parameter 232 wft command 204 221 223 227 whitewashed FIDs 237 width of chart 232 width of FID 232 width of plot 77 232 Wilmad tubes 102 window closing and opening 50 windows on display screen 27 44 wnt command 204 wnt parameter 71 204 208 working direc
187. an error message and the parameter is unchanged Similarly some flag parameters can only be set to enumerated characters Attempting to enter a character string containing a character that is not one of the enumerated characters of a flag parameter produces an error message and the parameter is unchanged Entering parameters may not have an immediate effect For instance if temp 60 is entered no temperature is regulated until an acquisition is started with the go command or until the hardware setup command su is executed Parameter Entry Limitations Some parameters such as ct number of completed transients cannot be entered from the keyboard Attempting to enter such a parameter in the normal way produces the error message that the assignment is not allowed 5 3 Command Line Editing and Reentry 96 You can reenter a command or series of commands that you previously typed Editing the previous or current commands is accomplished with the arrow keys special keys and key combinations For details move the mouse to the VNMR input window hold down the Control key and press the right mouse button to open an instruction menu window Perhaps you entered the command cat vnmr psglib noesy c to display a particular pulse sequence You thought you saw what you wanted but a few minutes later you need to enter the same command again Rather than retype that long file name you can Getting Started VNMR 6 1B 01 999083 00 A1298 5 3 C
188. an output window text input occurs only in the input panel near the top of the screen Some output to the dg program might produce more information than can be displayed on a single screen In this case a scroll bar appears along the edge of the window On some systems the scroll bar is always present Click on the scroll bar with the mouse to retrieve material that has scrolled out of view You can edit text in this window by highlighting the text you want to copy or move using the left mouse button and then pressing the right mouse button to pop up an Edit menu If the Tcl version of the dg window is not active the t cl command does nothing For more information about Tcl scripts see VVMR User Programming 01 999083 00 A1298 Getting Started VNMR 6 1B 47 Chapter 2 VNMR Basics 48 Selecting the Interactive dg Window The dg interface is selected by setting the UNIX environmental variable vnmrt ext to the full path of the dg program The following line in the login file selects the interactive dg window setenv vnmrtext Svnmrsystem tcl bin dg Deselecting the Interactive dg Window If you comment out the previous line with a character in front of it the noninteractive dg window will be selected Configuring the dg Window The dg window has a built in configuration tool You can activate this tool by simultaneously holding down the Control key and pressing the left mouse button over a label tab Use this tool to move items
189. an to make the spectrometer sweep from the minimum to maximum allowable frequencies Figure 27 Pull Down Menu For Span e Select CW to temporarily stop frequency sweeping and to make the transmitter put out a CW signal This sets the frequency to the currently selected center frequency This mode is useful for checking the reflected power on the tune meter or for making other tests that require a fixed frequency To Use Cursors Grid and Markers Cursors and markers appear on the Tune Display and are used the same way they are used in VNMR Cursors and markers are color coded and the frequency positions of each are displayed on the bottom of the Tune Display Cursor grid and marker controls are not available in minimal display Cursors In the Cursor field the Tune Control Panel provides three cursor modes see Figure Cursor Off Line Box Grid Off On 28 a Select Off to turn cursors off so that no cursors are displayed Figure 28 Cursor and Grid Controls e Select Line to display a single cursor that specifies one frequency The frequency position of the cursor and the signal amplitude at that frequency are displayed on the bottom of the Tune Display window e Select Box to display two cursors for use with the Expand button for setting the span to a narrower range After a region is expanded the cursor mode switches back to the 120 Getting Started VNMR 6 1B 01 999083 00 A1298 6 6 Tuning the Prob
190. and dconi Button Description Box OR If labeled Box select two pairs of cursors box mode If labeled Cursor Cursor select one pair of cursors cursor mode Trace Select trace display mode Proj Display the Interactive 2D Display Projection menu page 75 Expand OR If labeled Expand expand to area between cursors box mode Full If labeled Full display full area cursor mode Redraw Repeat the last 2D or image display with current parameters Plot Plot current trace Peak Display the Interactive 2D Peak Picking Main menu page 75 Return Return to previous menu Getting Started VNMR 6 1B 01 999083 00 A1298 4 9 Processing Menus Interactive 2D Display Projection Menu dconi Program The Interactive 2D Display Projection menu part of the dconi program is activated by selecting the Proj button in the Interactive 2D Color Map Display Main menu Button Description Hproj max Hproj sum Vproj max Vproj sum Plot Cancel Horizontal projection of the maximum intensity at each frequency Horizontal projection of the summed intensity at each frequency Vertical projection of the maximum intensity at each frequency Vertical projection of the summed intensity at each frequency Plot current projection Display the Interactive 2D Color Map Display Main menu page 74 Interactive 2D Peak Picking Main Menu ll2d Program The Interactive 2D Peak Picking Main menu part of the 112d progr
191. and Plotting Commands and Parameters Commands be 1D baseline correction cde Cancel drift correction cz lt freql freq2 gt Clear integral reset points de Calculate spectral drift correction dli Display list of integrals dlni Display list of normalized integrals dpir Display integral amplitudes below spectrum dpirn Display normalized integral amplitudes below spectrum isadj lt size lt neg_size gt gt Automatic integral scale adjustment nli Find integral values pir Plot integral amplitudes below spectrum pirn Plot normalized integral amplitudes below spectrum region Divide spectrum into regions z lt resetl reset2 gt Add integral reset point at cursor position be lt lt l1 unbc gt nsubregion lt minpoints lt minregion gt gt gt gt region lt tail_length relative_num threshold num_points tail_size lt num_regions gt Parameters dcg dc cdc Drift correction group ins number Integral normalization scale intmod off partial full Integral display mode liamp numbers Amplitudes of integral reset points lifrq numbers in Hz Frequencies of integral reset points lv1 number Zero order baseline correction tlt number First order baseline correction The 1D Data Display Secondary Menu appears 6 Click on Integrals The text window displays a list of integral intensities Fully Automated Method 1 Enter intmod partial region The integral display mode is changed s
192. and on the display of the transformed spectrum useful for modifying the weighting function on slow terminals or large spectra 8 3 Fourier Transformation The ft command Fourier transforms one or more FIDs without weighting applied to the FID To perform the same Fourier transform with weighting use the command wft Both ft and wft perform a shift and phase rotation according to the parameters 1sfid and phfid if these are set Any dc level in the FID is automatically calculated and removed except when wft nodc is used Alternatively the parameter dc rmv uses hardware information to remove the dc offset values from the FID when ct 1 For the Fourier transformation process the parameter fn is the number of points to be Fourier transformed Because of the type of algorithm used this number must be a power of two typical numbers are 16384 32768 or 65536 often written as 16K 32K and 64K where K is equivalent to multiplying the number by 1024 The most common entry for fn is n This value specifies that however many data points np were acquired the first 01 999083 00 A1298 Getting Started VWMR6 1B 223 Chapter 8 Data Processing power of two greater than or equal to np will be used as fn If fn is greater than np or if fnis n and np is not a power of two the remaining points in the transform are filled in with values of zero zero filling Thus there is no explicit zero filling command this process is an implicit one gover
193. any of the lower menus return directly to Main menu after the button actions on the lower menu are completed To make a choice on the Main menu and all lower menus move the mouse cursor over the button label with the action desired and click press down and release the left mouse button The Main menu is activated by selecting Main Menu in the Permanent menu or by entering the command menu main in the input window Button Description Workspace Display the Workspace menu page 67 for selection of the experiment workspace to be used Setup Display the Setup menu page 67 to set up parameters for data acquisition Acquire Display the Acquire menu page 70 to initiate data acquisition using one of several modes Process If a 1D experiment is active display the 1D Data Processing menu page 71 for processing data weighting Fourier transform If a 2D experiment is active display the 2D Data Processing menu page 73 for processing data weighting Fourier transform Display If a 1D experiment is active display the 1D Data Display menu page 77 for display of previously processed data If a 2D experiment is active display the 2D Data Display menu page 79 for display of previously processed data Analyze Display the Analyze menus page 81 for access to various spectral analysis tools including spin simulation deconvolution spectral add subtract regression and exponential analysis File Display the Files Main me
194. ap with other strong resonances Gradient shimming can also be done on a water sample of equal height of the sample of interest and then the sample of interest can be inserted For further information refer to the entries for gnapshim gmapsys and gmapz in the VNMR Command and Parameter Reference Gradient Shimming Menus The top level gradient shimming menu is the Gradient Shimming System menu which is opened by entering gmapsys Set Params Shim Maps Autoshim on z Set Shims Display Quit From this menu and submenus there are buttons to open the following menus e Gradient Shimming Setup menu Go dssh Gradient Nucleus Find gzwin Calculate gzwin Find tofl Add Params Return e Gradient Nucleus Parameter Setup menu Pfg H1 Pfg H2 Homospoil H1 Homospoil H2 Return 01 999083 00 A1298 Getting Started VNMR 6 1B 177 Chapter 6 Preparing for an Experiment 178 e Gradient Shimming Map menu Automake Shimmap Make Shimmap Shimmap Files Current Mapname Save As Return e Gradient Shimming Files menu Cd to Userdir Copy to Userdir Load Shimmap Load Shimmap amp Params Rename Return e Gradient Shim Setting menu Old Shims New Shims Min Shims Return e Gradient Shimming Display menu dgs List Shims Display Shimmap Display Fit Show Record Plot Return e Gradient Shimming Plot menu Print dgs Print Shims Plot Shimmap Plot Fit Plot b0 Return Two other gradient shimming menus are ava
195. aps The times required to plot a complete drawing on pen plotters depends on the number and size of the individual vectors in the drawing On raster graphics printers the time required to complete a drawing depends on the size of the drawing wcmax and wc2max and on the resolution The high resolution mode is usually about four times slower than the medium resolution mode The ThinkJet and the LaserJet use 8 5 x 11 in paper Selecting a Plotter From the Main Menu select the More button followed by Configure then Show Output Devices which invokes the showplotter macro to list the current plotter as well as your possible choices Select Plotter will step through the various choices Alternatively type in the name of the plotter such as plotter HP7550A This will run the set plotdev macro to configure the system for this plotter During the configuration wcmax wc2max and maxpen are set to the values described in table above but can now be changed to smaller and in some cases larger values if required After the system has been configured for a given plotter the graphics display window represents the plotter graphics area Never change the plotter configuration during the preparation of a single output page because all commands of one page will go to the same plotter If several plotters are connected to the system it is possible to change the plotter definition between pages even if these pages are still waiting in a queue to be p
196. ar button choice will do Clicking on the button labeled Help in the Permanent menu which is always available causes a help screen to be displayed in the text window This screen provides an explanation of each of the menu buttons and explains the function of the three buttons on the mouse for the menu buttons on view 01 999083 00 A1298 Getting Started VNMR 6 1B 59 Chapter 4 Using the VNMR Menu System 4 1 Working With Menus 60 At all times two rows of menu choices are accessible to you on the screen The upper row which can be selected only by using the mouse and not by function keys is the Permanent menu Although the labels and actions of these buttons are customizable see the manual VNMR User Programming their functions do not change during a VNMR session Abort Acq Cancel Cind GLIDE Main Menu Help Flip Resize Acqi Located below the Permanent menu is another row of up to 20 buttons whose choices vary depending upon which menu is on display The default is the Main menu which contains the following buttons Workspace Setup Acquire Process Display Analyze File More The Main menu can always be activated by clicking on the Main menu button in the Permanent menu You can make selections in the Main menu by either clicking on the button or by pressing one of the F1 F8 keys for example to select Setup press F2 Making a selection on the Main menu causes a different set of buttons to replace the Main menu For
197. arameters alfa 0 to 100000000 in ms at number in seconds ct number non user enterable d1 number in seconds d2 number in seconds dhp n ynumber dlp n snumber dm dm2 dm3 dm4 string dmf dmf 2 dmf3 dmf4 number in Hz dmm dmm2 dmm3 dmm4 string dpwr dpwr2 dpwr3 dpwr4 number in dB dpwrf dpwrf2 dpwrf3 number dpwrm dpwrm2 dpwrm3 number dres dres2 dres3 dres4 number in deg dseq dseq2 dseq3 string fb number in Hz gradtype string homo homo2 homo3 homo4 y n np number constrained to multiple nt number pl number in microseconds pad number in seconds pfgon y or n for each channel pw number in ms pw90 number in ms rofl number in ms rof2 number in ms seqfil string ss n 32768 to 32767 temp n number in celsius tpwr number in dB tpwrf 0 to 4095 4095 is max tpwrm 0 to 4095 4095 is max vtc 0 to 50 in celsius Adjust tip angle resolution time for 1st decoupler Adjust tip angle resolution time for 2nd decoupler Adjust tip angle resolution time for 3rd decoupler Adjust tip angle resolution time for 4th decoupler Display pulse sequence Calculate the Ernst angle pulse Set alfa and rof2 according to Hoult Enter pulse width for p1 in degrees Plot pulse sequence Enter pulse width for pw in degrees Set up parameters for standard 2 pulse sequence Display experiment time or recalculate nt Set a
198. articular feature is standard on the instrument UNITYTNOVA MERCURY VX Mercury UNITY plus UNITY GEMINI 2000 Gemini GLIDE VXR XL VNMR VnmrS VnmrX Vnmrl VnmrV VnmrSGI MAGICAL AutoLock AutoShim AutoPhase limNET Ultraenmr Indirectenmr Autosnmr Tripleenmr MagicAngleenmr Protonenmr Bioprotonenmr ASM and SMS are registered trademarks or trademarks of Varian Associates Inc UNIX is a registered trademark of AT amp T Information Systems OpenWindows Sun Solaris Suninstall SPARC and SPARCstation are registered trademarks or trademarks of Sun Microsystems Inc and SPARC Int Oxford is a registered trademark of Oxford Instruments LTD Ethernet is a registered trademark of Xerox Corporation VxWorks VxWorks Powered and WindRiver Systems are registered trademarks of WindRiver Systems Inc Other product names in this document are registered trademarks or trademarks of their respective holders Overview of Contents SAFETY ae 2 8 0 een eee 17 WAEPOGUCHON MEPE E E damcneeemeeneee 21 Chapter 1 Overview of Varian NMR _ q cccssssseecessseeeeeeseeneeeessseeeeneseeeeees 23 Chapter 2 NNMR Basics ssssnnnnnnsennunenrennnnenonnnnennnnnnnnnnnnnnnnnnnennnnnnnnnnnnnnnnnn ennan 39 Chapter 3 Using GLIDE ici eicecseieelee eee eee 53 Chapter 4 Using the VNMR Menu System c cccssseeeeeeseeeeeeeeeeeeeeeeeeeees 59 Chapter 5 Using the Command Mode ss ssecccssseeeeeeseeeeeeesseeeeeesneeeeees 9
199. at in most pulse sequences to get best use of pulse power the transmitter frequency during pulses should be kept in the center of the spectrum especially for 180 degree pulses 01 999083 00 A1298 Getting Started VWMR6 1B 219 Chapter 7 Acquiring Data 220 Getting Started VNMR 6 1B 01 999083 00 A1298 Chapter 8 Data Processing Sections in this chapter e 8 1 Weighting Function this page e 8 2 Interactive Weighting page 223 e 8 3 Fourier Transformation page 223 e 8 4 Phasing page 224 e 8 5 Advanced Data Processing page 226 After data are acquired the next step in the process is applying a weighting function to the FID which is an optional part of the process and Fourier transformation which is not Both processes are accomplished together with the command wft weight and Fourier transform command the command ft performs only the Fourier transform and skips the weighting step 8 1 Weighting Function Table 31 lists weighting and Fourier transform parameters and commands The weighting function used is governed by the following parameters e 1b results in exponential weighting A positive value gives the desired line broadening in Hz which is then used to calculate a decaying exponential function A negative value gives a resolution enhancement function e gf is a Gaussian time constant in seconds and defines a Gaussian function of the form exp t gf 2 e gfs shifts the center of
200. ation process and the message PSG aborted appears Use aa or halt only if the data is not to be used or if a block size storage has taken place so that the data at the time of the last block is present otherwise the data is irretrievably lost Data Precision and Overflow Single precision 16 bit dp n is mainly designed for a single application related to imaging Because DSP digital signal processing can give you 20 bits of data in a single acquisition the 16 bit data size is usually not desirable The console will detect a numeric overflow in hardware and post an error Even without DSP the standard 16 bit ADC boards can theoretically overflow after one transient Therefore dp y is the preferred setting Overflowing dp y with dsp r real time DSP is possible with greater than 4000 transients Hardware DSP scales to 16 bits with dp n so that it will not overflow As a result many of advantages of hardware DSP are discarded Under some conditions dp n is useful The main example is flash imaging where only one transient is typically taken using very large data sets under fast conditions In these experiments the DTM memory data to memory board memory typically 16 Mbytes can be filled up with rapidly acquired single shot acquisitions The dp n mode doubles the capacity of the DTM memory increasing the number of increments in the experiment If a cancellation experiment is carefully designed to avoid o
201. ausing spectra to be acquired processed plotted etc But VNMR software also includes an extensive series of menus which at any time provide a number of buttons that allow access to the essential functions of operating an NMR spectrometer experiment setup acquisition data processing display plotting analysis and more Many users will be able to operate their spectrometer for hours at a time with little or no resort to the keyboard The VNMR menu system provides an excellent mechanism for new users to begin acquiring or processing data with little or no training It isn t necessary to know that wft is the command that performs a weighting of the FID and a Fourier transform because the button marked Weight Transform is self explanatory It also isn t necessary to know that dpcon to displays a 2D contour plot because a button marked Contour Plot is available Using the buttons is simplicity itself move the mouse arrow or cursor to a point over the desired menu button then click press the mouse button and release the left button on the mouse The function keys F1 F2 or F8 etc on the keyboard can be used as an alternative method for selecting the first eight menu buttons on all menus except the Permanent menu described in the section Permanent Menu on page 65 key F1 selects menu button 1 F2 selects button 2 F8 selects button 8 Despite the user friendly labels on the menu buttons you may be unclear about what a particul
202. ay Plotting and Printing 258 VNMR Color Selection 20_PH 2D_AV l Inage l GhostWhite WhiteSmoke F gainsboro Floralwhite linen Anti queWhite Papayalhi p BlanchedAlmond A 5 bisque arameter PeachPutt threshhold Color selection File name Delete Load Figure 68 Color Selection Window color Program The buttons for the 2D Phase window for the display shown in Figure 69 allow you to set colors for the contours of the display The buttons in the 2D Absolute Value window for the display shown in Figure 70 allow you to assign colors to the contours of the display The Image window for the display shown in Figure 71 allows you to set the colors for the display background and foreground Setting Colors You can select colors from either the color list box in the center of the window or the color palette For every color on the palette there are ten values in the list box To set the background color of the graphics window to gray for example do the following steps 1 Click on the background button 2 Click on a gray button in the color palette The name of the button and its values appear in the scrollable list box directly to the left of the palette To change the color shade click on a value in the list e g gray 13 To set colors for the remaining eight areas of the display repeat steps 1 and 2 Saving A Color File When you are satisfied with the color assignments you can sa
203. ays and plots Data truncation limit Data truncation limit Data display mode directly detected dimension Reference peak position Reference peak frequency Threshold Vertical position of spectrum Vertical scale Set plot display or full display 01 999083 00 A1298 9 5 Spectral Display and Plotting Table 38 Spectral Plotting Commands and Parameters Commands aexppl lt expansion_factor gt Automatic plot of spectral expansion pl Plot spectra plex pltmod gt Plot carbon spectrum plh lt pltmod gt Plot proton spectrum pll lt x y minimum_y gt Plot a line list plp lt pltmod gt Plot phosphorus spectrum plot Automatically plot spectra plotid Plotting macro for simple non arrayed 1D spectra ppf Plot peak frequencies over spectrum pscale Plot scale below spectrum or FID pl lt lt start finish step gt lt int gt lt all gt lt options gt gt ppf lt lt noll gt lt pos gt lt noise_mult gt lt top gt gt ppf lt lt noll gt lt pos gt lt noise_mult gt lt leader gt lt length gt gt pscalex lt lt fid gt lt axis gt lt vertical_start gt lt plot_start gt lt pen gt gt Parameters hzmm number Scaling factor for plots pitmod Plotter display mode sp number in Hz Start of plot wp number in Hz Width of plot pltmod off fixed full standard user variable The vertical position in mm of the spectrum with respect
204. be used once and the second method three times Hardware Autoshim Hardware autoshim methods vary according to which system is involved UNITYINOVA Systems The hdwshim parameter enables the commands go ga or au to turn on and off hardware autoshimming which is done using a software emulation of hardware autoshim Shimming is active only while a pulse sequence is executing e If hdwshim y shimming is active only during the first delay of the pulse sequence e If hdwshim p shimming is active only during the first presaturation pulse defined as a change in power level followed by a pulse e g presat c Shimming during subsequent delays or presaturation pulses can be activated by using the hdwshiminit statement before the delay or presaturation pulse Shimming uses the z1 shim by default If the parameter hdwshimlist is created shimming uses the specified list of shims to shim on Only the following shims are allowed zi ZUG ZA a 2c ed jy 01 999083 00 A1298 Getting Started VNMR 6 1B 145 Chapter 6 Preparing for an Experiment 146 Shimming is done in the order of z1 z1c z2 z2c x1 y1 regardless of the order in which the shims are used in hdwshim1list and is performed on each shim in intervals of 20 seconds The fine shims z1 z2 x1 and y1 are recommended for routine use UNITY and VXR S Systems with Z1 Shimming Hardware The hdwshim parameter enables commands go su au etc to turn on and off the Z1
205. beade 39 VNMR Interface and Display Tools 00 0 ee eeeeeeeeeecseessecaceaeceecaececeseeeeseeeeeseeeeeeeeas 42 VNMR Menu System Part 1 Of 4 eeeceeeeseesccesceeeceseeseeeseeeeeneeseecaeeseecaeceaeceeneeerenaees 61 VNMR Menu System Part 2 Of 4 eeeceeceesessscesceeeceseeeeeeeeeseeeneeaeecaeesaecaeceaeceeneeereesees 62 VNMR Menu System Part 3 Of 4 ceeecesccessssscesceeeceseeseeeeeeeeeseeaeecaeeaaecaeceaececneeeeeesees 63 VNMR Menu System Part 4 Of 4 cececeesceesessecescesecesceeeecceeeeeeeseeeaecaeecaeceeecaeseaeeaeenaees 64 Special Keys for VNMR Line Editing oo eee eeeeeeeeecnecneeeeeseceeceeesesaecaeeeesaeaeeeseeenaens 97 Automated Acquisition Macros oc ceeeeesesseesscesceseceeceeeeeeeeeeeeaeeseecaeeaaecaecsaecaesnaeeeeaees 98 Automated Calibration Macros oo ce eeseseeseesecesceseceeeeeeeeeeeeeeenseseecaeesaecaeceaecaesnaeeeeenaees 98 Automated Plotting Macros oo ce eeceseesecsseesecescesecesceseesseeseseneeseecaeesaecaecsaeceessaeeeeenees 99 Automated Processing Macro o0 eccseesesseceseeseceseeseceeeeseeeeeeseeeneeseecaaesaecaecaecsessseeneensees 99 Sample LUbE Depths oi siies cis saceess ea secesanbelasasbins svces sasbesuevasnnvssveusscevodaueasssavebadounacaunsubccogesens 102 Sample Changing Commands and Parameters 20 0 0 eee eeseeseceeceeeceeeeeeeeeeeeeseeeeaeeenes 104 Retrieving Parameter Sets Commands and Parameters 0 0 0 0 eeeeeeeeeeeeeeeeeeeeeenes 107 Probe File Macros and Parameters 0 eccc
206. board and Remote Status Module cee eeeeeseeceeeeeneceeeeeeteeeneeeeee 27 VNMR Display SCteen lt 0 0 csssedicssvesssosssscescunseuessordesecudeeungeviessssseeossdeccsgeossicess 27 Using Multiple Windows 0000 cee eeeeeessececeseceeceaeeseceseeseceseeeeceeeeeeseaeeeaeeaeeaaeenee 28 TiS Advanced Feat res ccsciss sisceasceveeuicsebs ace s5s secseqessseace sdguetecugeauasiess is tuueydtesavsec R EE 29 CQUICUIND rcasessseesvadendib cites E E Aoatent Nii hee ieee ase E 30 IMMUN ASU Bs sices canes shcesactae sidesdbssecdbesigeavads shies dductanebssusntouseacesebsdeesitssouaanesoauedeaneess 30 Experiments 2553 ses cessdeveesiensacesnesscesecenedancsdendscastessiebedecd pusevodeienase sbvegsbaeaadaSetacensbes 31 Multiple Related PUD 8 2 s s5 sccscehcesesti Hote irese severe EEEE aE EEEE E 31 Multiple Unrelated Sets of Data eee eeeessesecseceeeseesecaeeeceseaeeersesaeseeeeeeeenee 32 MAGICAL II Macro Language oe e eee eeeeceeeeeeeeseeeeecaeesaecaeesaecseceaesneeeeeneens 32 Optional Specialized Software eee eeeeeceeseeseeseceeeeeeseeaeceseecsaesaeeeeeesasseeeees 33 1 4 Introduction to UNIX and VNMR Files ceeccccccesescessseceseeceesseceseeeeeceeesenssseeenenaes 33 UNIX File Systemi sassees cacdssecsndees scevscenss ces oroe eE E ENEE EAE EATE Ea 34 VNMR Directories and Files ccccccecesseeessecesecceeesnecesesaeecseeceeseeecseeaeeeseeeeneeee 34 NMR System Administrator and Other Users eseeccessessceeeeeee
207. button in the 1D Data Display menu or by entering the command menu size_1D Button Description Left Set display for left half of the screen page Center Set display for center of the screen page Right Set display for right half of the screen page Full Screen Return Set display for full screen page Display the 1D Data Display menu page 77 1D Plotting Menu The 1D Plotting menu is activated by selecting the Plot button in the 1D Data Display menu or by entering the command menu plot_1D Button Description Plot Plot the selected spectrum If the integral is currently displayed plot the integral as well Scale Plot an axis below the spectrum HP Params Plot parameters below the spectrum in a special format when the plotting device is a Hewlett Packard plotter Params Print parameters in the left upper corner of paper using English language format All Params Print parameters in the left upper corner of paper using mnemonic format Peaks Plot peak frequencies above peaks Page Plot out the currently buffered plot and change paper Return Display the 1D Data Display menu page 77 1D Data Display Secondary Menu The 1D Data Display Secondary menu is activated by selecting the More button in the 1D Data Display menu or by entering the command menu display_1D_2 Button Lines Integrals Dssh Dssa Getting Started VNMR 6 1B Description Display list of spectral l
208. cal cursors will be displayed on either side of the mouse arrow 01 999083 00 A1298 Getting Started VNMR6 1B 241 Chapter 9 Display Plotting and Printing 242 and a single vertical cursor will be displayed in the middle of the region where 1v1 was being updated The mouse will now control the first order baseline correction parameter tlt Clicking the left or right mouse button above or below the horizontal cursor will now increase or decrease t 1t and will also change 1v1 so that the total drift correction at the single vertical cursor in the middle of the previous region will be held constant This process eliminates or substantially reduces the necessity to iteratively adjust the two parameters 1v1 and t 1t As with the zero order correction placing the mouse arrow right on the horizontal cursor and clicking the mouse button will restore the initial baseline correction values Each time the mouse arrow is moved outside the two vertical cursors and the mouse button is clicked a new vertical and horizontal cursor is displayed The parameter adjustment alternates between adjusting only the 1v1 parameter and adjusting both the 1v1 and t1t parameters The left and right mouse buttons both adjust the baseline correction parameters and differ only in their sensitivity The left button causes changes a factor of eight times larger than the right button and hence you can consider the left button the coarse adjust and the right button t
209. calculated automatically when sw or at is changed If a particular number of data points is desired however np can be entered in which case at is calculated based on sw and np Values of at that give a number of data points not a multiple of 2 UNYINOVA UNITYplus and UNITY systems or 64 MERCURY VX MERCURY and GEMINI 2000 and VXR S will be readjusted automatically actually depends on the output board refer to the description of at in the VNMR Command and Parameter Reference 01 999083 00 A1298 Getting Started VNMR 6 1B 187 Chapter 7 Acquiring Data 188 ss is the number of complete executions of the pulse sequence not accompanied by data collection prior to the acquisition of the real data In a multi FID experiment if ss is a positive value the steady state pulses are applied at the start of the first FID only if ss is a negative value the steady state pulses are applied at the start of every FID nt is the number of transients to be acquired the number of repetitions or scans performed to make up the experiment To set up an indefinite acquisition set nt to a very large number e g le9 The parameter ct for completed transients is an informational parameter that changes during the course of an experiment to reflect the number of completed transients For normal 1D NMR p1 and d2 are zero The parameter d1 used to allow recovery of magnetization back to equilibrium is often zero as well reducing th
210. calls the macro paros to create the oversampling parameters oversamp oscoef oslsfrq osfb and filtfile While inline DSP is active the filter bandwidth parameter fb is set to Not Active 2 Set parameters sw and at to the values desired for the final spectrum 3 As required adjust the values of the oversampling parameters oversamp oscoef oslsfrq osfb and filtfile e oversamp specifies the oversampling factor 68 or less for the acquisition As a result no oversamp data points are acquired at arate of sw oversamp Once the data has been transferred to the host computer it is digitally filtered and downsampled to give np points and a spectral width of sw sw oversamp and np oversamp are limited by the values given in Table 30 Table 30 Maximum Values for sw oversamp and np oversamp Maximum Maximum System h n Sw oversamp np oversamp UNITYTNOVA 500 kHz 2M MERCURY VX MERCURY 100 kHz 256 K UNITYplus UNITY VXR S 100 kHz 512K GEMINI 2000 Broadband 100 kHz 128K GEMINI 2000 H 3c 23 kHz 64K The maximum np oversanmp is given for double precision data dp y For dp n multiply the value by 2 The value of oversamp might need to be decreased further for rapid arrayed experiments because of host computer memory and speed limitations Setting oversamp to n causes normal acquisition to be done without digital filtering e oscoef specifies the number of coefficients used in the digital filter The default is 7 5 ov
211. ccept button and remove the 50 ohm load from the tune port 12 After all three tests are finished click the Save button The old calibration files are moved to bak files and new calibration files std_ed cal std_es cal and std_er cal are calculated These files are stored in Svnmrsystem tune tunecal If the files cannot be saved the program produces a beep and an error message 13 Click the Close button To Restore the Previous Calibration File If you have an incorrect calibration file and do not want to re run the calibration tests restore the previous calibration files 01 999083 00 A1298 Getting Started VNMR 6 1B 123 Chapter 6 Preparing for an Experiment 124 1 Click the Calibrate button on the Tune Control Panel The Tune Calibration window opens see Figure 31 2 Click the Restore Backup button The program replaces the new calibration files with the bak files If the program does not find all of the backup files an error message appears z Tune Control Panel Exit Display Save 7 Center C13 75 455 JH To Restore the Original Calibration Files Span 10 000 MHz calibration r gt 3 i Calibrate System backup files can be installed by copying ee the following cal files on top of the Cursor Off Line Box Gr Cursor i 7 Displa corresponding sys files Marker 1 C13 75 455 ae e std_ed cal to std_ed sys Marker 2 off Expand std_es cal to std_es sys Marker 3 Off
212. cessing menu or by entering menu procpar_2D Button Description No WT Clear all weighting parameters Sinebell Select sinebell weighting over the whole FID length Pseudo Select pseudo echo weighting gt AV OR If labeled AV switch to the absolute value mode gt PH If labeled PH switch to the phase sensitive mode The value of the parameter dmg determines the button label FN Small Select Fourier number for quick transform Normal Select Fourier number for normal size transform Large Select Fourier number for large transform with zero filling Return Display the 2D Data Processing menu above 2D Interferogram Processing Menu The 2D Interferogram Processing menu is activated by selecting the Transform F2 button in the 2D Data Processing menu or by entering menu process_IF Button Color Map Adj Weighting F1 Transform Reprocess Description Display the Interactive 2D Color Map Display Main menu below Display the Interactive Weighting menu page 72 Perform second Fourier transformation along f1 Display the 2D Data Processing menu page 73 to repeat first Fourier transformation Interactive 2D Color Map Display Main Menu dconi Program The Interactive 2D Color Map Display Main menu part of the dconi program is activated by selecting Transform F2 or Full Transform in the 2D Data Processing menu by selecting Color Map in the 2D Interferogram Processing menu or by entering the comm
213. command 246 dscoef parameter 217 dseq parameter 194 dseq2 parameter 194 dseq3 parameter 194 dsfb parameter 217 dshim macro 139 dslsfrq parameter 217 DSP digital signal processing 209 compressing DSP FID files 293 dsp parameter 211 Dssa button 78 Dssh button 78 dtune macro 124 dwell time 185 E e macro 104 E shimming criterion 140 01 999083 00 A1298 eaddr command 283 285 Edit button 75 82 91 edit macro 197 edit text files 91 197 efficient mode decoupling 194 Eject button 55 eject button acqi 150 Eject button GLIDE 104 eject command UNIX 291 ejecting a sample 104 150 elist command 283 English language parameter format 78 261 enlarge graphics window 47 enter program 55 entering commands 94 entering VNMR 39 enumerated characters 96 enumerated string values 96 eread command 282 284 285 ernst command 188 errlog command 45 209 errloglen parameter 45 209 error codes 208 error handling control 134 error messages display 45 error messages on limNET 285 Ethernet communication 24 Ethernet network 281 ethers file 285 ewrite command 283 284 285 excellent shimming criterion 140 exit command 41 Exit VNMR button 46 91 exiting VNMR 40 51 91 Exp button 67 exp file name 277 expl through exp9 experiments 31 67 exp5 experiment 82 expactive command 208 Expand button 71 73 74 75 76 83 234 239 243 experiment abort 65 active
214. connection to public socket Client connection refused The limNET server is no longer functioning error obtaining internet host name The file etc hosts is not present or does not contain the address of the local node ether_hostton failure no such file or directory The file etc ethers is not present version 2 0 of limNET only This message is produced by the eaddr command and the limNET server Incorrect number of arguments Use exactly three arguments for eread and ewrite as described above Network timeout The local system software found the address of the remote node and attempted to send it a request but failed to receive a response This can occur if the remote node does not have limNET installed if the node is down or otherwise disabled if the Ethernet address for the 01 999083 00 A1298 Getting Started VWMR6 1B 285 Chapter 10 Storing Retrieving and Moving Data remote node is wrong if the Ethernet hardware has not been installed or configured correctly of if the local node is not physically connected to the network If this error message is a result of a read or write transfer initiated from a VXR Gemini or XL host the cause might be that the destination directory does not have read or write permission set for the world Public socket connect error Network unreachable Public socket connect error Connection refused Either one of these messages indicates that the local host is not connected to the Ethern
215. controlling the observe L O local oscillator line The first decoupler rf amplifier and preamplifier are gated only if dm y If dm n no gating of these signals takes place When homo y the parameter dmm should be set to c for continuous wave CW modulation Setting homo to n specifies no gating On UNITY and VXR S systems setting homo to y selects time shared decoupling which is appropriate for homonuclear decoupling in which the receiver is gated off when the decoupler is on Setting homo to n disables decoupler time sharing which is appropriate for heteronuclear decoupling or for cases in which the decoupler is off during acquisition 01 999083 00 A1298 Getting Started VNMR 6 1B 191 Chapter 7 Acquiring Data GEMINI 2000 broadband systems low band 0 to 63 5 dB 15 31 p steps of 0 5 dB tpwr 14 dB linear 0 to 1023 steps of 1 high band 19F 1H 0 to 63 5 dB steps of 0 5 dB dlp tpwr dpwr GEMINI 2000 H 8C systems low band 83e 0 5 or 1 W decoupler high band H full power pulses dhp for decoupling power 0 to 2047 homo decoupler steps of 1 dlp MERCURY VX and MERCURY systems 48 dB linear low band 20 dB step 1 dB dpwr tpwr 0 63 dB step1 dB r 48 dB linear high band 10 dB 20 dB step 1 dB tpwr dpwr 0 63 dB step 1dB homo decoupler gt Th dpwr 0 63 step 1 dB Figure 59 Attenuator Configurations Part 2 of 2 On
216. ct More than one command can be entered at the same time for sequential execution by separating each command with a space e g type ds 3 pl paand press Return Commands and parameters can also be interspersed on input e g nt 16 at 2 0 go Command Arguments Arguments for commands come in two types numeric and string e Numeric arguments can be integer or real although integer parameters are stored as real and can be entered with or without a decimal point e g 16 16 0 16 5 e Strings are distinguished by being enclosed in single quote marks such as SAMPLE 12 or 3456 Any character can appear between the single quotation marks but a few special characters such as a single quotation mark must be proceeded with a backslash if the character is to be enclosed within a text string for example You can t enter a single quote without special care To insert a backslash character itself in a string it must be used twice e g A B is written A B As do numeric arguments the string becomes an argument by appearing inside parentheses For example by using the command text the operator can store alphanumeric text in a file that accompanies the current experiment Thus to record a sample number and date the operator can enter text SAMPLE 307 3May Some text arguments are free form as in the text command just described In other cases however certain specific values of a text str
217. ctory e g exp1 but multiple shim commands can be queued Getting Started VNMR 6 1B 01 999083 00 A1298 7 4 Performing Acquisition To move an experiment to the head of the queue of a ae experiments to be submitted to the acquisition system enter the go next command This command coarse also has the effect of es e9 ae i synchronizing VNMR so 2 ee eee ee command execution with the e starting lock level 77 2 submission of experiments to current lock level 77 6 the acquisition system To accomplish this BLE Sa synchronization without SHIH coarse z x 1 best First putting the experiment at the 21 E 110 1 4 16 64 head of the queue enter the 22 i EEE a Ea EN go sync command 21C 105 1 4 16 64 Experiments do not need to 22C E 227 1 4 16 64e all be submitted at the same time If you have started an experiment in exp1 for example you might wait until that experiment is partially done and then using those partial results set up a follow on experiment perhaps a decoupling experiment in exp2 Later when exp1 has completed and exp2 is active you could set up a third experiment and use exp3 to set up and submit it Figure 62 SHIM Window During Acquisition acqi Program When an experiment is active on all systems except the UN TYINOVA you cannot use the Acquisition window to shim and th
218. d VNMR 6 1B 01 999083 00 A1298 4 11 Analyze Menus Button Description params Display parameters and allow for changes assign Run the dla program and display the Spin Simulation Line Assignment menu page 85 display Calculate and display the simulated spectrum iterate Perform an iterative optimization and display the resulting spectrum observe Fourier transform and display the experimental spectrum Return Display the Spin Simulation Main menu page 83 Main Display the Main menu page 66 Spin Simulation Line Assignment Menu The Spin Simulation Line Assignment menu is activated by selecting the Assign button in the Spin Simulation Secondary menu or by entering menu spins_assign Button Il use Il use fitspec auto assign iterate Return Main Description Perform a line listing on the current spectrum Use the last line listing as a reference for the line assignments Use last deconvolution as a reference for the line assignments Run the assign macro to assign lines for iterative optimization from a dll or n11 listing Perform iterative optimization and display resulting spectrum Display the Spin Simulation Secondary menu above Display the Main menu page 66 Deconvolution Menu The Deconvolution menu is activated by selecting the Deconvolution button in the Analyze menu or by entering menu fitspec Button Description Use Line List Use Mark Fit Results
219. d person is the generally the primary button Selecting choices from menus activating windows positioning cursors and similar actions are accomplished by clicking the left button or dragging the cursor with the left button held down e Within VNMR the center button of the mouse is always associated with vertical scale vertical scale of the spectrum of the integral of a 2D spectrum etc e Within VNMR the right button of the mouse is associated with the presence of a second cursor and is typically used for selecting expansions of 1D and 2D spectra The center and right mouse buttons are used with VNMR software only within the graphics window and when using the pulldown menus within the GLIDE user interface A special use of the left and right mouse buttons is in the Acquisition window such as setting the values of shims If you move the cursor over a button where is a number e g 1 and then press the left button the value shown reduces by the number on the button If you press the right button the value increases instead Specific functions will be described in conjunction with the relevant software Note that these buttons serve other functions within the windowing environment provided by Sun IBM or SGI Keyboard The operator enters commands parameters and other alphanumeric information into the data system through a keyboard The keyboard is similar to keyboards used with other computers with keys for letters and
220. d by selecting Write Pulse Sequence in the Secondary Main menu or by entering menu psg_main This menu is the first of seven menus to assist you in generating pulse sequences For detailed information about the menus and on menu driven pulse sequence programming refer to Chapter 2 Pulse Sequence Programming in the manual VNMR User Programming 01 999083 00 A1298 Getting Started VNMR 6 1B 91 Chapter 4 Using the VNMR Menu System 92 Configuration Menu The Configuration menu is activated by selecting the Configure button in the Secondary Main menu or by entering menu configure Button Description Show Output Devices Select Plotter Select Printer Hardware Return Show all printer and plotter output devices that have been defined as active on this system Select the next plotter on the list in vnmr devicenames Select the next printer on the list in vnmr devicenames Enter the config program the NMR system administrator vnmr1 must use config at least once to set up the proper system hardware configuration Display the Main menu page 66 Getting Started VNMR 6 1B 01 999083 00 A1298 Chapter 5 Using the Command Mode Sections in this chapter e 5 1 Commands this page e 5 2 Parameters page 94 e 5 3 Command Line Editing and Reentry page 96 e 5 4 Macro Automation page 98 Commands macros and parameters can be entered by typing them in the VNMR input window
221. d dm 2 to dmf 4 is inactive on UNITY but active on MERCURY VX MERCURY YINOVA and UNITYplus systems see the VVMR Command and Parameter Reference for details The macros dmfadj dmf2adj dmf3adj and dmf4adj adjust the values of dmf dm 2 dmf3 and dmf4 respectively when using waveform generator programmable decoupling Starting with VNMR version 4 2 significant changes were made in the values for the parameter dmm which sets the first decoupler modulation mode Although dmm c still sets the decoupler to continuous or single frequency decoupling the values of dmm s and dmm e in previous versions of VNMR are no longer valid and if used generate an error message Before VNMR version 4 2 dmm s could be used to set WALTZ 16 decoupling This is no longer true dmm w must be used to choose WALTZ 16 decoupling and dmm f must be used to choose fm fm efficient decoupling Several other efficient decoupling schemes are available on MERCURY VX MERCURY UNITYINOVA and UNITYplus systems and are chosen with dmm dmm g sets GARP decoupling dmm m sets MLEV 16 decoupling and dmm x sets XY32 decoupling Refer to the description of dmm in the VWMR Command and Parameter Reference for other modulation modes available In the standard two pulse sequence dmm normally has just a single state since the decoupler modulation remains normally unchanged during the pulse sequence Multiple states are possible for example dmm ccw
222. d minimum shimming time samples should be prepared to be the same height as much as possible Above 0 7 ml there is little sensitivity to sample length as long as the bottom of the tube is positioned properly You should make every sample up to the same height and obtain your shim values using samples of that height For Wilmad 528 or 535 tubes with no restricting plugs typical samples with volumes listed in Table 9 should be placed at the Volume Length Depth Range depths shown in the table where 700 uL 50 mm 68 mm 65 69 mm depth is the distance in mm from Table 9 Sample Tube Depths f 600 uL 42 mm 65 mm 63 67 mm the bottom of the green spinner 506 ut 7 D EA turbine to the bottom of the H er miii 00 04 mimi sample tube 400 uL 28 mm 59 mm 58 62 mm Sample Position Use the depth indicator provided to set the sample position to a repeatable position Figure 21 shows the depth indicators on the spectrometer for 10 mm and 5 mm sample tubes The larger spinner is available in both 10 mm and 5 mm versions To Position a Sample Using the Depth Indicator The procedure here is for the 5 mm tube using the larger spinner Other tube sizes and spinners are done similarly e Place the bottom of the flange along the line indicated in the figure and lower the sample until the sample tube bottom equals the Maximum Sample Depth line for the smaller 5 mm sample tube The length from the bottom of the flange to the bottom
223. d new horizontal and vertical cursors are displayed Subsequent first order phase changes causes the zero order phase to be adjusted such that the phase angle at the center of the previous region bracketed by the vertical cursors remains constant If you wish to return to the zero order phase correction the Phase button in the menu must be reselected The middle mouse button adjusts the vertical scale of the spectrum In addition it causes the latest phase correction to be applied to the entire spectrum To do this position the mouse arrow at the very top of a peak that is on scale and click the center button This leaves the vertical scale unaffected but recalculates the phase of the entire spectrum Clicking the center button above or below the peak raises or lowers the vertical scale To exit the interactive phasing mode make another selection from the menu the first button Cursor or Box is always an appropriate choice if no other choice is desirable Interactive Integral Reset Mode The resets button activates the interactive integral reset mode No cursors are displayed The left mouse button defines an integral reset at the current mouse arrow position The right mouse button removes an integral reset closest to the current mouse arrow position The middle mouse button adjusts the scale as described above The integral does not have to be displayed However if the integral is displayed in the partial mode the normally blanked
224. d then describes methods of controlling lock Lock loop time constant control is also described Table 15 lists the lock commands and parameters discussed in this section Getting Started VNMR 6 1B 01 999083 00 A1298 6 8 Optimizing Lock Table 15 Lock Commands and Parameters Commands acqi Open the Acquisition window acqmeter lt host gt Open the Acqmeter window lock Submit Autolock experiment readhw Read acquisition hardware values sethw Set acquisition hardware values lock related acgi lt par disconnect exit standby gt lt ret gt readhw parl par2 lt vall val2 gt sethw lt wait nowait gt parl vall lt par2 val2 sethw lock on off Parameters alock Automatic lock status in n Sw yT Lock and spin interlock lockacqtc Lock acquisition time constant lockgain Lock gain lockphase Lock phase lockpower Lock power locktc Lock time constant shimset Type of shim set z0 ZO field position alock y n a auto s samp u on UNTYINOVA alock y n a s on GEMINI 2000 MERCURY VX and MERCURY lockacqtc 1 2 4 7 12 48 in sec on UNTYINOVA lockacqtc N A on GEMINI 2000 MERCURY VX and MERCURY lockgain 0 to 48 dB 1 dB steps on UNTYINOVA lockgain 0 to 30 dB 10 dB steps on GEMINI 2000 lockphase 0 to 360 degrees in 1 4 degree steps lockpower 0 to 68 dB 1 dB steps on UNTYINOVA lockpower 0 to 40 dB 1 dB steps on MERCURY VX and MERCURY
225. d to learn to use MAGICAL II Optional Specialized Software Much advanced specialized software is available for VNMR including the following optional packages sold by Varian e Bayes software uses Bayesian probability theory to directly analyze 1D time domain data providing signal amplitude frequency and linewidth for all statistically significant resonances e Diffusion software performs acquisition and analysis for the determination of diffusion constants using the pulse gradient echo method e FRED software discovers carbon connectivities at previously unattainable levels of sensitivity FRED analyzes data from the insensitive but powerful carbon carbon connectivity experiment e STARS software simulates single pulse experiments on solids 1 4 Introduction to UNIX and VNMR Files The current VNMR software package runs in the Solaris 2 x computing environment which includes SunOS 5 x Sun s implementation of UNIX the OpenWindows and CDE windowing environments and desktop tools such as Clock and File Manager 01 999083 00 A1298 Getting Started VNMR 6 1B 33 Chapter 1 Overview of Varian NMR 34 No attempt is made in this manual to teach you more than is necessary about Solaris OpenWindows CDE and UNIX except for you to run VNMR Sun provides extensive information about their products both online and hard copy UNIX File System Like any high level system data on your disk is found in files which are
226. d use the same arguments as dfs e dfsn functions the same as dfs except the graphics screen is not erased before the display starts This allows composite displays of many FIDs to be created e dfsa displays one or more FIDs automatically by adjusting the parameters vo and ho to fill the screen in a lower left to upper right presentation wc must be set to less than full screen width for this to work The position of the first FID is governed by parameters wc sc and vpf e dfsan functions the same as df sa except the graphics screen is not erased before the display starts This allows the creation of composite displays of many FIDs e dfsh displays one or more FIDs horizontally by setting vo to zero and adjusting ho sc and wc to fill the screen from left to right with the entire array The position of the first FID is governed by parameters wc sc and vpf e dfshn functions the same as df sh except the graphics screen is not erased before the display starts This allows composite displays of many FIDs to be created The p1 fid command plots one or more FIDs as a stacked display This command uses the same arguments as dfs and functions the same as dfs except instead of displaying FIDs plfid plots the FIDs and instead of a screen color p1fid can be supplied with a pen number penl pen2 pen3 etc as an optional argument Whitewashed FIDs The dfww command displays whitewashed FIDs a display in which FIDs after the first
227. d used in the current experiment For routine operation on undemanding samples for example polymers with broad lines this may be completely sufficient The different computer controlled shim gradients are always set to the values at the end of the last shimming operation therefore it is never necessary to retrieve old shim values when starting a new sample If it is possible to assume that the previous sample was run by a reasonably skilled operator on a sample comparable to the current one shimming can be resumed where it was terminated on the previous sample This mode is selected by setting the parameter load n meaning do not load new shim values If on the other hand the state of the shims is unknown it may be preferable to start by resetting the shims to known values This is done by retrieving a set of shim values or by entering values as desired and then setting load y followed by su 01 999083 00 A1298 Getting Started VNMR 6 1B 137 Chapter 6 Preparing for an Experiment 138 Shim settings can be stored to reflect different combinations of probe solvent sample height nucleus or magnetic environment At a minimum a shim set should be saved for each solvent name cdc13 acetone etc Using the Input Window to Save Shim Coil Settings Enter svs file where file is the name of a file for saving shim coil settings e g svs acetone If file is an absolute path svs uses it to save the file Otherwise it saves
228. data conversion Converting Text Files Text files have a different format the byte order is reversed on the UNIX based systems than they do on VXR style systems To enable moving text files such as pulse sequences from one system to another the following commands with the file names as arguments perform a format conversion The syntax for UNIX text to VXR style text From VNMR unix_vxr UNIX_file VXR_file From UNIX unix_vxr UNIX_file VXR_file Getting Started VNMR 6 1B 01 999083 00 A1298 10 5 Converting Data Between Systems Table 50 Data Conversion Commands Commands convert VXR_file Convert data set from VXR style system convertbru file lt options gt Convert Bruker data VNMR convertbru file lt options gt Convert Bruker data UNIX cpos_cvt VXR_file Convert data set from VXR style system UNIX decomp lt VXR_file gt Decompose a VXR style directory sread file lt template gt Read converted Bruker data into VNMR unix_vxr UNIX_file VXR_file Convert UNIX text files to VXR style VNMR unix_vxr UNIX_file VXR_file Convert UNIX text files to VXR style UNIX vxr_unix VXR_file lt UNIX_file gt Convert VXR style text files to UNIX VNMR vxr_unix VXR_file UNIX_file Convert VXR style text files to UNIX UNIX The syntax for VXR style text to UNIX text From VNMR vxr_unix VXR_file lt UNIX_file gt From UNIX vxr_unix VXR_file UNIX_file In using this syntax VXR_file cannot be the same as UN
229. developed to run as a part of GLIDE interface or to automate systems with sample changers but they can be used directly by the user or modified as needed The following tables in this section list automation macros according to type e Table 5 lists automated acquisition macros e Table 6 lists automated calibration macros e Table 7 lists automated plotting macros e Table 8 lists automated processing macros For further information about these macros refer to the entry for the macro in the VVMR Command and Parameter Reference or examine the source code for the macro in the maclib directory Table 5 Automated Acquisition Macros Macros autolist Set up and start chained acquisition c13 lt solvent gt Automated carbon acquisition capt lt solvent gt Automated carbon and APT acquisition cdept lt solvent gt Automated carbon and DEPT acquisition 19 lt solvent gt Automated fluorine acquisition getdim dimensions Return dimensionality of experiment hl1 lt solvent gt Automated proton acquisition he lt solvent gt Automated proton and carbon acquisition heapt lt solvent gt Automated proton carbon and APT acquisition hecorr lt solvent gt Automated proton carbon and HETCOR acquisition hcdept lt solvent gt Automated proton carbon and DEPT acquisition hcosy lt solvent gt Automated proton and COSY acquisition p31 lt solvent gt Automated phosphorus acquisition autolist
230. dow secesecseeseeseeeeerteeeeeeaees 270 Saving VOUT Plot sisiraan eai a EEA E O E RE 270 Printing Your Plot nicieni E REES 270 01 999083 00 A1298 Getting Started VNMR 6 1B 11 Table of Contents Getting Help rrecn ariere ns sabeca chee Wacwset sve NTER EERE ENSE 270 Exiting Plot Designer s scssscasssssaredancsseasSbstsiesbeiaeseubssedeesnssevvantaanseaaiesbacsneeas 271 99 PANUS sanae aea E E E E E aasteaae abe 271 9 10 User Controllable Line Drawing sesessesesssesrssreresrsressesresesreresreserrererresrerssreresre 272 Chapter 10 Storing Retrieving and Moving Data ss secesssssereeeeees 275 10 1 Working with Directories and Files sseessesessesesessesrsssresssreersrterrsresesreseerrsrenrsreesss 275 Default DireCtOry secuencia engien iiia a a cece nii aao esaii 275 Creating and Manipulating Directories essseeesseeessresreresreesreresresrsrrerrrresrereee 276 Creating and Manipulating Files seseeeessesesseresessesrsrresrsrssreresrrsesresrsreerrrresrerese 276 10 2 Storme Dala sessrreecicpc tnc iseer a E E EE Ea REE EE TEE ESERE SE 277 Experiment HUES sraon ere eree rnEeE a OE AEEA NEE EA AAE EAA 277 OAVINE Data iss cccrctavedopesstassbtecesccanhtusesdepsctvacedaanvbnd sdavaensasesedsdsusbevaessdaaseadscbossduecs 277 Saving Parameters on isis sahvs causes cesvesecades lenstsesebevbsvaes s enen Ea EE CERN SEEE TEE EENES 278 Saving Shim Coil Settings sc sccsssesccasescescsesssssuncsoasessvacssasesea
231. dpar the entries shown are typically for following directories C13 par F19 par Hl par H2 par N15 par P3l par Using the Inout Window e Enter the command 1 lt directory gt where directory is the name of the directory containing the parameter sets e g 1f vnmr stdpar or 1 vnmr tests To list parameters sets if any exist in your home directory enter cd then 1 The command cd with no argument changes to your home directory by default 108 Getting Started VNMR 6 1B 01 999083 00 A1298 6 3 Retrieving Parameter Sets To Recall Any Parameter Set You can retrieve an existing parameter set a number of ways Once a parameter set is recalled the text window displays the retrieved acquisition and processing parameters for the set in the text output window Using GLIDE GLIDE can also be used to retrieve data However use this method to retrieve only data on parameters and FIDs Perform the following steps to retrieve data with GLIDE 1 Activate GLIDE by clicking the GLIDE button in the Main Menu 2 Click on Recall 3 Inthe Recall Setup window type the full path of the FID file that you want 4 Click on Retrieve The data file is recalled If the data was acquired with GLIDE the def files are also recalled into GLIDE Using the CDE File Manager This method can be used to retrieve data on parameters FIDs or shim files To use this method the 1istenon macro must be or must have been execu
232. drawing 272 list of choices 36 number of pens 255 pen number 272 plotter devices 92 queue 255 resolution 256 selection 257 size of plot area 255 312 Getting Started VNMR 6 1B speed 257 plotter parameter 255 plotting automated 99 general rule 232 plotting commands 254 plp macro 250 pltext command 262 pltmod parameter 249 points to Fourier transform 223 pop up menu 150 portrait view plot configuration 270 Pos Only button 80 position plots and displays 250 postacquisition DSP 210 217 Postscript devices 262 PostScript output 255 Postscript raster printers 255 power mode 225 ppa macro 261 ppf command 249 ppm scales calculation 183 ppm to plotter units 273 ppm units 95 pps command 189 preacquisition delay 187 preamplifier saturation 227 preparing samples 101 preprinted chart paper 262 previous command line 97 primary lock 206 print all parameters 261 exponential least squares analysis 81 gray scale image 80 parameters 78 80 261 text file 271 working directory 37 Print button 81 printcap file 271 printer attached to computer 36 devices 92 list of choices 36 printing 271 color printing 257 printoff command 271 printon command 271 Printout button 82 probe 23 25 insertion 113 protection 198 removal 112 ringing 227 tune interface panel 114 tuning 25 113 116 probe file macros 113 probe file parameter 113 probe_protection parameter 198 proc pa
233. e Off mode The frequency positions of the cursors as well as the delta and the signal amplitudes are displayed on the bottom of the Tune Display window Grid In the Grid field select Off or On see Figure 28 to control a grid display in the Tune Display window The grid helps in reading the reflected power levels off of the graph The grid does not slow down the drawing time of the graph Markers In the Marker 1 Marker 2 and Marker 3 fields the Tune Control Panel provides three markers for marking fixed frequencies Each marker has a pull down menu see Figure 29 that lists the same nuclear frequencies and the Center pull down menu Each marker also has an entry field for entering a frequency You can use markers for observing fixed frequencies for example the two nuclear frequencies of a double tuned probe You can then vary the span and the markers will appear and disappear depending on whether their frequencies are being scanned in the current experiment Attempting to set the markers to values beyond the system frequency limits causes the message window to beep and produces an error message To Change the Vertical Scale TJ Tune Control Panel Exit Display Save Help Center C13 75 455 MHz MHZ G3 Gta Span 10 000 Cursor Off Line Box Grid Off On Marker 1 C13 Marker 2 lt __ H1 300 050224 Marker 3 H2 46 059600 H3 320 047397 He3 228 5
234. e forexample pen graphics red A drawing mode xor or normal for the graphics window output can be specified In the xor mode if a line is drawn such that one or more points of the line are in common with a previously drawn line the common points are erased In the normal mode the common points remain The default mode is normal move lt graphics l plotter gt x y sets an absolute location with coordinates x and y such as move 10 20 This becomes the point from which to start drawing the line draw lt graphics Il plotter gt lt xor l normal gt x y draws a line with attributes set by the pen command from the current location set by the move command to the absolute location with coordinates x and y The pen move and draw commands below show two typical sequences of commands In the first sequence a yellow line is displayed on the graphics window at the th level 1 pen graphics yellow Select the graphics window and yellow as the active color move wcmax Sc wc vpt th Move to left edge of chart as x and the threshold level as y draw wcmax sc vp th Draw a line to the right edge of the chart and at the threshold level as y In the second sequence two cursors are drawn on the plotter using pen 3 1 pen plotter pen3 Select the plotter and pen 3 move wcmax sc wc cr sp wp 20 Move to the cursor position along x and the bottom of the chart along y draw wc
235. e Contents of a Directory on a Remote Node The elist command displays a listing of the contents of a directory on a remote VXR style system The syntax is the following From UNIX list remote_node remote_dir From VNMR list remote_node remote_dir where remote_dir is the name of the directory on the remote system For example entering from UNIX elist gemini fidlib or entering from VNMR elist gemini fidlib provides a list similar to the following APT DR 5 45 HETCOR DR 5 141 C13 DR 5 45 DEPT DR 5 144 H1 DR 5 23 COSY DR 5 141 The contents are listed in the order they appear in the remote directory To Display Local Node Address The eaddr command address of your local node This command is entered without arguments and can be used from either VNMR or the UNIX shell File Suffixes Whenever limNET is used to transfer a file from a VXR style Gemini VXR 4000 or VXR system to a UNIX based VNMR MERCURY VX MERCURY UN YINOVA UNITYplus GEMINI 2000 UNITY or VXR S system a suffix is appended to the UNIX file name by the VNMR system This lets other software on the VNMR system know what type of VXR style file the UNIX file represents 01 999083 00 A1298 Getting Started VYNMR 6 18 283 Chapter 10 Storing Retrieving and Moving Data 284 Similarly when limNET is used to transfer a file from a VNMR system to a VXR style system the VNMR system uses a suffix to determine what kind of V
236. e Setup menu which is used to set up a new NMR experiment To complete the setup additional menus can be displayed from the Setup menu to select the nucleus solvent and pulse sequence Setup Menu The Setup menu is useful for setting up new experiments from scratch or modifying existing experiments for example switching from a normal 1D carbon experiment to an APT experiment You can also enter menu setup to display the Setup menu Button Description H1 CDC13 Set up a standard proton experiment with CDC13 as solvent C13 CDCI3 Set up a standard carbon experiment with CDC13 as solvent Nucleus Solvent Display the Nucleus Selection menu page 68 to set up a standard experiment using menus to select nucleus and solvent Sequence Display the 1D Pulse Sequence Setup menu page 68 to select a sequence from a list of 1D and 2D pulse sequences App Mode Display the Applications Mode menu page 70 Acquire Display the Acquire menu page 70 01 999083 00 A1298 Getting Started VNMR 6 1B 67 Chapter 4 Using the VNMR Menu System 68 Nucleus Selection Menu The Nucleus Selection menu sets the value of the transmitter nucleus parameter tn using input from the user then displays the Solvent Selection menu The Nucleus Selection menu is activated by selecting the Nucleus Solvent button in the Setup menu by entering the command setup or by entering menu nucleus Button Description H1 Set nucleus for H H
237. e User Guide Solid State NMR e User Guide Imaging e VNMR Command and Parameter Reference e VNMR User Programming e VNMR and Solaris Software Installation All of these manuals are shipped with the VNMR software These manuals other Varian hardware and installation manuals and most Varian accessory manuals are also provided online so that you can view the pages on your workstation and print copies Types of Varian Spectrometer Systems In parts of this manual the type of system Y YINOVA MERCURY VxWorks Powered shortened to MERCURY VX throughout all manuals MERCURY GEMINI 2000 UNITY plus UNITY or VXR S must be considered in order to use the software properly e UNITYINOVA and MERCURY VX are the current systems sold by Varian e UNITYplus UNITY and VXR S are spectrometer lines that preceded the UN YINOVA e MERCURY and GEMINI 2000 are a separate line of spectrometers that preceded the MERCURY VX 22 Getting Started VNMR 6 1B 01 999083 00 A1298 Chapter 1 Overview of Varian NMR Sections in this chapter e 1 1 Varian NMR Spectrometer System this page e 1 2 User Interface page 25 e 1 3 Advanced Features page 29 e 1 4 Introduction to UNIX and VNMR Files page 33 1 1 Varian NMR Spectrometer System The Varian research NMR spectrometer system consists of four major units e Host computer A workstation that controls the spectrometer thus receiving most of your attention in day to day use As
238. e a decoupled spectrum without NOE pl pw dl d2 at A B Cc Figure 57 Logical Periods A B C in Standard Two Pulse Sequence Observe Transmitter and Decoupling Parameters On all systems transmitter power levels are set through attenuators which are in turn controlled through a number of parameters Figure 58 and Figure 59 show schematics for the attenuator configuration for different systems The parameter t pwr sets the observe transmitter power which is under computer control on systems with linear amplifiers tpwr can be given values from 0 to 63 or from 16 to 63 depending on the range of attenuators present in the system In both cases 63 is the maximum possible power The first decoupler mode parameter dm determines first decoupler output if dm y the first decoupler is on and if dm n the first decoupler is turned off On YNITYYZNOVA and UNITYplus systems setting dm to a or y specifies the asynchronous mode In this mode the decoupler rf is gated on and modulation is started at random places in the Getting Started VNMR 6 1B 01 999083 00 A1298 7 2 Setting Pulse Sequence Related Parameters UNITY NOVA and UNITY plus systems for all channels 60 GB linear 16 to 63 dB 0 to 4095 steps of 1 steps of 1 dB tpwrm dpwrm dpwrm2 dpwrm3 tpwr dpwr dpwr2 or tpwrf dpwrf dpwrf2 dpwrf3 dpwr3 dpwr4 UNITY and VXR S for systems with linear amplifiers 6dBlinear 0 to 63 dB or
239. e spin rate is at the requested rate 01 999083 00 A1298 Getting Started VNMR 6 1B 43 Chapter 2 VNMR Basics 44 Input q window Abort Acq Cancel Cmd GLIDE Main Menu Help Flip Resize Menu Workspace Setup Acquire Process Display Analyze File DATA AutoProcess Autoplot More buttons Graphics window dg interface VNMR Display Screen The VNMR display screen shows the operator what is happening with the data Figure 9 shows a typical configuration of the windows in the display screen after logging in on a data station system not configured for acquisition Status window a vnmr ma Seq stdih Exp 1 Index 1 Acquisition Sample Acq amp Obs Spect width 5998 8 Hz o Nucleus ia Date Jul 29 96 Decouplers Acq tine 250183 sec f Spect Freq 400 075 miz File fidld fid Acquired complex pts 15008 offset 0 0 Hz of Solvent _ enci3 Sequence Recycle delay io sec muf obs pulse 7 75 us temperature 29 Ta riage Bion Transients ie pover 55 Steady state fo Process Calibration Channel Nucl Status Process2 p i a panne pi 2 pulse 7 75 us Observe HL aie power 55 Decoupler Hl mn Decoupler2 display2 Decoupler3 Gradient Type nng Label tabs Figure 9 VNMR Display Screen We will describe these windows according to their position in Figure 9 but like other windowing systems you can move and clo
240. e su command which is used to set up the spectrometer hardware for temperature changes probe tuning etc is irrelevant but would be queued if started from another experiment On UN YINOVA systems you can shim on your sample while an acquisition is in progress see Shimming During an Acquisition on page 200 Chained Acquisition The autolist macro sets up parameters for chained experiments by executing the experiments given as arguments and then starting a chained acquisition for example autolist h1 c13 dept The macro au is executed as part of autolist and should not be included in the arguments to autolist To start a new experiment based on the results of another experiment use the wexp parameter To prevent another queued experiment from being started between two experiments use the wait argument with the macros go ga and au wait specifies that no acquisition will be started until wexp processing of an experiment is finished Use the next argument to change the processing order of experiments next puts an experiment next in line to the front of the queue for acquisition next is most useful for chained acquisitions and in automation 01 999083 00 A1298 Getting Started VYNMR 6 18 201 Chapter 7 Acquiring Data 202 If a third experiment is to be started based on the results of the first or second experiment use both the wait and next arguments with au The resume command re enables exp
241. e the signal of a frequency standard such as TMS or any line such as a solvent signal with a known chemical shift in ppm or a position in the spectrum where you expect such a line to appear rfp Reference position The difference between the reference line and the reference frequency zero position of the scale in Hz If you reference a spectrum using the signal of a frequency standard such as TMS then rfp is 0 The distance of the reference frequency from the right edge of the spectrum is rfl rfp sfrq Spectrometer frequency The absolute frequency in MHz of the center of the spectrum the transmitter position In order to see the accurate value of the s frq parameter you should use the spc f rq command reffrq Reference frequency The frequency in MHz of the frequency standard i e the zero position of the frequency scale and the divider unit for the calculation of ppm scales refpos Used only for internal housekeeping and is normally set to zero It also indicates whether the referencing is used on or not refpos n The r1 command is used to reference a spectrum based on the current cursor position If you want to reference the spectrum based on a line position in the spectrum first use the nl command to place the cursor at the exact position of that line If no argument is given r1 defines the current cursor position as the reference frequency reffrq sfrq cr rfl sw 2 le6 At the same t
242. e total pulse sequence to a pulse of pw us followed by an acquisition time at in seconds Before each pulse the receiver is gated off for rof1 us rof1 is normally fixed as 10 us On systems where the amplifiers are normally blanked to give the best possible signal to noise i e they are turned off when the receiver is turned on pulse sequences must be written so that the receiver is turned off for a sufficient time prior to a pulse to allow the amplifier to fully turn on before the start of the pulse Most pulse sequences are written so that this time is rof1 On INOVA and GEMINI 2000 systems the receiver is off during the pulse sequence and on only during at The amplifier can be unblanked at any time but no longer than 10 ms Blanking and unblanking are implicitly done around pulses After the final pulse in each pulse sequence the receiver is gated off for rof2 us before the acquisition begins If pulse breakthrough effects are seen spike in the beginning of the FID increasing rof2 can reduce or eliminate the problem The parameter pw90 stores the length of the 90 pulse in us This parameter is not used by pulse sequences directly but is used by a number of commands to assist in setting up special experiments It is also used by certain output programs to be able to print the value of the pulse width in degrees instead of us Setting this parameter is the responsibility of the operator and is a function of the sample
243. e weighting r gt ft lt options gt lt nf gt lt start gt lt finish gt lt step gt gt ft inverse exp_num expansion wft lt options gt lt nf gt lt start gt lt finish gt lt step gt gt wft inverse exp_num expansion Macros gaussian Set up unshifted Gaussian window function pi3ssbsq Set up pi 3 shifted sinebell squared window function pi4ssbsq Set up pi 4 shifted sinebell squared window function sqcosine Set up unshifted cosine squared window function sqsinebell Set up unshifted sinebell squared window function Parameters awc n number Additive weighting const in directly detected dimension dcrmv string Remove dc offsets from FIDs in special cases fn power of 2 number Fourier number in directly detected dimension gf n number in sec Gaussian function in directly detected dimension gfs n number Gaussian shift constant in directly detected dimension 1b n number Line broadening in directly detected dimension math 1 f Fourier transform mathematics sb n number Sinebell constant in directly detected dimension sbs n number Sinebell shift constant in directly detected dimension wtfile file User defined weighting in directly detected dimension Although the system allows the combination of sinebell exponential and Gaussian weighting a combination of those can be difficult to understand and should only be used after experimenting with the individual parameters The use
244. eak s of interest 3 Enter gf 4 Inthe Acquisition window click on Connect FID Spectrum 5 Ifthe spectrum is not at the correct vertical intensity adjust the vertical scale multiplier with the up and down buttons 6 Ifaphase correction is required click on IPA in the PANEL menu then adjust phfid as an alternative to rp hence phasing the spectrum Getting Started VNMR 6 1B 01 999083 00 A1298 6 10 Using the Acquisition Window 7 Click on Shim in the PANEL menu then shim in the normal way using the lineshape of the peaks as a shimming criterion 8 If the sample is not locked adjust z0 to shift the spectrum 9 If you wish to make changes to the display such as altering sp wp make the changes in VNMR by entering the command ds to display the spectrum and altering the required parameters When you have a satisfactory display enter gf or acqi par to send the changes to the Acquisition window Then click on LOCK FID The next display should reflect the changes SHIM Display The SHIM display appears when the SHIM button is clicked from any Acquisition window Figure 46 shows a typical SHIM display The buttons at the top of the window CLOSE LOCK FID LARGE and the menus and buttons in the lower panel SHIM x1 best shim adjustment first lockgain were described previously In the upper panel are the SPIN and SHIM menus e SPIN sets sample spinning on or off This menu was described in t
245. ecceeseecseeseeeceeeeeeeseecsecaeecaecsasaecsaeeaeeneensees 113 Probe Timing Commands iss isselsaciseececgasicveesicestetediScisesehadassesncunceceetesverdedscnseeseevbes 113 Sample Spinning Commands and Parameters eee eee eeeseeeseceeeeseceeeeaecnaeeecnseesees 128 Lock Commands and Parameters e cee eeceeeesecscesseceeesaecseaecseeseceeeeseeeeeeseeseaeeeaes 131 Homogeneity Adjustment Commands and Parameters 000 0 eeeeceeeeeeeeeeeeeeeeenes 137 Permissible Shimming Criterion Values oo eee ce cssessecsseeseceeeeeeeeeeeeeeeeeeseneeaeeenes 140 Codes for Standard Shim Gradient Combinations 0 eeeeeccsecseeeeeeeeeeeeeeeeaeeeeeeeene 141 Hexadecimal Codes for Shim Groups cssececeseeeseeceeceeeeeesecnecaeesesaeeaeeaeeacaeeeseeeeas 143 Interactive Acquisition Commands and Parameters 00 eee eeeeeeeseceeeeceseeeeeeensees 148 Gradient Shim Availability viecsaiceiascisiesciscttes yl ccuacesheebstbesacevcasbsaave ovcessassncasnsebeesvnstes 168 Gradient Shimming Commands and Parameter cc eeseeeceeceseceeeeeeeeeeeeeeeeeeseeenes 169 Typical 2H Gradient Shimming Parameters for Common Solvents seeeeeeeee 174 Acquisition Frequency Related Commands and Parameters 00 0 0 eee eeeeeeeeeeeeees 184 Acquisition Pulse Sequence Related Commands and Parameters eee 186 Experiment Text File Commands 000 0 eee eeceeeecseseeeeceseeeeecaeeceecaeecaecaeaessaeeaeensensees 197
246. ecoupler modulation frequency Temperature Related Control For systems equipped with the optional variable temperature controller the t emp command opens the Temperature Control window shown in Figure 60 The Temperature Control window can be used for the following purposes Turn off temperature control e Set temperature control on at a specified temperature in degrees C 01 999083 00 A1298 Getting Started VNMR 6 1B 195 Chapter 7 Acquiring Data 196 e Enable temperature control from within an experiment using Temperature Control the temp parameter y Turn temperature control off and the su go ga Turntemperature controlon at 30 degrees C or au commands 30 and macros E EES 150 100 50 50 e Alternatively turn off experiment Experiment Control control of the E Allow temperature control in an experiment with go temperature and Vv allow only the Vv Temperature Control Reset YT Press Reset YT when VT cable is reconnected toa probe window shown in _ResetvT Figure 60 and the command sethw to set the temperature Figure 60 Temperature Control Window e Reset the temperature controller when the temperature cable is reconnected to a probe If the temperature is controlled only through the Temperature Control window two actions to be taken after a temperature error can be selected e Display a warning but continue acquisition e Stop acquisition and display a warning
247. ectory Display the Files Main menu page 87 Getting Started VNMR 6 1B 89 Chapter 4 Using the VNMR Menu System 90 Files Data Menu The Files Data menu is activated by selecting Data in the Files Main menu or by entering files files_data Button Description Load Save FID Show Shims Load Shims Save Shims More Return First mark one file in the files display and then click on this button If you have selected an entry that has Varian NMR data including data from a Gemini VXR or XL system that parameter set and data is loaded into the current experiment If it is a parameter set only the parameters are loaded Show prompt File name enter name and lt return gt and save data in current experiment there Show the contents of the system shim directory the shim directory in the VNMR system directory and the user shim directory the shim directory in your VNMR user directory First mark one file in the files display and then click on this button If you have selected an entry that is an NMR data set the program loads the shims stored with that NMR data Otherwise the program assumes the entry is a shim data set and attempts to load the shims from that entry Show prompt File name enter name and lt return gt and save shims in current experiment there Display the Files Data Secondary menu below Display the Files Main menu page 87 Files Data Secondary M
248. ed to the log file if the lock level falls below a preset hardware level about 20 on the lock meter or if the spin parameter is set to a particular value and the spin speed goes out of regulation however acquisition is not stopped e y makes the system check the lock level and spin speed Acquisition is halted if the lock level falls below a preset hardware level about 20 on the lock meter or if spin is set to a particular value and the spin speed goes out of regulation The in parameter can be set to one or two characters e If set to two characters the first character specifies the action for lock failure and the second character specifies the action for spinner failure e If set to only one character that character specifies the same action for either lock or spinner failure Lock Loop Time Constant Control During acquisition the lockacqtc parameter sets the lock loop time constant the time constant by which the lock feedback corrects disturbances of the magnetic field On a UNITYINOVA or UNITYplus lockacqtc is 1 2 3 or 4 which corresponds to time constants of 1 2 4 7 12 or 48 seconds respectively On a UNITY or VXR S lockacqtc is 1 or 2 for 1 or 200 seconds MERCURY VX MERCURY and GEMINI 2000 do not use lockacqtc When the system is not performing an acquisition idle lock display shim display FID display autoshim etc the Locktc parameter not available on MERCURY VX MERCURY and GEMINI 2000 controls the
249. eeaeeeneeaes 288 Converting Bruker Data s ccci ssssssscscssestisestesessedecsssovensesossoeessessasedeaseaasegaanscases 289 10 6 Magnetic Tape Operations o s ccccscsciesscsuts sicdesestestevestavsesoesetevessvensasavstesestsenssesbess cases 289 Reading Tapes from Gemini VXR 4000 and XL Systems 0 0 eee eee 290 Reading Bruker Data Files from 9 Track Tape 0 0 cece eeeese eee ceseeeeeeseeeeeeeeees 290 Sharing a Tape on a Network ooo ceceeseceseeseceeceseceeeeeeeeeeeeeeeeeaeeeaeeaaeeaeeaee 291 Moving Data to PCs and Macintoshes via Floppy Disk 00 eee eee eee 291 19 7 Compressing Data crase sivssvescnsev soncosteectenenseesssesatetesusentaguissiateteseteansenesscests 292 Compressing and Uncompressing FID Data Files o oo eeeeeeeee cere 292 Compressing Digitally Filtered FID Files oo eee cee eese cee ceseeeeeeseeeeeeeeeee 293 Compressing Double Precision VNMR FID Data o00 eee ceeeeeeeeeeeeeeeeeee 293 7 s 9 Jane ee eee ee ee ee eee ee 295 WAGON E sess gunaseesaasenavansessanesssessacsenasienaciexesdenessdaczadsenaaie 299 12 Getting Started VNMR 6 1B 01 999083 00 A1298 List of Figures Figure 1 Magnet Probe and Associated Electronics ccccesceeseesseeseeseeeeeceeeseceeeeaeceeceseeerensees 26 Figure 2 VNMR Display Screen nesesario iets esse dc aS ace Eae a get Enae A a aie 27 Figure 3 GLIDE User Interface oe ee eesscseeseessesecsceecesesaeeeceeesaesecsceeecneeacsecaecaseeeeaecaseserenaeeees 28 Pigu
250. eecceeceseneeeeceecneeseescenecaeeeeaecaeeeceeseaeeees 51 Figure 18 GLIDE User Interface Window ou ee essseecesessseeceseseseeseenecsceacesecaecoseeeaecasseeeeenaeeees 53 Figure 19 COSY Customization Window sescseccesessseeceecssesesreeecsceseesecaecaseeesaecaseeeeeesaeeees 57 Figure 20 HMQC Customization Window 0 eesesesssesecseesceeesecaceecesesaeeeseesseseeseeseeneeseeeeen 57 Figure 21 Sample Depth Indicator ote eesessesecsceecesesseeeceeesseneeseceeenecseeseenecaeeeesaeceeeeseessaees 103 Figure 22 TUNE INTERFACE Panel oo esessesecsceecesesseeeceecssesecscceeeneescsecnecaseeeeaeceseeeeeesaees 114 Figure 23 Probe Tuning Window qt une Program ou eee eeceseeceeeeseeneeseeeeesecaeeeeeaeeaeeeseeeeaees 117 Figure 24 Minimal Display Mode for the Tune Display 0 eeeeeeeseseceeceeseeseeeeeeeeaeeereeeerenee 118 Figure 25 Tune Control Panel qt une Program oo eceeeseseeeecseceeseeseceeeeseeesaecaseecsecneeeeeseenes 119 Figure 26 Pull Down Menu for Center Frequencies 00 0 scecesessesecseeeeeseeseceeeeceaeseeeeceeenaeneeeees 119 Figure 27 Pull Down Menu For Span eecsesssecseesessesseeeceeceaesceeceesneeseeseenecaeeeesaesaseeseeseaees 120 Figure 28 Cursor and Grid Controls eeceesessssecsceccesesseeeceecsaesesscceeeneeseeseenecaeeeeeaecaseeseeesaees 120 Figure 29 Pull Down Menu for Marker 1 oo cece eecsecsesessecseeeceseeceseeeecneeseesecnecaeeeeeaecaeeeeeessaees 121 Figure 30 Scale Conttols si2 2105 iesetise
251. eeceecaececeseeeeeseeeeeeeeees 174 Homospoil Gradient Shimming for or eea ener nee 174 Full Deuterium Gradient Shimming Procedure for Lineshape eee 175 General User Gradient Shimming o00 ee ee ee ceeeeeceeeeeecnecesececeseeeeeeeeereneeees 176 Suggestions for Improving Results eee eeceseceeceseeeeeeseeeeeeaeeeeseaeeeneeaes 176 Gradient Shimming Menus 0 00 cece eeeeceeeeeeeeceeeeeceeesaecaeceaeceeceaeseeeeeeereeetees 177 Chapter 7 Acquiring Data cies ccscse sei sdedenec ee ececcccntvadaveaaedntexiaceneteateeeaatenece 183 7 1 Setting Frequency Related Parameters 0 0 0 0 cecesceseeseceeceeceeceseeeeeeseeeeseeeeeeeeaeeees 183 Frequency Setting ieissar ceio e ae een E eeror E a R RE ares E a Esisi 183 Transmitter and Decoupler Positioning essseeeseeeeseseseesesreseereresresrrreerrrresrerese 184 Spectral WiNdOW sssini E E REO EEE 185 7 2 Setting Pulse Sequence Related Parameters ss ssseeeseeeesssreseseesrsreserrrerreresreresreresre 185 Standard Two Pulse Parameters essseseeseeeesseeesesresesresrereererrereeresreresreerrrrereens 187 Commands for Setting Parameters eeeseesessereeesseersreesrsrssresesreesresrsreererresrereee 188 The Status COMES Pt esis s seceicd salaadsscteatess ean esnea EEEE EE EENE EE NEEESE E 190 Observe Transmitter and Decoupling Parameters esesseeeseeeseseeersrrerrrrereerse 190 Decouplet Modes a s seicsscseisebscaecesisssa hisses tasbhjocuhaysetsdtuentvoassin ses pudeechaveb
252. een To return to the standard size graphics window click the SMALL button notice that the SMALL button appears in place of the LARGE button when the LARGE button is selected 01 999083 00 A1298 Getting Started VNMR 6 1B 149 Chapter 6 Preparing for an Experiment 150 If the spin control hardware is installed the Acquisition window also contains the SAMPLE menu with the following choices insert Turns off the eject air waits for the sample to slowly drop then turns off the slow drop air After sample is seated all buttons are displayed again eject Turns on the eject air and slow drop air to eject the sample from the probe At this point most buttons disappear and a sample must be inserted or at the least the insert button selected before continuing Making a Choice in a Display As you make choices in the LOCK FID Spectrum and SHIM displays the contents of the window change and the indicated actions take place To make a choice in a display the quickest way in most cases is to move the mouse cursor arrow on top of the choice you want then click once with the left mouse button To see the range of choices for a menu 1 Move the mouse cursor arrow to the menu button 2 Click on the eft mouse button to cycle through all possible choices To use a pop up menu instead of a regular menu 1 Move the mouse cursor arrow to the menu button 2 Hold down the right mouse button A pop up menu appears with a menu of the
253. een selecting only those peaks greater than th high Among the options for dpf are noll pos and noise_mult The command dpf noll displays peak frequencies using the last previous line listing and dpf pos displays positive peaks only Any subsequent changes in the display will require a new ds command to erase the displayed frequencies The noise_mul1t argument suppresses noise peaks and uses the same values as given for the d1 1 command above Control of label position is available through the optional leader top and length arguments The dscale command displays a scale under the spectrum or FID The syntax is dscale lt lt axis gt lt vert_start gt lt display_start gt lt color gt gt where axis specifies the units vertical_start is the vertical position display_start modifies the start of the plot and color is the color of the scale Getting Started VNMR 6 1B 01 999083 00 A1298 9 5 Spectral Display and Plotting Line Resolution The dres command displays the resolution of a line as well as the limiting digital resolution of the spectrum selected by the displayed cursor The resolution is determined by a width at half height algorithm and not by least squares Referencing VNMR frequency referencing is based on a number of parameters rfl Reference line The distance of the reference line from the right edge of the spectral window This line is the spectral position used to set the referencing It can b
254. eesreeuteesdeassntcesueesingonsdeesseetoutecosesss dees 221 6 2 Interactive Weighting aicnin disaiie nai ae iii aE NE Ea 223 8 9 Fournier Transformation ssi isea enei r aeee Ea EEE EEES Ta ES Pa ie wed 223 8A PI ASIN D ciscascescecescsgibnsen nuedevevscseascvanstennsdaavesunesdeadasdneadas Ee ERE EAEE ERR Er EE EEE E aasit 224 Phase Parameters sisien teins irea guess est a E OEE EE C R EE rE eaaa 224 A tophase AlgorithM sisses rica eseni eeir Ee rea EE E E EEEE E Eai 225 Spectrum Display nesieme ennen eae a E E EE R EES 225 8 9 Advanced Data Processio i sicsecicscssccscdessesesesssiecestcuscgundensusnesccevensstbasesscevedigevscssectices 226 FID Phase Rotation enesenn a E E E E REESE 226 Frequency Shifting 0 eee esecsecceseeseceesecsseseeeessecseeseseseecseeaesseseesaeeeeeaeeaees 227 Data Processing Methods cceessesccesseceececeseeeeceeeeeecseceececeeeeesaeceneecsaeeeneeesees 227 Linear Prediction sisi oc ietids aeea Series than ioatii nematic AE aie 227 Solvent Subtraction Filtering ccccssscisssessessssesvasesseacevansseasessnsessscssonssansssiosecoses 228 Interleave FIDE riren aiea ads ate asinine aemapad enacted 229 Chapter 9 Display Plotting and Printing ccccsseeeceesseeeeeeeseneeneeeeeees 231 9 1 Interactive FID and Spectrum Display 00 cece ceeeseeeseeeceeceseceseeeeeeseeeeeeeeaeeens 231 Display Parameters a iccscsciiscbvas clesscisas dekh eats ian ediebees a EE TEER ESE EEE 232 PI QUIS secss
255. efault filter coefficients calculated by VNMR i1t file should be set to the empty string i e two single quotes with no space between them 4 Once the parameters have been set the filtered and downsampled dataset can be saved by using the macro digfilt exp_number lt option gt to write the digitally filtered FIDs to another experiment The data can then be saved by joining the other experiment and using the svf command to write the digitally filtered FID to disk The possible options available with the digfilt macro are nodc zero and t2dc Use these options if you used the same option when processing the data with ft wft ft 2d or wft2d If ct 1 it may also be useful touse dcrmv y during data processing If proc 1p linear prediction will be done prior to digital filtering Apodization will also be done prior to digital filtering 5 Carry out the digital filtering and Fourier transformation by entering wft or in the case of 2D datasets by entering wft 2d The digital filtering and downsampling step takes place after all other processing on the FID dc solvent suppression linear prediction apodization etc If desired the filtered downsampled data can be written to another experiment and then saved using the svf command Removing Quadrature Artifacts Using DSP Normally NMR spectra are acquired with the receiver in the center of the spectrum and the center zero frequency glitch and quadrature artifacts fa
256. elect a method from the menu and click Start Autoshim The buttons at the bottom left of the control panel allow you to load save and delete shim values in named files Click the left mouse button to load save or delete the named file or click the right button to select a file name from the menu The Best button at the bottom right resets the shim values to the best seen in the current session when clicked with the left mouse button The Best button may not give correct results if the DC Correction status has been changed Select Reset Best from the menu to reset the record of best shim values The main display screen shows the FID or spectrum in real time depending on what has been selected on the control panel On UNITYplus and older systems the displayed data is signal averaged over nt transients 01 999083 00 A1298 Getting Started VNMR 6 1B 157 Chapter 6 Preparing for an Experiment Style 2 Interface On N YINOVA systems there are two toggle switches Phase Cycle and Signal Avg next to the DC Correction switch As in the Style interface they allow you to phase cycle and or signal average the data over bs transients The vertical scale is controlled by the Up and Down buttons and the horizontal scale by the Expand and Compress buttons Each click of one of these buttons changes the scale by a factor of two The Real Imaginary and Envelope choice buttons allow you to view either channel alone or the square root of the s
257. eline correction lvltlt number Control sensitivity of 1v1 and t1t adjustments phasing 10 to 100 in Control update region during interactive phasing rp 360 to 360 in deg Zero order phase on directly detected dimension tlt number First order baseline correction vp 200 to 200 in mm Vertical position of spectrum vs le 6 to 1e9 Vertical scale Interactive 1D Spectrum Display Menus Upon entry to ds the screen contains a spectrum similar to Figure 67 Figure 67 Interactive Spectrum Display ds program At the top of the display is the Interactive 1D Spectrum Display Menu with the following buttons the labels change on some of the buttons according to the mode the program is in Box Part Integral Full sp wp Mark Phase Th Resets Dscale Lvl Tlt Set Int Ref Pbox Return 238 Getting Started VNMR 6 1B 01 999083 00 A1298 9 4 Interactive Spectrum Display The buttons on the Interactive 1D Spectrum Display Menu function as follows The first button is Box or Cursor depending on if you are in the box or cursor mode Box Change to the box mode with two cursors Cursor Change to the cursor mode with one cursor The second button is No Integral Full Integral or Part Integral depending on which integral display mode you are in No Integral Hide the integral display Full Integral Display all integral regions Part Integral Display every other region The third button is Expand or Full dependin
258. ely the left button on the mouse can be held down and the cursor tracks movement of the mouse arrow Moving the cursor updates the parameter crf Pressing the right mouse button displays a second cursor to the right of the original cursor Pressing the right button of the mouse or holding the right button down causes this new cursor to move to the mouse arrow The second cursor may not be moved to the left of the first cursor Movement of the second cursor updates the parameter deltaf the difference in seconds between the two cursors If both cursors are displayed pressing the left button on the mouse enables both cursors to be moved by the same amount this changes the parameter crf but not the parameter deltaf The middle mouse button controls the FID intensity Pressing this button adjusts the vertical scale of the FID parameter vf so that the FID intensity at the position of the mouse arrow equals the vertical position of the mouse arrow If the mouse arrow is positioned at the left edge of the display the vertical position of the display is adjusted to the vertical position of the mouse arrow Parameters affected are vpfi if the imaginary channel of the FID is displayed and vpf if the imaginary channel is not displayed After an FID is displayed with the df command parameter entry updates the FID The left and right mouse buttons differ only in their sensitivity Full scale top to bottom of screen corresponds to approximately 180 for
259. ements in the COSY experiment The values that you choose are shown as depressed buttons Figure 19 COSY Customization Window 9 When you have made your choices click the OK button in the popup window to close it and add the COSY experiment to the experiment list The list is displayed in the VNMR text window and now has the entries PROTON and COSY 10 Click on the HMQC button in the middle row of the experiment selection menu to open the HMQC customization window shown in Figure 20 Figure 20 HMQC Customization Window 11 Make your selections and click on OK to add the HMQC experiment to the list that appears in the VNMR text window 12 Click on the Close button to remove the Acquisition Setup window 13 Click the upward pointing triangle at the bottom of the Custom icon to close the Custom menu 14 Click the Go button in the main GLIDE menu Processing and Plotting Combination Experiments Some processing and plotting automatically happens in GLIDE combination experiments The 1D proton spectrum is always processed and plotted as is a COSY if it is run Phase sensitive experiments are saved in the data directory for this sample specified in the Save As field in the setup window To process and plot these experiments the data must be 01 999083 00 A1298 Getting Started VNMR 6 1B 57 Chapter 3 Using GLIDE recalled and specific plotting actions must be taken Data can be recalled and processed with either Co
260. ems l Sample insertion a hole LA N Magnet Srat selector Magnet switch Probe console hemes Tuning rods Flow lll Po ae Tune display ee _ Attenuation a switch 9 Quarter wavelength i ae cable ee Spin eject button Spin rate knob Not on MERCURY VX LHe LN flowmeters Tune Spin Rate meter Green LED __ Tune Spin switch Tune knob Quarter wavelength cable MERCURY MERCURY VX and GEMINI 2000 Systems AS jo OL e Preamplifiers Sample insertion hole Magnet VT Cooling flowmeters Probe Tuning rods Figure 1 Magnet Probe and Associated Electronics Getting Started VNMR 6 1B 01 999083 00 A1298 1 2 User Interface Mouse Keyboard and Remote Status Module The mouse is a three button pointing device that controls one or more cursors that appear on the display screen although only one cursor can be controlled at a time On the keyboard you enter commands parameters and other alphanumeric information into the data system The optional remote status module is a small case containing indicators and displays usually placed next to the host computer display The YINOVA and UNITY plus versions of t
261. ensitive COSY 69 phase sensitive mode 72 74 79 80 225 phasing interactive 235 mode 234 240 Getting Started VYNMR 6 18 311 Index spectra 224 phasing parameter 235 240 phfid parameter 156 159 223 226 233 235 phosphorus spectrum plot 250 pi3ssbsq macro 222 pi4ssbsq macro 222 pir command 254 pirn command 254 pl command 249 plfid command 237 plh macro 249 pll command 249 plot axis below spectrum 78 columnar line list 249 currently displayed region 249 customizing a 263 editing with Region Editor 266 exponential analysis spectra 81 FIDs 237 finish current plot and change paper 78 80 importing from VNMR graphics window 265 integral with spectrum 78 integrals 250 parameters 80 232 261 parameters on HP plotter 78 peak frequencies 249 peaks frequencies above peaks 78 phosphorus spectrum 250 proton spectrum 249 pulse sequence 188 pulse sequence as a graph 189 scale under spectrum 249 simulated spectrum 86 spectrum 78 start 232 text file 262 width 232 Plot button 74 75 77 78 79 81 82 86 87 243 Plot Correlations button 82 Plot Designer program 262 271 plot macro 250 plot menu file 266 plot output positioning 262 plot parameters adjusting and restoring 269 plot importing into a region 266 plotid macro 250 plotter attached to computer 36 choices 257 code 255 color printing 258 configuration 255 257 convert Hz or ppm 273 draw box 273 line
262. ent combinations Table 18 Codes for Standard Shim Gradient Combinations Standard Hexadecimal Code Gradients Code z1 Z1C 0000008 z2 Z2C 0000020 z3 Z3 0000040 z4 Z4 0000080 z5 Z5 0000100 zq Z1C Z2C 0000028 2t Z1C Z2 Z3 0000068 zb Z1C Z2C Z4 0000048 za Z1C Z2C Z3 Z4 Z5 00001E8 ze Z2C Z4 0000040 ZO ZIC Z3 Z5 0000148 e Z1C Z2C Z5 0000128 zm User selected gradients User entered tx X Z1 0010004 ty Y Z1 0020004 t1 X Y Z1 0030004 t2 X Y XY YZ X2Y2 Z1 03B0004 Ez X Y XZ YZ Z1 0270004 tt X Y XZ XY X2Y2 YZ Z1 03F0004 E X Y XZ2 YZ2 Z1 5030004 t4 X XZ X3 XZ2 Z1 4450004 t Y YZ Y3 YZ2 Z1 1A20004 t XY X2Y2 ZX2Y2 ZXY Z1 A180004 E7 X Y XZ XY X2Y2 YZ X3 Y3 YZ2 FFF0004 ZX2Y2 XZ2 ZXY Z1 ta X Y XZ XY X2Y2 YZ YZ2 XZ2 Z1 53F0004 tm User selected gradients User entered Refer to the description of the shimset parameter in the VNMR Command and Parameter Reference for a list of shims in each type of shim set The following examples show the meaning of a few standard shim methods e szq cmm means set shims Z1C and Z2C with a medium to medium criterion 01 999083 00 A1298 Getting Started VNMR 6 1B 141 Chapter 6 Preparing for an Experiment 142 e sza clm means shim all Z gradients with a loose to medium criterion e szt clm szb clm szq cmm means shim ZIC Z2 and Z3 with a loose to medium criterion then shim Z1C Z2C and Z4 with a loose to mediu
263. ent to be shimmed 141 gradtype parameter 196 graphical probe tuning 116 graphics screen line drawing capability 272 graphics window 44 46 covering text window 65 enlarge 66 grayscale image 79 80 Grid button acqi 155 grid lines 155 Grid Off button aqi 155 grid magnetizing and demagnetizing 263 grid showing and hiding 263 gshimlib directory 172 gzip command UNIX 293 gzsize parameter 177 gzwin parameter 170 H H1 button 68 hl parameter set 145 H1 CDCI13 button 67 H2 button 68 halt command 203 hard disk drive 23 Hardware button 92 hardware caused distortions 227 hardware configuration 92 hardware simple Autolock 132 hardware Z1 Autoshim 139 01 999083 00 A1298 Index Hd All button 77 Hd Box button 76 Hd Lbl button 77 Hd Pk button 76 HdNum button 76 hdwshim parameter 139 145 hdwshiminit parameter 145 hdwshimlist parameter 145 heat exchange bucket 196 helium contact with body 18 helium gas flowmeters caution 20 Help button menu system 59 65 help directory 34 70 help files customization 64 Help screen 59 65 HET2DJ button 70 HETCOR button 69 heteronuclear correlation 69 heteronuclear decoupling 194 195 heteronuclear J resolved 2D 70 Hewlett Packard plotters 78 255 Hewlett Packard printers 255 Hewlett Packard raster mode 255 hexadecimal codes for shim group 143 high rf band 184 high power amplifiers cautions 20 high resolution plotter
264. enu The Files Data Secondary menu is activated by selecting More in the Files Data menu or by entering files Button files_data2 Description Load Params Save Params Return Start by marking one file in the files display and then click on this button If you have selected an entry that has NMR data the parameters from that data are loaded into the current experiment Show prompt File name enter name and lt return gt and save the parameters from the current experiment there Display the Files Main menu page 87 Files Secondary Menu The Files Secondary menu is activated by selecting More in the Files Main menu or by entering files files_main2 To mark a file place the mouse cursor over the file name and click the left mouse button The file name will appear in reverse video when marked To deselect a file name click on it again Button Display Getting Started VNMR 6 1B Description Start by marking one or more files in the files display and then click on this button to display the files you marked This action is appropriate for text files only 01 999083 00 A1298 4 13 Secondary Main Menu Button Description Edit Start by marking one or more files in the files display and then click on this button to edit the files you marked This action is appropriate for text files only Copy Start by marking one file in the files display and then click on this button
265. envelope display that shows the outline of the FID envelope The FID display is controlled by the acquisition parameters active when the gf or go acqi command is executed and by the processing parameters 1sfid phfid and if present dmgf The gf macro is recommended instead of running go acqi directly Using gf prevents certain acquisition events from occurring such as spin control and temperature change Changes to acquisition parameters become active in the Acquisition window after the execution of gf or go acqi Changes to the three processing parameters become active in acqi after the execution of acqi par The lower panel of the FID display window contains menus and buttons for changing the shim parameters e SHIM menu selects the group of shim parameters up to six to be manually adjusted e g the axial z menu is shown in Figure 41 e x button toggles the magnitude of the shims adjustment buttons Selecting x32 changes the increments from 1 4 16 64 to 32 128 512 2048 e best button reloads shims that gave the best lock level in the current session valid only if the Llockgain lockpower and lockphase parameters are unaltered e first button reloads shims to the values that existed at the start of the current session Below the SHIM menu are the shims controls Each shim can be adjusted between minimum and maximum values by the buttons to the right of the value Clicking a button
266. ep 1997 To add a single line of text to the end of the current experiment text file enter atext string e g atext Series 10 appends this string to the text file Series 10 To use a text editor to edit the text file of the current experiment enter textvi The textvi macro lets you edit the text file from VNMR using the UNIX text editor vi If you want to edit the file with a text editor other than vi set the UNIX environmental variable vnmreditor to the name of the editor you want e g emacs and use the macro edit file instead of textvi Refer to the description of edit in the manual VNMR Command and Parameter Reference for further information To clear or remove all the text presently in the text file of the current experiment enter the ctext command Displaying and Handling a Text File To display the text file in the current experiment enter text without an argument To return text from a data file to the current experiment use gett xt file where file is the name of a VNMR data file Text can be retrieved from a file on disk or from another experiment e g gett xt vnmr fiblib fidld gets file fidld To save the text from the current experiment into a VNMR data file use the command puttxt file Text can be updated from a file on disk or from another experiment 01 999083 00 A1298 Getting Started VNMR 6 1B 197 Chapter 7 Acquiring Data 7 4 Performing Acquisition 198 Data are acquired through the macro
267. er Before using dpwr 49 for continuous decoupling ensure safe operation by measuring the output power This safety maximum may be adjusted in the config program On systems with class C amplifiers on the first decoupler channel the parameter dhp controls the decoupler high power level and the parameter dlp controls the low power level usually for homonuclear decoupling dlp is only active if dhp n dhp runs from 0 to 255 maximum in uncalibrated non linear units Specific values of dhp should be calibrated periodically for any particular instrument and probe combination dlp specifies dB of attenuation of the decoupler below a nominal watt value In addition on GEMINI 2000 broadband systems with fast switching attenuators dlp controls a fine attenuator over 14 dB in 1023 steps in line with the coarse attenuator For GEMINI 2000 H 3C systems dhp control the heteronuclear decoupler power 0 5 or 1 watt dlp controls the homodecoupler power 0 to 2047 On systems equipped with a linear amplifier on the first decoupler channel the parameter dpwr sets the decoupler power which is under computer control dpwr can be given values from 0 to 63 or from 16 to 63 depending on the range of attenuators present in the system In both cases 63 is the absolute maximum power However the output power should be measured to make sure a maximum of 2 watts is applied to switchable probes This safety maximum which limits the value that can be ente
268. er details 10 4 Transferring Data Using Ethernet and limNET One of the most efficient mechanisms for transferring data from one location to another is over an Ethernet network Ethernet can be used to transfer data and hence to store and retrieve data remotely on a wide variety of systems including VNMR systems MERCURY VX MERCURY YN YINOVA UNITY plus GEMINI 2000 UNITY and VXR S VXk style systems Gemini VXR 4000 and XL and VAX computers Ethernet encompasses a number of ideas but for our purposes here only hardware and software or protocol is considered On the hardware side Ethernet is a standard feature of the VNMR data system Ethernet hardware is optional on VXR style systems On the software side VNMR includes standard UNIX software using the Internet Protocol IP that enables data transfer between one VNMR system and another or between a VNMR system and other computers supporting IP VNMR software includes a proprietary Ethernet protocol named limNET Laboratory Information Management Network a Varian trademark This protocol is required for exchanging information with VXR style systems on which only the limNET protocol is supported The limNET protocol is also available for VAX and IBM RS 6000 computers where it is used to transfer data from VXR style systems Table 49 lists commands associated with data transfer over Ethernet and limNET Table 49 Ethernet and limNET Data Transfer Commands
269. er setup menu Getting Started VNMR 6 1B 01 999083 00 A1298 6 12 Gradient Autoshimming Button Description Find gzwin Run a calibration experiment to set parameters tof and gzwin to optimize the spectral window for a given gz1v1 Pulse length and gain should be correctly set before using this button Calculate gzwin Determine tof and gzwin from the profile spectrum using cursor positions Find tof Run a calibration experiment to set tof Pulse length and gain should be correctly set before using this button Add Params Add parameters for gradient shimming Return Return to the Gradient Shimming System menu Gradient Nucleus Parameter Setup Menu The Gradient Nucleus Parameter Setup menu is used for setting parameters according to type of gradient and nucleus Recabling may be required to observe IH or 7H nucleus Check the value of gradt ype when done To open this menu click on Gradient Nucleus in the Gradient Shimming Setup menu Button Description Pfg H1 Set parameters for pulsed field gradient on IH Pfg H2 Set parameters for pulsed field gradient on 7H Homospoil H1 Set parameters for homospoil gradient on IH Homospoil H2 Set parameters for homospoil gradient on 2H Return Return to the Gradient Shimming Setup menu Gradient Shimming Map Menu The Gradient Shimming Map menu is used for making and retrieving shimmaps To open this menu click on Shim Maps in the Gradient Shimming System menu Button Description
270. eriments to be submitted to the acquisition system even if the wexp processing of an experiment that was started with au wait is not yet finished resume can be useful if the processing macro extracts enough information to start the next experiment identified by au next but still has more processing to do Stopping and Resuming Acquisition An experiment that has been submitted for acquisition can be stopped with the sa command If the experiment is waiting for execution no action is taken If the experiment is active itis stopped and data is retained Options are available for stopping the experiment at several user specified places during acquisition only the first option is supported by MERCURY and GEMINI 2000 systems e At the end of the next data accumulation ct e g sa or sa ct e Ata multiple of the value of ct can be used to complete a phase cycle before stopping e g sa 4 e At the end of the next block size e g sa bs e At the end of the next complete FID e g sa nt e At the end of the next complete interleave cycle i e the latest block size has been complete for all FIDs in the interleave cycle e g sa il The command ra resumes an acquisition stopped with sa When experiments are queued the behavior of sa and ra is more complex If an experiment is active in exp1 and queued in exp2 entering sa from exp1 stops that experiment and immediately begins acquisition on exp2 Entering sa
271. ersamp 1 A larger number of coefficients gives a filter with sharper cutoffs a smaller number of coefficients gives a filter with more gradual cutoffs The value of oscoef does not need to be changed when oversamp is changed because oscoef is automatically adjusted by VNMR to give filter cutoffs that are the same regardless of the value of oversamp e oslsfrq is used to select a bandpass filter that is not centered about the transmitter frequency os 1sfrq is specified in Hz and works much like lsfrq A positive value of oslsfrq selects a region upfield from the transmitter frequency and a negative value selects a downfield region The oslsfrq parameter can be used to perform frequency shifted quadrature detection see Removing Quadrature Artifacts Using DSP on page 218 e osfb specifies the digital filter bandwidth If os fp n the bandwidth defaults to sw 2 A value less than sw 2 rejects frequencies at the edges of the 212 Getting Started VNMR 6 1B 01 999083 00 A1298 7 5 Applying Digital Filtering spectrum a value more than sw 2 aliases noise and signals at frequencies outside of sw 2 filtfile specifies the name of a file of finite impulse response FIR digital filter coefficients The file must be in the user s vnmrsys filtlib directory The filter coefficient file is a text file with one real filter coefficient per line Complex filters are not currently supported To use the default filter coefficients calculated by V
272. ertical cursors Click the left or right button to adjust the FID phase parameter phfid Click the mouse above the horizontal cursor to increase phfid Click below the horizontal cursor to decrease phfid Place the mouse arrow right on the horizontal cursor and click the left button to restore the initial phase 3 To exit the interactive phasing mode make another selection from the menu Select the Cursor or Box button if no other choice is desirable 01 999083 00 A1298 Getting Started VWMR6 1B 235 Chapter 9 Display Plotting and Printing 9 3 Stacked and Whitewashed FID Display and Plotting Table 35 lists commands and parameters available for stacked and whitewashed FID display and plotting All new parameter sets have the FID display parameters dot flag axisf vpf vpfi crf and deltaf defined Because old parameter sets might not have these parameters defined the macro addpar fid is provided to create these parameters in the current experiment the macro fidpar functions the same as addpar fid Table 35 FID Display and Plotting Commands and Parameters Commands addpar fid Add parameters for FID display in current experiment dfs Display stacked FIDs dfsa Display stacked FIDs automatically dfsan Display stacked FIDs automatically without screen erase dfsh Display stacked FIDs horizontally dfshn Display stacked FIDs horizontally without erasing screen dfsn Display stacked FIDs without erasi
273. eseeeeeeeeeeceeescecaeesaecaecsaecsecaeeeeesseeeeseetee 112 6 4 Removing and Inserting the Probe 0 0 eee eee cee ceseeeeceeeeeceseeeeeeeeeeseaeeeeseneeaeeeas 112 To Remove the Probe isc seissisciszeessestacasssteaes aseidgs has E a e E RER SS 112 TO Umsert the Probe cxion opcao aro aereis E ENEE EREE 113 6 5 Using Probe Files and Templates ccccscccascscsisccsssesssssvasscnsceveassessatasneesgoasssnesapesonaeds 113 6 6 Tuning th Probs eicocon e Ei eE TEESEEISE NOTEN EES ra SE nih 113 To Tune Probes on YNITYZNOVA and UNITY plus osesseeseeeeeereeseerserreerereeeees 114 Tuning Probes on MERCURY VX MERCURY GEMINI 2000 cccscceeseeees 124 Tunning Probes on UNITY and VXR S Systems 0 eee eee eee eeseeeeeeeeeee 126 6 7 Spinning the Samples ics wiih dalek edi Wain eae eA 127 6S Optimizing LOCK saroien neok E R A EARR R 130 Lock Power Gain and Phase cccccesseesssscssecececccccseececescececesesesssseestreaueeees 131 Lock Control Methods a c ieiesctsstsviiieas vnces st saneren ren Erene Ea EEn NE EEEE 132 Leaving Lock in the Current State esessesesseeeersereresreerrsreerssrrrsrrrrsrrererrereereee 132 Running an Experiment Unlocked ooo cece ceeseeceeeeeeceeceseceeceseeeeeeseeereeeeees 132 Simple AULOLOGK scacciare see E snades shasnsestvaanes hee ssasntbsbeanesebpesedts 132 Optimizing AULOlOCK wis scscssccestascessscsntsdbids edaraten EESE EE NEER EEE NE EEEE 133 Pll Optima ZATION aces icerisine sdvesanesbeie
274. eshsstisesessssavensssbusessastagshesaxedancssuac ET EE E EEr e E Ee Eae ipe ea E EEEE 232 10 Getting Started VNMR 6 1B 01 999083 00 A1298 Table of Contents O2 Interactive FID IDISplay oisciscctesnsesias siseachaessbsas dessauavsskstbvi ses stuveasieassdavensvesuaebeneadeessasts 233 FID Display Menu isicvceccissessestassstaaredanteseacs Gastapesederaeseubcsnssesussepassdansenadesuatanaead 233 Controlling Cursors and FID Intensity eee cee ceeceeceseeeeeeseeeeeeeeees 234 Interactive FID Windowing o 0 eee eeeeeeeeeeeeeceeeeecaeeeaecaeceaecaeeeseeeeeneeeeeeeeees 235 Interactive Phasing Mode ooo ee ecceeeeeeseeeeeceeeseeceeesaecaecaececeseeeeeeeeeeeeetees 235 9 3 Stacked and Whitewashed FID Display and Plotting 0 0 ee eeeeeeeeeereeeee 236 Stacked FIDS pirmi e mentees ua iee eA ease aesliees 236 Whitewashed FIDS cicccs sci sibesrsc Wascies eki EEEE EEEE EREA EAEE EEEE 237 9 4 Interactive Spectrum Display sc sisaiccsscssssseeascsespssesscssessscnsscesceneaasecusdanssezonsnaeesapesneates 237 Interactive 1D Spectrum Display Menus 2 00 0 cece ceeceseceeceseeeeeeseeeeeneeees 238 Controlling the Cursors and Spectral Intensity eee cesses eeeeeeeeeeeeee 239 Interactive Spectral Windowing Mode ou eee eee ceeeecneceseceeceeeeeeeseeereneeees 240 Interactive Phasing Mode 00 ee eee ecceeeeeeeeseeeeeceeessecaeesaeceecaeceeceseeseeeeseeeeeeee 240 Interactive Integral Reset Mode 0 eee eeceeecseceenceeeecenseceececeeeeesaeceeeecsaeeeaeeenee
275. esolved 2D spectra for HET2DJ HOM2D J after rotation Foldcc Perform a symmetrization in 2D INADEQUATE for CCC2D CCC2DQ Rotate Rotate spectral data by 45 for HOM2D J Normalize Normalize vertical scale for 2D display Return Display the 2D Data Display menu page 79 2D Plotting Menu The 2D Plotting menu is activated by selecting the Plot button in the 2D Data Display menu or by entering the command menu plot_2D Button Description All Contours Pos Only Image All Params Params Page Return Calculate a contour plot of the current data Calculate a contour plot of the positive current data Print a grayscale image on a dot matrix printer LaserJet QuietJet or InkJet does not work on pen plotters Print parameters on printer Plot parameters in the left upper corner of the paper Plot out the currently buffered plot and change paper Display the 2D Data Display menu page 79 2D Data Display Secondary Menu The 2D Data Display Secondary menu is activated by selecting the More button in the 2D Display menu or by entering the command menu display_2D_2 Button Stacked Plot F1 Mode OR F2 Mode AV OR PH Reference Analyze Return Getting Started VNMR 6 1B Description Display data stacked and whitewashed and allow for interactive adjustment If labeled F1 Mode select the fq axis to be horizontal If labeled F2 Mode select the f2 axis to be horizontal
276. esult in misset shims Calibrating gzwin The parameter gzwin is the percentage of the spectral window used in calculating the field maps gzwin should be adjusted only when making a new shimmap If this parameter is not calibrated correctly you may see excess noise data at the edge of the shimmaps which corresponds to the region in the profile spectrum where the signal goes to zero It is normal to have a few noise data points at the edge of the shimmap but if it is more than a few data points greater than 25 of the window gzwin may be miscalibrated This can occur if there is low signal to noise or if gzwin has not previously been calibrated for the current parameter set If the gain is too high wings will appear on the sides of the spectra and may result in miscalibrated gzwin This can also occur if there are multiple chemical shifts in the presence of a weak gradient Getting Started VNMR 6 1B 01 999083 00 A1298 6 12 Gradient Autoshimming SELSRS varoot 30000 20000 10000 0 410000 20000 30000 Frequency bz ws Field hz Figure 49 Shimmap Plot Automatic Calibration of gzwin Clicking the Automake Shimmap button causes the following actions 1 Enter gmapsys and click on Set Params gt Find gzwin which calibrates gzwin and sets tof to center the window used for calculation 2 Click on Return gt Shim Maps gt Make Shimmap which makes the shimmap with the current values of
277. et hardware In this situation the system administrator must terminate the limNET server connect the local node to the network and then restart the server The system administrator can stop the limNET server by taking the following steps 1 Enter the UNIX command ps e on Solaris to find the process ID of the limNET server The name of the process is limnetd 2 Enter the UNIX command kill a PID where PID is the process ID of the limNET server Only root can execute this ki 11 command Remote host busy The remote node is currently involved in another limNET transfer The VXR 4000 system allows only one transfer at a time Try the command again in a few minutes Remote node not found The remot e_node argument could not be located in the node file 10 5 Converting Data Between Systems 286 Files transferred from VXR style systems Gemini VXR 4000 or XL or Bruker systems are in a format that must be converted to a usable format for VNMR and then stored for later use e Forall text files the unix_vxr and vxr_unix commands convert the files between VNMR and VXR style systems e For VXR style system data files the convert command makes the transferred data usable for VNMR and decomp breaks up transferred libraries and stores the files in a VNMKR subdirectory e For Bruker data files the convertbru and sread commands convert the Bruker data and read the converted data into VNMR Table 50 summarizes the commands used for
278. eters Resolve Select default resolution enhancement parameters Broaden Select standard line broadening parameters gt AV OR If labeled gt AV switch to the absolute value mode gt PH If labeled gt PH switch to the phase sensitive mode The value of the parameter dmg determines the button label FN Small Select Fourier number for quick transform Normal Select Fourier number for normal size transform Large Select Fourier number for large transform with zero filling Return Display the 1D Data Processing menu page 71 Interactive Weighting Menu wti Program The Interactive Weighting menu part of the wt i program is typically entered by selecting the Adj Weighting button in the 1D Data Processing menu in the 2D Data Processing menu or in the 2D Interferogram Processing menu or by entering the command wti lt index gt If called with an index number as an argument the desired FID number in a multi FID experiment is selected otherwise the current index is used This menu is not user programmable Button Description next fid Increment FID interferogram index Ib Select line broadening or exponential weighting Negative gives resolution enhancement sb Select sinebell constant Negative gives squared sinebell sbs Select sinebell shift constant only if sinebell is active gf Select Gaussian time constant gfs Select Gaussian time constant shift only if Gaussian time constant is active awc Select
279. etup Menus tisessa eine eaea ane EE aE E E SEEE EAEE REEERE RE EOE E 67 Setup Ment es ssasekiccds ick cetchon oE rE EE EE ENEA A gees 67 Nucleus Selection Menu sscsscicsresssrrneioscicsocsuesrusierevsrredtossresesrisui tanisa isisisi 68 Solvent Selection Men sistonreceserieei ternare ethos eines fhe oubesuevbeaneteabes 68 1D Pulse Sequence Setup Menu o oo ceecseeecsseeseceeceeeeseeseeeeeteeseeseaeeenes 68 1D Pulse Sequence Setup Secondary Menu eee ese ceecsecsseeseeeeeneeeeeeeees 69 2D Pulse Sequence Setup Menu eee ceeceseeseceeeeeceseeseceeeeseseaeeeeseneesaeeaee 69 2D Pulse Sequence Setup Secondary Menu 0 cee ceeeecesceeceeeeeeeseeeeeeeeaeenee 70 Applications Mode Menu 000 eee ecesecsecseeceeceseeseceseeseceseeeceeeeeseseseeeeaeesaeenee 70 AG Acquire Ment i cicssdiscess ibs obese caeestdstabeeccecesateeibes choedehlas Ea Ea E e EEE E E E iia R 70 4 9 Processing Menus 8icckciiesiaiiisienitiad iol EE EEE EEE ET E E aelabadeaees 71 ID Data Proces sine Ment srera tees ceateced cb esdtvaubcsedstveaheeeerdannssbadsccansacdabes 71 Interactive 1D FID Display Menu df Program sssessessseessereeesreessererrerseeeresen 71 1D Processing Parameter Setup Menu ssessesseessssesrsesrerrsreersreeresrererrnserrrererrsre 12 Interactive Weighting Menu wti Program sseseseseseesssrerrsrerrsreersrrererreeeereeen 72 Interactive 1D Spectrum Display Menu ds Program ssseseseeeseeeeseeeerereereren 73 2D Data Pr
280. eul svocsugavecuuvelsevannseawisauen te 53 Closing GUDE see erento rieira re o AE E EER E E EE EE EE E E EE 53 De Usine GUIDE sireno loses E E a A E E EE S 54 Running a Standard Experiment sseeseseesesseeesesresrseresrsresreresrrrsrerrsrenrrrsseerese 54 Customizing a 1D Experiment oo eee cee ceeeseceseeseceeeeeeeeeeeeeeeseeeeeeneesaeenee 55 3 3 Customizing Combination Experiments 0 0 0 eee ee eceseeseesceeseceecaecnaeeseseseeeeeseeeeees 56 Processing and Plotting Combination Experiments eee eee eeeeeeeeeeeeenee 57 Walkup NMR victessciiventaniesas tistn adie eae ETETEN EE ER T R NE EEEE EEG 58 Chapter 4 Using the VNMR Menu System ccccessseecesseeeeeeeeseeeeeeneeeeeees 59 4 1 Working With Menus cissscsccccsssceisseescssasasenscasnsgaicessacesesevesbesdnsceedeuvensyonsecapnssiadndanstanctoas 60 Interactive Programs with Menus 0 cece eseeseceseeeeceeeeeceeceseeeeeeeeseeeeaetenes 60 4 2 Customizing the Menu System 00 eee ee eeceeeeeeceseeeeeceeeceeeaeesaecnaesaesseeseeneeeeeeneenes 64 4 3 Menu System Step by Step st esesscessessceeseonseeessevscesscesscesseessessessseesscssessesnenees 64 4 4 Permanent Menu ce cee ccccccecseesssecessceeceneceeesaeecseseeeceneeceeaaeecseeeeeceeeceeaeeesseaeeesneeeeneas 65 43 Main Menu fe csccscicastese das Natiesscsslstabe ce casvateetieai a entice eneatell ausneascets 66 MB Workspace Menu sredis seo ienei eei reene A EE En teases scsusacve bess EEE E ENNE E 67 AT S
281. eve a few parameters from a file stored with svf or svp enter the command rtv lt file parl lt par2 gt gt with the file name and one or more parameter names as arguments If rtp or rtv are entered without an argument you are prompted for a file name In that case the file name can be given without single quotes To retrieve shim settings the command rts file locates a preexisting file of shim settings saved by the svs command and copies the settings into the current parameter set of the current experiment If the file name entered as an argument is a relative path rts looks fora shims subdirectory in the following order 1 If shims exists in your VNMR user directory rts copies the settings 2 Ifthe shims subdirectory does not exist rt s looks for a global parameter named shimspatnh If it is present shimspath is expected to contain the name of a 01 999083 00 A1298 Getting Started VWMR6 1B 279 Chapter 10 Storing Retrieving and Moving Data 280 directory If this directory exists rt s copies the settings if it locates the requested file 3 Ifstep 2 does not work rts tries to locate the file in vnmr shims If the name of the file entered as an argument is an absolute path the file is located directly A message is displayed at the end about the success or failure of rts To retrieve Spinsight data into the current experiment use the rt cmx lt file gt command Using GLIDE to Retrieve Data GLIDE can
282. everal seconds the window appears for the program you wanted 01 999083 00 A1298 gy Workspace Acquisition Status YNMR Online vnmr Programs m Utilities is Properties Help Desktop Intro Exit Figure 15 Workspace Menu under OpenWindows Getting Started VNMR 6 1B 49 Chapter 2 VNMR Basics 50 If the item you want has a small triangle to the right of it that is the Programs and Utilities items on the Workspace menu that item has a submenu To open the submenu continue to hold down the right button and slide the mouse toward the right of the item across the triangle until the submenu opens then move the cursor to the item you want on the submenu and release the button Here are some programs accessible from the Workspace menu that you will probably frequently use Acquisition Status Opens the Acquisition Status window one of the VNMR acquisition programs discussed above VNMR Online Displays hypertext version of all your VNMR user manuals including all the entries in the VNMR Command and Parameter Reference and all the pulse sequence statements in the VNMR User Programming manual Many users leave this program on all the time for quick retrieval of useful operating information Vnmr Activates the VNMR display window If the VNMR display is already active selecting Vnmr creates a second instance of the display probably useless click on ExitVNMR to quit Programs Opens a s
283. ex Getting Started VNMR 6 1B 319 Index 320 Getting Started VNMR 6 1B 01 999083 00 A1298
284. exists Simple Locking Establishing lock using simple or manual locking uses the LOCK display The line that crosses the spectral window represents how close the deuterium resonance field is to the lock frequency When the two are matched the line should be flat with perhaps some noise depending on the lock gain and lock power The poorer the match the greater the number of sine waves in the line Figure 40 represents the changes from a bad match to a good match AVW CTN ON RESONANCE Figure 40 Finding Lock The following procedure for finding lock manually is typical 1 Make sure a sample is inserted and seated properly Spinning helps but is not required 2 Inthe LOCK menu at the top of the window click the off button 3 Using the slide control 1 4 16 and 64 buttons or entering values directly turn up lockpower and lockgain and look for some sinusoidal variation in the signal The actual value needed for lockpower and lockgain depends upon the concentration of the deuterated solvent the nature of the deuterated solvent the number of deuterium atoms per molecule and the relaxation time of the deuterium At this point do not be too concerned about optimizing power and gain just look for a sine wave 4 If you see no sine wave perhaps just noise click on the 16 button for ZO until some discernible wave appears 5 If you know the concentration of the lock solvent is high sa
285. f moving the transmitter frequency outside the current spectral window The macro sd sets the first decoupler offset dof to place the first decoupler at the cursor position in the spectrum Similarly sd2 sets dof2 and sd3 sets dof 3 for the second and third decouplers These macros assume homonuclear operation the decoupler nucleus dn dn2 or dn3 is the same as tn To set an array of decoupler offset values use the macro sda for the first decoupler the macro sd2a for the second decoupler and the macro sd3a for the third decoupler These macros also assume homonuclear operation Spectral Window Spectral window size is adjusted with the spectral width parameter sw see Figure 52 The spectral width determines the sampling rate for data which occurs at a rate of 2 sw points per second actually sw complex points per second The sampling rate itself is not entered either directly or as its inverse known on some systems as the dwell time e_ __ sw a Figure 52 Positioning the Spectral Window With two cursors displayed the macro movesw lt width gt uses the parameters cr and delta to calculate a new spectral width sw and a new transmitter offset tof If referencing was used it is also adjusted The macro also sets sp and wp to display the spectral window Entering a width argument to specify the spectral width allows making an adjustment more precise than if based on the cursors The macr
286. f these programs you can look at the disk contents on your desktop and automatically translate text files basically stripping out line feeds so you can read them Mac OS 7 5 and later can read a PC floppy disk without additional software You can also use the floppy disk as a UNIX file system 1 After entering fdformat to format the floppy enter 01 999083 00 A1298 Getting Started VNMR6 1B 291 Chapter 10 Storing Retrieving and Moving Data newfs dev rfd0c Alternatively you can avoid the usual 10 percent free space in the file system from the command above by entering instead newfs m 0 dev rfd0c 2 Create a directory and mounting point by entering mkdir floppy mount dev fd0c floppy Now floppy is just a normal file system that you can read and write to 3 When done with the floppy enter umount floppy 4 To insert a floppy with data already on it insert it into the drive and enter mount dev fd0c floppy There is no need to reformat or create a new file system Sun has an unofficial method to get around the fact that only root has the privileges to do all of the above In this method root carries out each of the following steps 1 Ifusing Solaris create a shellscript mount floppy like this bin csh b mount F pcfs dev fd0c floppy If not using Solaris the shellscript mount floppy is slightly shorter bin csh b mount dev fd0c floppy 2 Create another shellscript eject floppy
287. first restores the parameters of the current experiment n to the plot then applies the adjusted parameters to the plot jJplotunscale jexpn jplotscale If you do not want to use the adjusted parameters enter the following command jplotunscale jexpn 01 999083 00 A1298 Getting Started VWMR6 1B 269 Chapter 9 Display Plotting and Printing 270 jplotunscale isa macro that restores the original parameters of the current experiment to the plot Moving Objects and Changing Object Size You can move an object by double clicking on it and dragging the mouse across the workspace To move a region click anywhere inside the region or on its border You can shrink or enlarge an object by double clicking on it placing the cursor on a border anchor and dragging it Changing the Shape of the Plot Designer Window Plot Designer can be viewed in two orientations Landscape or Portrait which is the default orientation You can change the shape of the Plot Designer window in the Orient menu Changing the Size of the Plot Designer Window Increase or decrease the size of the Plot Designer window by clicking on the sizes listed in the Magnify menu Saving Your Plot After you are satisfied with the plot that you have created do the following procedure to store your file 1 Click on File in the Main Menu then Save Data to open the Plot Save window shown in Figure 79 Directory list File list 2 Scroll down the list of
288. frequency A coil tuned to a specific frequency usually the frequency of the nucleus the user wants to observe reflects little power at that frequency The acquisition system then sweeps through the desired frequency range and gathers data on reflected power interactively The user can adjust certain parameters interactively during the experiment To Tune a Probe with qtune This procedure describes how to use the qt une program to tune an NMR probe 1 Set up the system for tuning UNITYTNOVA and UNITYplus leave the switch set to observe mode Getting Started VNMR 6 1B 01 999083 00 A1298 6 6 Tuning the Probe Tune Display B Tune Control Panel EF Show Control Panel Exit Display Save v Help v Center T H1 300 047 MHz Span 7 10 000 MHz Display Full Minimal Audio On Off Cursor Off Line Box Grid Off On Marker 1 Off MHz Marker 2 off MHz Marker 3 5 Off MHz Scale dB Linear Max 1 00 EJE Step 0 10 __ _ div Smoothing m 1 2 3 4 5 Line width o EE Calibrate Q calculation off on Figure 23 Probe Tuning Window qtune Program MERCURY VX connect the following cables e Connect the appropriate cable from the probe J5102 or J5302 to the TUNE J5402 connector on the inside of the magnet leg e Connect the appropriate cable from the transmitter J5602 or J5603 to the TUNE J5604 connector e Connect the appro
289. from exp2 on the other hand removes exp2 from the queue without affecting the active experiment 1 Entering sa from an experiment that is neither active nor queued has no effect Entering ra likewise applies to the experiment from which it is entered If exp1 was stopped with sa you must be joined to exp1 to resume that acquisition with ra If both exp 1 and exp2 were stopped with sa you can resume either one or both depending on whether you are joined to exp1 or exp2 when you enter ra Note also that experiments resumed with ra go to the end of the queue if other experiments have started in the meantime Pausing Halting and Aborting Acquisition Once an acquisition is in progress it generally continues to completion however several situations can stop acquisition early The system may detect an error it may detect an overflow or the operator may stop the system with an aa or an sa command The UN YINOVA system only detects data overflow at 16 bits for do n and 32 bits for dp y and responds with an error message MAX TRANSIENTS ACCUMULATED Except under unusual circumstances do y should be used at all times see also the section Data Precision and Overflow below Overflowing dp y with real time DSP dsp r is possible with greater than 4000 transients Another alternative if do n is to change the maximum scaling constant mxconst to add additional scaling refer to the VWMR Command and Parameter
290. g 127 128 161 tubes 103 sample changer 314 Getting Started VNMR 6 1B changing samples 106 sample position 102 sample macro 106 SAMPLE menu 150 151 sampling rate 185 saturated lock signal 139 saturation of the lock signal 163 save button 83 Save FID button 90 Save Params button 90 Save Shims button 90 saving compressed FID 292 display parameter set 243 experiment data 277 FID data 90 parameters from current experiment 90 shim settings 90 278 sb button 72 223 sb parameter 221 sbs button 72 223 sbs parameter 221 sc parameter 232 236 250 sc wc button 243 sc2 parameter 250 Scale button 78 scale image to full window 250 scale integral value 253 scaling constant 202 scientific notation arguments 94 scroll bar 47 scrollable window 44 45 SCSI high speed link 24 sd macro 185 sd2 macro 185 sd2a macro 185 sd3 macro 185 sd3a macro 185 sda macro 185 search spectrum for peaks 185 second cursor 42 234 second Fourier transformation 74 Secondary Main menu 60 91 second level menus 66 Select button 83 Select Params button 71 73 Select Plotter button 92 Select Printer button 92 271 seqfil experiment time 189 seqfil parameter 185 seqlib directory 36 sequence 70 Sequence button 67 sequential execution of commands 94 sequential sampled data 227 serial communications 34 set cursor position to zero 79 Set Default button 88 Set Directory button 87 set display 78
291. g Printer device Printing from within VNMR is initiated with the printon command All output which normally appears in the text window is saved and when the printoff command is issued sent to a printer This output includes the following e Parameter listings from dg dg1 da etc e Line listings from d11 e Integral listings from dli e System configuration parameters generated by config display e Text files using the text command e Results of calculations from h2cal adept t1 t2 etc e Any other information that some program or macro may write to the text window This output is saved in a temporary file in the VNMR subdirectory tmp The VNMR parameter printer determines the printer to which the output is directed To select a printer select the More button from the Main Menu followed by Configure then Show Output Devices which invokes the showplotter macro to list the current printer as well as your possible choices Select Printer will step through the various choices For more information refer to Plotting on page 254 When the printoff command is issued VNMR executes a UNIX script called vnmrprint that sends the temporary file to the printer using standard UNIX printing utilities This script is supplied with the name of the temporary file to be printed the name of the printer corresponding to a printcap entry and the type of printer corresponding to a devicetable entry Note that devicetable informat
292. g a ZO slider button array The range is 2000 Hz Buttons are labelled in Hz and allow the lock frequency to be modified in increments of 1 Hz 4 Hz 16 Hz and 64 Hz Find the lock in exactly the same manner as you would finding lock using z0 However on UN TYINOVA the granularity of resolution for lock frequency is approximately 2 3 Hz so changes in the lock frequency of 1Hz or even 2 Hz might not change the frequency sent to the lock circuit in the probe Alternatively the value of each parameter can be changed by clicking on the four buttons marked 1 4 16 and 64 on the GEMINI 2000 Lockgain only has a 10 button and it can only be set to 0 10 20 or 30 Each click with the left mouse button on one of these buttons subtracts the value shown each click with the right mouse button adds the value shown For example to add 14 to the parameter Lockpower move the mouse cursor arrow to the 16 button in the row for lockpower and click the right mouse button once Next move the arrow to the 1 button in the same row and click the left button twice Using lockfreq to Find Lock Resonance In VNMR 6 1 and only on YN TYINOVA you can find the lock signal or resonance by using either the z0 parameter or the lock frequency If you use the lock frequency then less shimming when switching solvents and less adjustment to the lock phase should be required To choose z0 you must activate z 0 to choose lock frequency you mu
293. g on if you are in the box or cursor mode Expand Expand spectral region between cursors to the full width of chart Full Set displayed spectrum to its full spectral width The remaining buttons do not change labels sp wp Open an interactive spectral windowing mode described below Mark If selected in the cursor mode the position and spectral intensity at that point are displayed and written into a file mark1d out in the current experiment directory file e g home vnmr1 vnmrsys exp2 markld out If selected in the box mode the values of both cursor positions the spectral intensity of the maximum between the cursors and the total integral between the cursors are displayed and written into the file Phase Open an interactive phasing mode described below Th Toggles the display of a horizontal cursor The left mouse button positions this cursor at the mouse arrow position The middle mouse button adjusts the scale as described below resets Open an interactive integral reset mode see below Dscale Toggle on and off the display of a scale below the spectrum LvI Tlt Open interactive zero and first order baseline correction mode see below Set Int Set the value of an integral Ref Set spectral referencing Return Return to the last menu active before entering ds Controlling the Cursors and Spectral Intensity The cursor is controlled by moving the mouse arrow and pressing the left mouse button Alternatively the left mouse bu
294. g the Return key is assumed For example to find the value of sw type sw and the monitor displays the value of sw Unlike parameter entry only one parameter value can be requested at a time If the parameter to be displayed is an arrayed parameter the number and type of array elements are displayed For example if nt is arrayed entering nt might display the message nt array of 8 reals To display an individual element of an array provide the index in square brackets e g nt 3 might display nt 3 2 Certain parameters can be turned off by setting the parameter to n The display of a parameter that is turned off is the phrase Not Used followed by the actual value in parentheses For example if 1b is set to 1 5 and then set to n entering 1b will display lb Not Used 1 5 Parameter Value Limitations Some parameters have restricted value ranges The parameter nt number of transients cannot be negative for example Attempting to enter an illegal value results in the system assigning the parameter a minimum or maximum value An error message is also displayed explaining the actual value assigned to the parameter Certain numeric parameters nt is an example again are limited to integers and a non integer number entered is rounded to the nearest integer Some string parameters can only be set to enumerated string values Attempting to enter a value that is not one of these values produces
295. geneity at the conclusion of the shimming must be specified e Method used to shim For routine tweaking of the resolution adjustment of Z1 and Z2 is sufficient and the method z1z2 would be selected In the interactive Autoshim mode this is one of six methods accessible by pull down menu after auto is selected A variety of standard shim methods are available in the vnmr shimmethods library You can use the dshim macro to display the available shim methods You can also create your own shim method and store it in your user shimmethods for vnmr1 the path would be export home vnmr1 vnmrsys shimmethods on Solaris or vnmr1 vnmrsys shimmethods If you decide on a particular method for routine work it would be wise to save it in the standard parameter set for each nucleus to which it is applicable Automatic shimming relies on a non saturating lock signal on which an optimizing process can be performed If too high a lock power is used the shimming process can become unreliable since it may be chasing a moving target Since it is customary to increase lock power until the lock level maximizes if done manually it is clear that lock signals will be partially saturated This follows directly from the shape of a saturation curve where signal amplitude increases linearly with lock power until a point where it flattens out becomes oscillatory and eventually declines Adjustment for maximum lock level puts the lock power near the
296. ghting constant 72 221 223 addpar macro 111 228 236 address of local Ethernet node 283 Adj IS button 77 Adj VS button 77 Adj Weighting button 71 73 74 Adj WP button 77 Adjust button 75 adjust integral height 253 adjust integral scale 77 adjust vertical scale 77 adjust width of plot 77 advanced operating features 29 aexppl macro 250 ai command 232 245 aig parameter 245 alfa parameter 187 188 216 algorithm autophase 225 All Contours button 80 All Params button 78 80 allzs method 145 alock parameter 132 133 154 AM Bruker data 289 AMX Bruker data 289 analog anti aliasing filter 210 analog to digital converter ADC 24 209 Analyze button 66 80 Analyze menu 81 angled brackets lt or gt notation 21 ap command 261 aph algorithm 225 aph command 225 aphO algorithm 225 aphO command 225 aphb command 225 apinterface parameter 192 app defaults directory 45 append text to current experiment text file 197 Applications Mode menu 70 appmode parameter 70 APT button 68 apt macro 32 arguments to commands 93 array index 95 array macro 95 arraydim parameter 200 arrayed experiment dimension 200 arrayed experiments 278 arrayed parameters 95 arraying a parameter 31 32 assign button 85 assign macro 85 asynchronous decoupler mode 190 at parameter 140 187 atext command 197 Attached Proton Test 68 ATTEN pushbuttons 116 ATTEN re
297. gradient shimming method has these steps 1 Map the shims 2 Perform autoshimming The shims must be mapped before autoshimming is used Mapping the shims is necessary when a new probe is installed but can be repeated at any time Table 22 summarizes gradient shimming commands and parameters Table 22 Gradient Shimming Commands and Parameters Commands dg2 Display group of parameters gmapshim lt files quit gt Run gradient autoshimming get files and parameters quit gmapsys Enter Gradient Shimming System menu make shimmap gmapz lt mapname gt Get parameters files for gmapz pulse sequence gmapsys lt shimmap lt auto manual overwrite mapname gt Parameters gradtype Gradients for x y and z axes gzlvl DAC value Pulsed field gradient strength gzsize integer 1 to 8 Number of z axis shims used by gradient shimming gzwin 0 to 100 Percentage of spectral window used by gradient shimming pfgon nny if on PFG amplifiers on off control gradtype 3 character string from n w 1 p q s t u h Configuring Gradients and Hardware Control 1 Confirm that PFG or homospoil gradients are installed on your system See the chapter on PFG modules experiments in the manual User Guide Liquids NMR 2 Confirm that the gradients are active by checking that gradt ype and pfgon are set appropriately for your system Use config to change settings if necessary 3 Ifyou have the Ultrasnmr
298. gzsize is greater than 4 shimming is done first on Z1 Z4 and then proceeds with all shims specified by gzsize Gradient shimming takes longer and goes through more iterations but this may avoid the problem on some systems where a high order shim i e Z5 Z6 goes out of range because it contains impurities from lower order shims This parameter may be set at any time while shimming 01 999083 00 A1298 Getting Started VNMR 6 1B 173 Chapter 6 Preparing for an Experiment 174 from gmapsys In order to use this parameter in user autoshimming set it before making a shimmap or in the corresponding parameter set in gshimlib shimmaps Quitting the Gradient Shimming System Menu Enter gmapsys and click on Quit to exit from the gmapsys menu system This also retrieves the previous parameter set and data including any data processing done on the previous data set Deuterium Gradient Shimming Deuterium gradient shimming is feasible for most deuterated solvents because the lock solvent usually has a single strong deuterium resonance with sufficient signal The automated deuterium gradient shimming module is required to run deuterium gradient shimming If present this module automatically holds the lock at its current value and switches the transmitter cable to pulse the lock coil when an experiment is run with tn 1k The module is strongly recommended for all users who wish to run deuterium gradient shimming in automation See Table 21 for
299. gzwin and tof You may click through these steps separately to see if gzwin is calibrated correctly The box cursors at the end of step should be at either edge of the profile Manual Calibration of gzwin Manual calibration of gzwin may be used to avoid noise spikes in the spectrum or other artifacts To manually calibrate gzwin do the following 1 Click on Set Params gt Go dssh Wait until the experiment is done 2 Enter ds and set the box cursors near the edges of the profile 3 Enter gmapsys and click on Set Params gt Calculate gzwin 4 Click on Return gt Shim Maps gt Make Shimmap The parameter gzwin should be adjusted only when making a new shimmap The calibrated value of gzwin is saved when the new shimmap is saved at the end of the mapping experiment The same value of gzwin must be used in shimming as in making a shimmap and should not be adjusted when shimming 01 999083 00 A1298 Getting Started VNMR 6 1B 171 Chapter 6 Preparing for an Experiment 172 Shimmap Files and Parameters The parameters and shimmap files saved under a mapname are retrieved when that mapname is retrieved When reinserting a probe reload the shimmap for that probe If you are unsure if the shimmap is correct make a new shimmap which typically only takes a few minutes The last parameters and files used are automatically retrieved the first time gmapsys is entered If gmapsys is entered again the parameters are not retrieved
300. hapter 10 Storing Retrieving and Moving Data 290 If data has been written onto a magnetic tape on a Silicon Graphics computer and is to be copied back onto a Sun or IBM RS 6000 computer the byte order is again reversed The tar command cannot be used alone in this case instead use the command string dd if dev rmt 0lb conv swab bs 20b tar xvBfb 20 6 Note there is a space between the and the 20 at the end of the command string CAUTION Keep magnetic tapes away from the magnet Data stored on the tape can be damaged by the strong magnetic field Reading Tapes from Gemini VXR 4000 and XL Systems The command tape lt type gt keyword lt file gt displays the contents of a VXR style tape used on a Gemini VXR 4000 or XL system for use on a UNIX based system or reads one or files from a VXR style tape into the current directory t ype is the type of tape to be accessed default is the 1 4 in tape keyword can be help display entry options cat display catalog of files on tape read read file given by filename maximum of four file names can be specified rewind rewind tape 1 2 in tape only or quit release the tape drive 1 2 in tape only If you are using Vnmrl on an IBM RS 6000 computer or VnmrSGI on a Silicon Graphics computer tapes from V XR style systems can be read using the UNIX dd command For the IBM RS 6000 the following command is appropriate dd if dev rmt1 fskip 1 of
301. he fine adjust The overall sensitivity of these adjustments can also be controlled by the parameter 1v1t1t This parameter is a multiplier with a default value of 1 0 for the size of the changes To make larger changes make 1v1t1t larger than 1 0 To have finer control set 1v1t1t to be between 0 0 and 1 0 The middle mouse button adjusts the integral scale parameter is or the integral offset parameter io exactly as whenever an integral is displayed To exit the interactive baseline correction mode make another selection from the menu the first button Cursor or Box is always an appropriate choice if no other choice is desirable Setting the Integral Value 1 Position a cursor over an integral region and then press the Set Int button to display Current integral is xx New value 2 Enter the value you want to assign to that integral region Setting the Reference Position 1 Position a cursor on the reference line and then press the Ref button to display New reference value in ppm 2 Enter the value you want to assign to that line Interactive Inset Display The inset command displays the part of the spectrum between the two cursors in ds as an inset The vertical position of the inset spectrum is shifted up about one quarter of the height of the whole display window The old spectrum remains on the screen but the parameters shown at the bottom are now relevant to the inset display If present the integra
302. he section covering the LOCK display e SHIM sets the mode of shimming manual mode performs manual shimming and auto mode performs automatic shimming Each is described next Manual Mode troi ACQUISITION CLOSE LOCK FID LARGE SPIN off SHIM manual on auto SPINNER iquids solids mas coarse 0 20 40 60 80 100 E fine 0o 2 4 6 8 0 2 4 6 8 starting lock level current lock level E 188 L 278 E 119 C 170 Figure 46 SHIM Display Window acqi Program In the manual mode up to six shims can be displayed for adjustment Using the SHIM menu to select sets of shims and adjusting shim values is covered in FID Spectrum Shimming Windows on page 154 Auto Mode In the auto mode the bottom of the window changes to one button and two menus shown in Figure 47 01 999083 00 A1298 161 Getting Started VNMR 6 1B Chapter 6 Preparing for an Experiment 162 START button starts the shimming process START When shimming starts the button label d changes to STOP Clicking on STOP will stop QUALITY L gt M the shimming AUTO SHIM kd Z1 Z2 QUALITY menu selects the shimming criteria loose L medium M or tight Figure 47 Auto Mode Window T and the order used for example L gt M acqi Program means start with loose shimming and end with medium shimming The selection is made with the mouse in the normal way Refer to
303. he LOCK button 128 Getting Started VNMR 6 1B 01 999083 00 A1298 6 7 Spinning the Sample The LOCK display appears with the following spin related information see Figure 33 The SPIN menu near the top of the display e A readout of the actual spinning speed at the bottom of the graphics window e Controls for changing the value of the spin parameter at the bottom of the display The controls for changing spin consist of a readout with the current value of spin shown in square brackets e g 20 aslide control for adjusting the value of spin and four buttons labeled 1 4 16 and 64 also for adjusting the value of spin Check that the on button in the SPIN menu is selected Also check the current spinning speed displayed near the center of the LOCK display To adjust the spin parameter use either of these methods e Drag the mouse cursor across the slide control with the left button of the mouse held down The value changes proportionally as the mouse moves e Click on the 1 4 16 and 64 buttons as required Clicking on a button with the left mouse button decreases spin by the amount shown on the button clicking with the right mouse button increases spin by the amount shown on the button For further information see the LOCK Display on page 151 Using the Spinner Control Window The spinner command opens the Spinner Control window for control of sample spinning see Fig
304. he additional parameters sp wp dmg rp lp rfl rfp vs vp sw and fn The same limits on the acquisition et fol CaS mae a parameters as those described for the a FID display apply to the spectrum display Furthermore if the Fourier number parameter fn is greater than 64K it is reduced to 64K 64 Figure 44 Spectrum in FID Spectrum Display Window acqi Program These parameters are automatically sent to acqi when acqi is first invoked They can subsequently be changed and sent again to acqi with gf or acqi par This is exactly analogous to the way the FID parameters are sent to acqi Interactive Parameter Adjustment In interactive parameter adjustment IPA not available on MERCURY VX MERCURY and GEMINI 2000 if the pulse sequence used for go acqi or gf contains statements such as ipulse or idelay or if the parameter phfid is not set to NOT USED a menu labeled PANEL appears to the right of the FID Spectrum menu with the following choices e Shim selects the shim adjust button in the bottom panel to enable you to adjust the displayed shims while observing the FID To select different shims to adjust select a different choice from the SHIM menu At the bottom of the display are buttons for adjusting the shims or parameters To increase a shim or parameter value click with the right mouse button on the button with the value you want to increase to decrease a value click with the left mouse button instead Adjus
305. he current plot jobs in the plot queue for the active plotter To stop a plot in progress a plot in which you have not entered page use the command page clear The killplot macro stops all current plot jobs in the plot queue for the active plotter then removes the jobs from the plot queue Unless the user executing killplot is root only that user s plots jobs are deleted from the plot queue Plots can be sent to a file instead of to a plotter by supplying a file name argument to the page command In this way PCL HP GL and PostScript files can be captured for incorporation into other computer documents Plotter Configuration The VNMR software supports a variety of different plotter devices with different characteristics Pen plotters and raster graphics printers are supported For pen plotters the HPGL graphics language from Hewlett Packard is used For raster graphics printers the Hewlett Packard raster mode or PostScript is used The following parameters are used to describe the characteristics of different plotters e plotter contains a code for the selected plotter e wcmax is the maximum horizontal width in mm of the plotter area e wc2max is the maximum vertical size in mm of the plotter area maxpen is the maximum number of pens colors available on plotter When changing to a Hewlett Packard plotter the set pen macro allows the user to interactively define the maximum number of pens The parameters plotter wcma
306. he module display such information as the status and temperature of the variable temperature unit lock level acquisition and other information for each active rf channel MERCURY VX MERCURY and GEMINI 2000 systems use an indicator on the magnet leg VNMR Display Screen The VNMR display screen shows you what is happening with the data Figure 2 shows a typical configuration of this screen Acquisition Status window Status window Seq stdih Exp 1 Index 1 H unigem400 E STATUS Interactive P i USER EXP Interactive FID CT e opo Input EE completion Tine Acquisition I Remaining Time rome window window Abort Acq Cancel Cmd GLIDE Main Menu Help Flip Resize eer View Interactive Massage Size Reprocess Plot More Integrals ante aan te ant IE EE Menu TD SHIM LARGE buttons Graphics window Text window SPIN oft LOCK off SAMPLE iugert SPINNER iguids for fou eka solitsnas E e oe o G2 PY E CDE toolbar Figure 2 VNMR Display Screen The display is divided into several windows The menu buttons graphics window and text window are typically always visible Like most windowing systems these windows can be moved resized and even closed The windows are described here and throughout the manual according to
307. he reverse of the removal procedure above 6 5 Using Probe Files and Templates Table 12 summarizes the VNMR macros and parameters connected with probe files Refer to the manual Walkup NMR Using GLIDE for more information on probe files Table 12 Probe File Macros and Parameters Commands addnucleus lt nucleus gt Add new nucleus to existing probe file addparams Add parameter to current probe file addprobe lt probe_name lt system gt gt Create new probe directory and probe file getparam param lt nucleus gt Svalue Retrieve parameter from probe file setdecpars Set decoupler parameters values from probe file setdec2pars Set decoupler 2 parameters values from probe file setparams param value lt nucleus gt Write parameter to current probe file updateprobe Update probe file addparams param value nucleus lt tmplt gt lt system gt updateprobe lt probe tmplt gt lt system gt Parameter probe string Probe type 6 6 Tuning the Probe Probe installation and tuning varies with the spectrometer and the type of probe Table 13 summarizes the VNMR commands connected with tuning probes Different NMR laboratories also have different standards about probe tuning Table 13 Probe Tuning Commands Commands btune Tune broadband channel on GEMINI 2000 any channel on MERCURY ctune Tune 3C channel on H 3C GEMINI 2000 dtune Tune lock channel on GEMINI 2000 go Submit experiment to acquisiti
308. he right the coarse fine gradient control C F button is active in both the BANK and the FILE modes Files 2 through 63 are available for user storage Users can not write to file 0 which contains all zeros or write to file 1 which contains converged shim values Files are stored on a DOS formatted 1 4 MB floppy disk in a drive accessible from the front of the main unit The small cover panel at the right edge of the upper card cage must be removed to gain access to the system floppy disk New disks must be formatted using DOS version 5 0 or higher Numerous calibration files will be copied to that disk Copies of existing floppy disks can be made using the DOS diskcopy command on any machine running DOS version 3 3 or higher for example enter diskcopy a a ifthe particular floppy drive is configured to be drive A One of the selectable options in the MODE mode allows system lock out for security reasons If this feature is activated all knob button and toggle control is disengaged until the MODE BANK and VIEW buttons are simultaneously pressed It is also possible to disable turn off the lock from the interface box in the MODE mode This feature is contained in the ZO enable ZO disable option After Ultraenmr Shims are installed Z0 is not controlled via the Acquisition window but only from the Ultrasnmr Shims interface box All other lock parameters 1lockpower lockgain and lockphase remain controlled through the Acquisition wind
309. he screen and page The command is used to set the sp and wp parameters to display a full spectrum The zoom width macro adjusts the display limits to the width specified in Hz setting the limits to width 2 Also available is the split macro which repositions the left hand cursor halfway between its original position and the position of the left cursor A scaling factor helpful for 1D plotting is the hzmm parameter which contains the quotient of wp divided by wc The wysiwyg parameter is useful for scaling the image to a full window instead of the same size as the plot Setting wysiwyg n sets a full display and wysiwyg y sets a plot display the default 9 6 Integration 250 This section describes methods and tools for displaying and plotting integrals Table 39 lists the integration commands and parameters described in this section Displaying Integrals Step by Step The following methods should give you an opportunity to compare procedures Before starting each procedure be sure to obtain a typical spectrum by entering rt vnmr fidlib fidld wft full Menu Method 1 Click on Return The 1D Data Display menu appears It will also appear after steps 2 3 and 4 Click on Massage gt Region gt Return Optional Click on Massage gt BC gt Return Click on Massage gt Adj IS gt Return Click on More a oe Getting Started VNMR 6 1B 01 999083 00 A1298 9 6 Integration Table 39 Integral Display
310. hese two data sets to produce one data set according to the formula absorption spectrum real channelg cos imaginary channelg sin Eq 3 The process is complicated by the fact that phase angle 0 is a function of frequency 8 rp Wo lp Eq 4 where 1p left or first order phase and rp right or zero order phase are constants that must be determined The following is clear about the terms in Equation 4 e rp is frequency independent Changes in rp affect all peaks in the spectrum equally e lp is frequency dependent Changes in 1p affect peaks with a differing amount as a function of frequency There are several ways in which 1p and rp can be adjusted e Like any parameter they can be recalled with a particular parameter set Once entered they can also be entered directly e g lp 150 Getting Started VNMR 6 1B 01 999083 00 A1298 8 4 Phasing e Fully automatic phasing is also provided with the aph command which optimizes both the frequency dependent 1p and the frequency independent rp parameters and is independent of the starting point The aph0 command only adjusts rp The aphx macro optimizes parameters and arguments for the aph command aphx first performs an aph then calculates a theoretical value for 1p If 1p set by the aph is different from the calculated value by 10 per cent the calculated value is used and an aph0O is performed The command phase phase_change changes the phase of all
311. host computer occurs through the display screen three button mouse and keyboard The use of these devices is introduced in the section User Interface on page 25 A wide range of Sun desktop workstations can be used with a system The standard workstation contains a hard disk drive to store data and a magnetic tape unit for saving and transferring data If additional data storage is necessary a second hard disk drive can be 01 999083 00 A1298 Getting Started VNMR 6 1B 23 Chapter 1 Overview of Varian NUR 24 added to the system A CD ROM drive must also be available either local or on a network for installing the current versions of Sun and Varian software System printers plotters additional memory and other computer peripherals can be added to the basic system NMR System Console The NMR system console contains rf electronics including transmitters amplifiers and receivers as well as a complete computer system known as the acquisition computer Units in the acquisition computer control the pulses and timing of the acquisition process through the Digital Acquisition Controller board Pulse Sequence Controller board Acquisition Controller board or Output board depending on the system digitize the signal through the analog to digital converter or ADC and automatically sum the data and scale it when necessary the H 13C GEMINI 2000 uses software data summing The acquisition computer is also responsible for the cont
312. however It is possible to also use set ref to preestimate the position if the reference frequency in spectra from unlocked samples provided the spectrometer is first locked on a sample with similar susceptibility then in acqi the lock is disengaged and the field offset adjusted such that the lock signal is on resonance Now you can acquire spectra without lock and calculate their estimated referencing using set ref provided the solvent parameter is set to the solvent the system was last locked on The setoffset macro uses set ref to calculate offset frequency for a chemical shift The macros set ref1 and set ref2 are used to reference f and f in multidimensional spectra respectively They take the frequency relevant nucleus as argument tn for homonuclear nD spectra dn for f in heteronuclear 2D spectra etc and both call set ref with that nucleus as argument for the calculation of the referencing parameters Spectral Plotting The p1 command plots the currently displayed region of the currently active spectrum or spectrum plus integral or the region which would be displayed if there were a spectral display on the screen p1 int plots the integral only p1 pen2 plots the spectrum using pen number 2 of a multi pen plotter The pscale command plots a scale under a spectrum The syntax is pscale lt x lt axis gt lt vertical_start gt lt plot_start gt lt pen gt gt If the letter p h k etc is supplied as
313. hst number in milliseconds Homospoil time probe_protection n y Probe protection control wbs string When block size werr string When error wexp string When experiment completes wnt string When number of transients 01 999083 00 A1298 Getting Started VNMR 6 1B 199 Chapter 7 Acquiring Data 200 e Whenever data are acquired the current date is copied from the UNIX level calendar and written into the acquisition parameters thus maintaining a record of the date of acquisition The date parameter contains the date that is copied To calculate the dimension of an experiment enter the cal cdim command The result is put into the arraydim parameter If an experiment is arrayed arraydim is the product of the size of the arrays The celem parameter indicates the number of completed FIDs in an experiment When go or au is entered celem is set to 0 As each FID acquisition is completed celem is updated This parameter is most useful in conjunction with wbs wnt wexp and werr processing macros see Automatic Processing on page 191 Shimming During an Acquisition On UN TYTNOVA systems only you can use the Acquisition window to shim on your sample while an acquisition is in progress The procedure is as follows 1 Ifthe Acquisition window is not open enter acqi to open the window shown in Figure 61 troi ACQUISITION CLOSE SHIM LARGE 2 Enter su go orau to start an acquisition Figure 61 Acquisi
314. i se i sstscssasesseetasas coveeuscesttaes shassciacachacesus seesscaeseesenazesscubteds 145 Gradient AUtOSRINT 5266ssc5sceceds sevespewiescrie eeneioe ane E E R E REER 146 Which Shims to Use on a Routine Basis ssssessseessseseeseseeesrerrsrerrsrrererreseereee 147 8 Getting Started VNMR 6 1B 01 999083 00 A1298 Table of Contents Shimming Different Sample Geometries 00 ee eeeceeeseeeeeeececeeeeeeseceeeneeeees 147 6 10 Using the Acquisition Window o0u eee eeeeeeseceeceeceneeeceseeeceseeeeeeeeeeseaeeeeseaeeaeeeas 148 Opening the Window viscid siiicscaees ecicreseeeecseascdsec Ee e EEE e EE eiS 148 Connecting to the Acquisition System oo eee cseeecneceeceeceseeeeeeseeeeeeeeees 149 Making a Choice in a Display 0 ee ceeeeecseeseeceeaeceecaeceeceseeeeeeeeeeeeeeees 150 Changing Parameter Values ssssssssesssscssossseeseesseevonsseecseesseessersnessenetoes 150 LOCK Display si isciiii ai biiadiniwudtied amc uid E E RESE 151 Using lockfreq to Find Lock Resonance oe eee eeseeseceeceseceeceeeeeeeseeeeenetees 152 Using sethw to Set Lock Frequency 0 eee ee eeeeeecseeeeecneceseceeceseeeeeeseeereeeeees 153 Simple LOCKING 4s sesciees ssc ccen seo eresia ireira een steed stews EE TNES AEE EEEE EEEE 153 FID Spectrum Shimming Windows ssessesessesesesererssrererresrerssrrresreresrrererrereerese 154 Interactive Parameter Adjustment eseeseesesseesrserersrrererresesrssreresrerrsrrererrereersee 159 Shimming on the FULD
315. ibrary limNET automatically supplies this extension Note that when data is copied from a VXR style system all files should first be stored in a directory on the system and then stored on the tape as one file or transferred over Ethernet as one file Otherwise the command decomp will not work 01 999083 00 A1298 Getting Started VWMR6 1B 287 Chapter 10 Storing Retrieving and Moving Data Step by Step Example with limNET The VNMR command convert takes the FID file from a VXR style Gemini VXR or XL system into a format with which the VNMR program can work The reverse capability converting data from VNMR format into VXR style format does not exist The example below shows the interaction on a Sun system using limNET with the remote VXR style system a Gemini named gemini 1 The following commands are entered with the responses shown gt eread hl gemini fidlib hl 23 gt ls hi hL 5 gt vnmr 2 WNMR starts up In VNMR enter convert h1 5 The convert command works with the output from the VXR style command SVF An output of 23 from the eread command indicates the file fidlib h1 is 23 blocks in size The suffix 5 appears because the entry h1 is a VXR style directory with 5 entries as is typical for saved FIDs on VXR style systems 3 To save the data in VNMR format enter svf h1 4 Verify the operation was successful by entering 1s h1 VNMR displays the contents of the direct
316. ibration corrections respectively The default is enabled If valid calibration files are not present this button is not available 4 Connect a shorting load e UNITYINOVA and UNITYplus Connect a shorting load to the tune port e MERCURY VX Connect a shorting load to TUNE J5402 on the inside probe side of the magnet leg 5 Click the Short Test button 6 Remove the shorting device from the tune port 7 With no load on the tune port click the Open Test button The program divides the full range of the spectrometer into 32 frequency bands and runs 32 experiments This data is merged into one high resolution data set After enough data are collected the Accept button becomes available If ADC overflow occurs a warning message appears 8 After you see a strong signal the signal will be stronger at low frequencies than at high frequencies that does not cause ADC overflow click the Accept button 9 Attach a 50 ohm load e UNITYINOVA and UNITYplus Connect the 50 ohm load to the tune port e MERCURY VX Connect the 50 ohm load to TUNE J5402 on the inside probe side of the magnet leg 10 Click the 50 Ohm Test button The program divides the full range of the spectrometer into 32 frequency bands and runs 32 experiments The data is merged into one high resolution data set After enough data are collected the Accept button becomes available If ADC overflow occurs a warning message appears 11 Click the A
317. ic 225 G ga command 138 198 200 204 gain from real time DSP 215 gain parameter 154 206 GARP decoupling 194 Gaussian apodization 222 Gaussian line shapes 222 gaussian macro 222 Gaussian time constant 72 221 223 Gaussian time constant shift 72 223 GEMINI 2000 decoupling values 195 probe tuning 124 Gemini systems 281 generating pulse sequences 91 generic plotting macros 250 gettxt command 197 gf button 72 223 gf macro 154 156 159 gf parameter 221 222 gfs button 72 223 gfs parameter 221 GLIDE 01 999083 00 A1298 button 49 53 54 65 command 49 53 directory 34 files 34 opening and closing 53 user interface 28 49 global file 37 gmapshim macro 172 176 gmapsys macro 170 172 177 Go button 70 198 Go button GLIDE 55 go command 32 115 138 183 198 200 203 207 go acqi command 156 Go Periodic Wft button 71 204 Go Wft button 70 198 go_ macro 198 gotolink cpr_j jplotscale 269 gotolink cpr_r rtcmx 279 Gradient Autoshim on Z button 176 gradient autoshimming 168 Gradient Autoshimming Files menu 172 178 181 Gradient Nucleus Parameter Setup menu 177 Gradient Shim Setting menu 178 180 Gradient Shimming Display menu 178 180 Gradient Shimming Files menu 178 179 Gradient Shimming Map menu 178 179 Gradient Shimming Plot menu 178 180 Gradient Shimming Setup menu 177 178 179 Gradient Shimming System menu 170 177 178 gradient systems 24 gradi
318. ies and their contents is deleted Getting Started VNMR 6 1B 87 Chapter 4 Using the VNMR Menu System Button Description More Display the Files Secondary menu page 90 for additional options Return Display the Main menu page 66 Directory Menu The Directory menu is activated by selecting the Set Directory button in the Files Main menu by selecting Return in the Directories Secondary menu or by entering the command files files_dir Button Description Change Change to a new directory First mark a directory in the files display directories have a following their names and then click on this button If you have selected a directory that becomes the new current directory If you have not selected any entries a prompt appears requesting the name of the new current directory Default Set current directory to the value of parameter defaultdir Initial value is your home or login directory Set Default If you click this button and haven t marked any entries the current directory becomes the new value of parameter defaultdir Otherwise if you have marked a directory and then clicked on this button the directory you marked becomes the new defaultdir In both cases the new value of defaultdir is displayed An error is reported otherwise Parent Set the current directory to the parent of the current directory Home Set the current directory to the home or login directory Nmr Set the current directory
319. ifting linear prediction and interleaving FIDs Table 33 lists the tools discussed Table 33 Advanced Data Processing Commands and Parameters Commands addpar lp addpar ss dglp ilfid parfidss parlp tmove Parameters lpalg Ipfft Iparfft lpext number lpfilt number lpnupts number lpopt b f lpprint number lptrace number lsfid n number lsfrq number in Hz phfid 360 to 360 in deg proc ft rft lp ssfilter n 10 to sw 2 in Hz sslsfrq n number in Hz ssntaps 1 to np 4 ssorder n 1 to 20 strtext 1 to np 2 strtlp number FID Phase Rotation Create parameters for linear prediction in np dimension Create parameters for time domain solvent subtraction Display group of linear prediction parameters Interleave FIDs during data processing Create parameters for time domain solvent subtraction Create parameters for linear prediction in np dimension Left shift FID to time domain cursor Linear prediction algorithm in np dimension Linear prediction data extension in np dimension Linear prediction coefficients to calculate in np dim Linear prediction number of data points in np dim Linear prediction algorithm data extension in np dim Linear prediction print output in np dimension Linear prediction output spectrum Number of complex points to left shift np FID Frequency shift of the fn spectrum in Hz Zero order phasing constant for np FID Type of processi
320. igher order gradients causing less effect per DAC unit The following suggestions are offered e ZO use coarse only fine is too fine e Z use fine only coarse is far too coarse e Z2 Z3 ZA use coarse or fine whichever seems best e Z5 Z6 Z1 Z8 use coarse only e Radial shims use coarse with the possible exception of X and Y Remember that the gradients produced are purer more orthogonal so shimming methods subjectively generated on other shim systems may not behave the same If you adjust any axial shim you should probably touch up Z before touching any other gradients for example if you change Z4 then optimize Z before touching up Z2 In addition be forewarned that 80 of what might be corrected with Z4 using an Oxford shim system is probably corrected with Z2 when using Ultraenmr Shims Installing the First Probe Starting from the final converged results obtained with field mapping it is possible to obtain a lineshape of less than 7 12 Hz non spin in under an hour or two on 1 CHCl in acetone dg ASTM IH lineshape sample Z and Z2 typically change the most Z fine needs about 70 units Z2 about 400 units but Z3 Z4 Z5 X and Y will need adjustment The higher order radial shims are typically converged to a better value than a user can determine spectroscopically and should therefore not be adjusted manually only X Y ZX ZY and possibly C2 and S2 should need adjustment A simple maximization of the l
321. ilable for the general user e Automated Shimming menu To open click on Main Menu Setup Shims Lock Autoshim Lock Autoshim z1z2 Gradient Autoshim on Z Return e Gradient Autoshimming Files menu To open enter gnapshim files Cd to Userdir Copy to Userdir Load Shimmap Load Shimmap amp Params Rename Return A description of each menu in the same order as above the button or command for opening the menu and the action of each button in the menu is given in the following sections On all menus the left mouse button is used to click on the desired choice in the menu The other mouse buttons are not active Gradient Shimming System Menu The Gradient Shimming System menu is the top level menu for gradient shimming setup and shim mapping To open this menu enter gmapsys Button Description Set Params Enter Gradient Shimming Setup menu Shim Maps Enter Gradient Shimming Map menu Autoshim on Z Start gradient shimming using current parameters Fit is displayed with each iteration Set Shims Enter Gradient Shim Setting menu Display Enter Gradient Shimming Display menu Quit Return to previous experiment Gradient Shimming Setup Menu The Gradient Shimming Setup menu is used for calibrating gradient shimming parameters To open this menu click on Set Up in the Gradient Shimming System menu Button Description Go dssh Run and display profile spectra Gradient Nucleus Enter Gradient Nucleus paramet
322. ile 248 number of transients 187 188 numeric arguments 94 numeric parameters 94 numerical integral amplitudes 254 numrfch parameter 110 01 999083 00 A1298 O object preferences setting 265 observe button 85 observe receiver gain 157 opening a window 51 OpenWindows windowing environment 25 33 optimizing Autolock 133 optimum Ernst pulse width 188 optimum lock parameters 130 organic solvents 114 Original button 83 orthogonal data points 227 oscoef parameter 212 osfb parameter 212 osfilt parameter 214 oslsfrq parameter 212 218 Output board 24 output devices 92 oversamp parameter 212 214 oversampling amount 214 oversampling data 209 oversampling factor 212 213 P p suffix 95 pl command 188 pl parameter 187 188 P31 button 68 pacemaker warning 17 pad parameter 187 Page button 78 80 page command 255 pages of plotter output 254 panel menu 159 panels of shims 157 pap macro 261 paramedit command 112 261 paramedit macro 261 parameter sets 107 correct saved sets 280 filename storage 110 listing files 108 retrieval 109 standard parameter sets 110 storage 36 parameters acquisition 37 adjusting and restoring plot 269 arrayed 95 baseline correction 242 chemist style 261 common to experiments 37 create for current experiment 111 default values 96 defined 93 display groups 112 entering values by hand 231 entry 95 entry
323. ile lt options gt converts 32 bit Bruker AMX data and 24 and 32 bit Bruker AM data into a 32 bit format compatible with Varian s sread program The file argument to convertbru is the name of the input argument From UNIX the syntax is convertbru file options Refer to the VVMR Command and Parameter Reference for detailed information on convertbru including the options available and examples After converting the Bruker data into the new format the converted data can be read into VNMR using the command sread file cv lt template gt where file is the name of the file containing the converted data and template is the full path of a parameter template file do not append par to the file name for example sread brudata cv vnmr parlib bruker The name of the file containing the parameter template is optional the default is bruker par If no parameter template is specified and bruker par cannot be found in the user or system parlib directory sread aborts with an appropriate error message 10 6 Magnetic Tape Operations Table 51 lists UNIX and VNMR commands associated with magnetic tape operations Table 51 Magnetic Tape Operations Commands Commands dd lt option value gt Convert and copy a file UNIX mt lt f tape gt command lt count gt Magnetic tape control UNIX readbrutape file lt num_skipped gt Read Bruker data files from 9 track tape UNIX tape lt type gt option lt filel gt Read tapes fr
324. ime rf1 is set to the distance of the cursor from the right edge of the spectrum in Hz rfl sw 2 sfrq reffrq le6 and the parameter rfp is set to 0 because we have referenced the spectrum based on the position of the reference frequency itself Optionally r1 takes the position of the reference line in Hz as an argument For example if you reference a proton spectrum to the chloroform CHC14 solvent line you would position the cursor on that signal and enternl r1 7 24p r1 first calculates the absolute cursor position as absolute_cr sfrq cr rfl rfp sw 2 1l1e6 and can then calculate ref frq as vreffrq 1 1 argument_1 reffrq 1le6 absolute_cr refpos is set to 0 rf1 and rfp are calculated as follows rfl sw 2 absolute_cr sfrq le6 rfp absolute_cr reffrq le6 01 999083 00 A1298 Getting Started VWMR6 1B 247 Chapter 9 Display Plotting and Printing 248 The cr1 command clears the reference line by removing any spectral referencing present It also sets refpos n turns off referencing After this operation zero frequency appears at the right edge of the spectrum The tmsref command tries to locate a TMS line If found tmsref re references the spectrum to the TMS line and returns a to the calling macro if not found tms re f returns 0 and the referencing is left as it was In the case of other signals e g from silicon grease immediately to the left of the TMS line even if they
325. in taken from the nucleus table but then the set frq command is called by the system set frq immediately combines the frequency from the table with information about the lock solvent and small offset and stores the result in the parameter s f rq The result is that when a data acquisition is requested with go no further adjustment of the value of sfrq is needed In other words the value of s frq and dfrq dfrq2 dfrq3 dfrq4 for decouplers is the exact frequency that will be used The benefits of the new approach are that the frequency is readily apparent and more importantly the calculation of ppm scales which are based on the value of s frq are exact Also data that is stored can be recalled later on any system and the correct frequency at which the data were obtained will be known an essential part of good laboratory practice 01 999083 00 A1298 Getting Started VNMR 6 1B 183 Chapter 7 Acquiring Data Table 24 Acquisition Frequency Related Commands and Parameters Commands centersw minsw movesw lt width gt movetof lt frequency gt sd sd2 sd3 sda sd2a sd3a setfraq lt channel gt setsw downfieldppm upfieldppm Parameters cr number delta number in Hz dfrq dfrq2 dfrq3 dfrq4 number in MHz dn dn2 dn3 dn4 string dof dof2 dof3 dof4 number in Hz lockfregq n 1 to 160 in MHz rfband string using h T c rfchannel string using 1 2 3 4 sfrq number in MHz
326. ine frequencies and amplitudes The parameter th is used as the listing threshold Display list of integral intensities using the current set of integral reset points If parameter intmod partial every other integral is listed If intmod full or intmod of f every integral is listed The ins parameter acts as a divisor for this listing of integral amplitudes Display spectra horizontally with a scale under first spectrum Display spectra with automatic adjustment of the parameters ho and vo Display a scale under the first spectrum 01 999083 00 A1298 4 10 Display Menus Button Description AV OR If labeled AV switch to the absolute value mode PH If labeled PH switch to the phase sensitive mode The value of the parameter dmg determines the button label Reference Reference the spectrum so as to set the cursor position to zero on the chemical shift scale Return Return to the 1D Data Display menu page 77 2D Data Display Menu The 2D Data Display menu is activated by selecting the Display button in the Main menu while a 2D experiment is active or by entering the command menu display_2D Button Color Map Contour Image Size Massage Reprocess Plot More Description Display normal 2D contour display color image or map and allow for interactive adjustment Display a true 2D contour display comparable to plotter output this mode is slower than a simple color map Display grayscale i
327. ing Started VNMR 6 1B 01 999083 00 A1298 6 12 Gradient Autoshimming Automated Shimming Menu The Automated Shimming menu is used for running automated gradient shimming after a shimmap is made To open this menu click on Main Menu Setup Shim Button Description Lock Autoshim Start lock autoshim using current method Lock Autoshim z1z2 Start lock autoshim on z1z2 Gradient Autoshim on Z Start gradient autoshim on z axis shims Quit Gradient Shim End gradient shimming and return to previous experiment Return Return to Acquisition Parameter Setup menu Gradient Autoshimming Files Menu The Gradient Autoshimming Files menu is used for loading shimmaps To open this menu enter gmapshim files Button cd to Userdir or cd to Systemdir Current Mapname Load Shimmap Load Shimmap amp Params Return Description Change directory to userdir shimmaps Change directory to syst emdir shimmaps Show current mapname used for gradient shimming Load files and parameters for selected shimmap Load files and parameters for selected shimmap Return to Main menu 01 999083 00 A1298 Getting Started VNMR 6 1B 181 Chapter 6 Preparing for an Experiment 182 Getting Started VNMR 6 1B 01 999083 00 A1298 Chapter 7 Acquiring Data Sections in this chapter e 7 1 Setting Frequency Related Parameters this page e 7 2 Setting Pulse Sequence Related Parameters page 185 e 7 3 Creating and Editi
328. ing are required For example the command to plot a contour plot is pcon If you want to plot only the positive contours of a phase sensitive experiment then you enter pcon pos The text string pos and others like it are referred to as keywords A keyword must be entered exactly as shown in VNMR manuals and on line 5 2 Parameters 94 Parameter names have a variable number of alphanumeric characters e g nt temp axis There are only two types of parameters numeric and string Numeric parameters are numbers while string parameters are a collection of one or more letters Numeric parameters that are typically integers such as nt number of transients can be entered with or without a decimal point e g 16 or 16 0 Scientific notation is also acceptable for input e g 1e3 for 1 x 103 or 2 5e 4 for 2 5 x 10 4 Getting Started VNMR 6 1B 01 999083 00 A1298 5 2 Parameters Suffixes p d and k have been given the following meaning when inputting numeric parameters e The p suffix translates the input to ppm units For example entering sw 1 0p is equivalent to entering sw 10 reffrq e The d suffix translates the input to ppm units relative to the decoupler frequency For example entering sw1 10d is equivalent to entering swl 10 reffrq e The k suffix translates the input to thousands For example fn 1 6k setting the Fourier number parameter to 16k is equivalent to fn 16 1000 Note however that fn 1 6k
329. ing experiment noise Measure noise level of FID Resume acquisition stopped with sa command react lt wait gt Recover from error during werr processing sa lt option number gt Stop acquisition showstat lt remote_system gt Display information about acquisition status VNMR showstat lt remote_system gt Display information about acquisition status UNIX unlock exp_number Remove inactive lock and join experiment usergo Experiment setup macro called by go ga and au wbs string Specify action when bs transients accumulate werr string Specify action when error occurs wexp string Specify action when experiment completes wnt string Specify action when nt transients accumulate aux lt nocheck gt lt gt lt next gt lt gt lt wait gt gt autolist lt option gt experimentl lt experiment2 lt experiment3 gt go lt lt acqi gt lt nocheck gt lt nosafe gt lt next gt lt sync gt lt wait gt gt noise lt excess_noise lt last_noise lt block_number gt gt gt rl1 r2 r3 r4 r5 r6 Parameters acqstatus code number Acquisition status arraydim number Dimension of experiment bs 1 32767 transients n Block size celem number Completed FID elements date string Date from UNIX system dp y n Double precision errloglen number Number of lines in VNMR error message display gain n number in dB Receiver gain hs y orn for each period Homospoil pulses
330. ing sorted list is displayed in the VNMR text window Display the Files Main menu page 87 Files Tape Menu The Files Tape menu handles UNIX tapes only used on UN TYINOVA UNITY plus MERCURY VX MERCURY GEMINI 2000 UNITY and VXR S systems The Files Tape menu is activated by selecting the Tape button in the Files Main menu or by entering files files_tape The tape parameter defines the device the files program accesses when it is instructed to read or write to a tape Button Directory Sizes Write Read All Return 01 999083 00 A1298 Description Displays the contents of the streaming tape currently loaded in the tape drive Since UNIX tar tapes do not have a directory per se the entire tape must be read in order to produce this listing so the operation may be time consuming Reports the size of each entry in the current directory To report the size of selected entries only mark one or more entries in the files display first and then click on this button The size of the entries you marked is reported in the VNMR text window The size of each entry in a subdirectory is included in figuring the size of the subdirectory Write the entire contents of the current directory to tape To write selected entries only to tape mark one more entries in the files display first and then click on this button Only those entries you marked are written to the tape Load contents of the streaming tape into the current dir
331. inline DSP include no increase in disk storage and user defined filter functions A potential disadvantage is some additional load on the workstation Inline DSP software is compatible with all systems with Sun host computers e Real time DSP uses a dedicated embedded processor chip installed on the input board of certain systems such as the UN TYINOVA to filter the data prior to time averaging The advantages of real time DSP include no increase in data storage and compatibility with ultra rapid experiments because there is no additional loading on the workstation A disadvantage is that fewer parameters are available to control real time digital filtering Another type of DSP postacquisition DSP integrates the digital filtering and downsampling process into the Fourier transform commands ft and ft 2d The digitally filtered and downsampled FID can then be saved to disk The advantage is that the original FID is not altered in the original experiment multiple applications of digital filtering are possible no limitations exist on filter shape complexity and filter cutoff and user defined filter functions are possible The main disadvantage is the large disk storage required The usual disk storage requirements are directly multiplied by the oversampling factor which ranges from 2 through 68 Postacquisition DSP software is compatible with all systems with Sun host computers In all types of DSP the signal is initially filtered at the oversam
332. ion The data will be acquired processed and plotted using the values set within the Custom Setup windows 3 3 Customizing Combination Experiments 56 In addition to setting specific parameter values in 1D experiments GLIDE allows you to select an arbitrary combination of values from a list of available experiments and separately customize each selected experiment As an example to run 1D proton COSY and HMQC experiments on a sample do the following steps 1 Open the Experiment Setup window as described in Running a Standard Experiment on page 54 Select H1 and H1 detected Experiments from the Experiment menu Enter a name in the Save As field Your entry will be appended to the directory name in which all data will be stored i e vnmrsys data Click on Setup to retrieve standard proton parameters and activate the Custom menu Click on the Acquire icon to open the Acquisition Setup window Getting Started VNMR 6 1B 01 999083 00 A1298 3 3 Customizing Combination Experiments 6 Select the spectral window number of transients relaxation delay and pulse angle for your sample The spectral window you choose will be used for all experiments the other selections are used only for the 1D spectrum 7 Click on the COSY button in the top row of the experiment selection menu 8 Inthe new window shown in Figure 19 use the left mouse button to choose the number of transients per increment and the number of incr
333. ion 3 Menu The Regression 3 menu is activated by selecting the Next button in the Regression 2 menu or by entering menu regression3 Button Description dp linear Fit a straight line to the data points and display Getting Started VNMR 6 1B 01 999083 00 A1298 4 12 File Menus Button Description dp quad Fit a quadratic curve to the data points and display dp cubic Fit a cubic curve to the data points and display dp exp Fit an exponential curve to the data points and display plot Plot the displayed data and curves dp output Display the results of the analysis in the text window Return Display the Regression 1 menu page 86 4 12 File Menus A series of eight menus for handling files are accessible using th File button in the Main menu or by entering the files command The following applies to all files menus e To make a choice on a menu move the mouse cursor over the button and click press and release the button with the left mouse button e To select or mark a file in the list of displayed file names move the mouse cursor over the desired filename and use the left mouse button to click on the name so that the name changes to reverse video To deselect a filename click on it again File names with a slash after the name are directories e Some operations permit more than one filename to be selected To select additional file names simply click on them e If you do not select a file name when requ
334. ion is used to distinguish PostScript printers If desired the script vamrprint affords a place for user customizing The macro ptext file prints out the text file given as an argument For example the command ptext vnmr psglib dept c prints the text file dept c 01 999083 00 A1298 Getting Started VWMR6 1B 271 Chapter 9 Display Plotting and Printing Print jobs for the currently active printer in VNMR are held in a print queue The showprintgq macro displays the current print jobs in the print queue The killprint macro will stop a print job and remove it from the print queue Unless the user executing this macro is root superuser only that user s print job is deleted from the print queue 9 10 User Controllable Line Drawing 272 The pen move and draw commands provide the user with a line drawing capability for display on the graphics screen or output on the plotter By default the output device is the plotter plotter but the device can be changed to the graphics screen graphics in any of these commands The output currently selected is passed to subsequent pen move and draw commands and remains active until a different output is specified The commands are entered as follows pen lt graphics l plotter gt lt xor l normal gt pen color selects the pen for a plotter pen1 pen2 etc or the active color for the graphics screen red green blue cyan magenta yellow black or whit
335. ion of readultra in the VNMR Command and Parameter Reference In a multiuser environment it is probably best if each user has a separate floppy disk on which that user s particular shim files can be written In any environment backup floppy disks are always a good idea Two backup system disks are made at the time Ultrasnmr Shims is installed one is to be kept by the customer the other is sent to Varian Backup disks can be easily made on any DOS based computer using the DOS diskcopy command CAUTION Keep floppy disks away from the magnet dewar Data on the disk is susceptible to damage from intense magnetic fields When changing floppy disks observe the following procedure 1 Save the current shim values into one of the 62 available shim files 2 Load in file 0 3 Remove the current floppy from the drive and immediately insert the new system floppy into the drive Do not operate the controls on the interface box when there is no floppy in the drive Enabling the Acquisition Window The shims can be controlled with the Acquisition window instead of from the interface box To enable software control press the Mode button on the interface box to activate the mode select feature Use the NO direction on the YES NO toggle switch to toggle through to display RS232 TERMINAL MODE on the interface display screen Toggle the YES NO switch to the YES position to select the serial mode The interface box screen will display RS232 TERMINAL MOD
336. ion parameters 6 4 Removing and Inserting the Probe 112 If you want to use another probe or must remove the probe for cleaning you need to know how to remove the probe and reinsert it Since many types of probes are available only general information is given here Refer to the manual NMR Probes Installation for more information on Varian probes To Remove the Probe To remove the probe you do not need to turn off the air supply or the transmitter 1 If acquisition is in progress stop the acquisition Enter dm n su 2 Ifa sample is in the probe remove the sample 3 Remove the cooling line from the blue nipple on the probe 4 Remove the cables from the collar attached to the probe Typically there are cables for lock observe and decouple and VT control The VT cable is a 9 pin cable attached to a connector with steel screws or a steel clamp If there are screws carefully remove them with the small nonmagnetic screwdriver provided If there is a clamp squeeze the connector to unplug it 5 Loosen the two knurled small bolts that hold the probe to the bottom of the magnet body support the probe with one hand and guide it slowly out of the magnet with Getting Started VNMR 6 1B 01 999083 00 A1298 6 5 Using Probe Files and Templates the other hand As the probe begins its descent remove the rubber VT connector from the glass protrusion on the rear of the probe To Insert the Probe Reinsertion of the probe follows t
337. ired VNMR displays a prompt requesting the entry of the file name in the input window Files Main Menu The Files Main menu is activated by selecting the File button in the Main menu or by entering the command files Button Set Directory File Info Tape Load Data Delete 01 999083 00 A1298 Description If a directory has been selected in the files display directories have a 7 following their names that becomes the new current directory If you haven t selected a directory the Directory menu below is displayed for you to select a new current directory Display Files Information menu page 89 to list the files in the current directory sorted by size or data of modification Display Files Tape menu page 89 to read and write tapes See Chapter 10 Storing Retrieving and Moving Data for other types of tapes First mark one entry in the files display and then click on this button If you have selected an entry that has Varian NMR data including data from a Gemini VXR or XL system that parameter set and data is loaded into the current experiment If the entry is a parameter set the parameters are loaded Display Files Data menu page 90 with choices for accessing NMR data and related files First mark one or more files and or directories in the files display directories have a following their names and then click on this button Each entry you have marked including subdirector
338. is deactivated at the start of acquisition Simple Autolock Simple Autolock is available on MERCURY VX MERCURY and YINOVA UNITY plus or GEMINI 2000 as a software function and on UNITY and VXR S as a hardware function e Software simple Autolock searches for the correct ZO value in software but does not adjust lock power gain or phase e Hardware simple Autolock searches for the lock resonance over an approximately 10 ppm range turning up the lock power by 3 dB from its preset value during the search and then turning the lock power back down when lock has been found and captured 132 Getting Started VNMR 6 1B 01 999083 00 A1298 6 8 Optimizing Lock Once energized this type of lock remains energized until simple Autolock is selected again or optimizing autolock is selected A danger in hardware simple Autolock is that if the lock signal falls below a certain level the system reenters the lock capture phase and boosts the lock power This can have unfortunate consequences during for example a shimming operation Using the Acquisition Window Applies only to UNITY and VXR S systems configured for acquisition 1 Ifthe Acquisition window is not open enter acqi in the input window then click on the Connect button in the window when it appears 2 Click on the LOCK button The LOCK display appears The LOCK menu near the top of the display has three choices off on and auto 3 Click on auto Using the Input Windo
339. is menu changes the FID Spectrum display to display the spectrum for the FID described on page 159 To the right of the SMALL LARGE button is the style button that allows you to switch between Style 1 and Style 2 FID shimming Shimming on the FID is discussed on page 160 Below this menu are two toggle buttons shown as Single and Grid Off in Figure 41 On the INOVA system there might be two more buttons see the following subsection Style 1 Interface The currently selected choice is displayed The toggle button on the top left alternates between the choices Single and Summed e Single button displays the last acquired FID A yellow box indicates the ADC limits and two short yellow lines indicate the zero point of the ADC If the display is down scaled the ADC limit is indicated by short red lines in the display e Summed button displays the summed FID The toggle button on the below left alternates between Grid and Grid Off Clicking on this with the left mouse button toggles the display of grid lines overlaying the FID display The grid lines are provided as an aid to monitoring the effects of changing the shims 01 999083 00 A1298 Getting Started VNMR 6 1B 155 Chapter 6 Preparing for an Experiment 156 Style 1 Interface On UN TYINOVA systems on the right of the Single Summed and Grid switches are two more toggle switches the Signal Avg switch to the right of the Single Summed switch and the Phase Cycle switch
340. is way to resets that were established automatically by the region command 7 Enter vp 12 The spectrum moves up to allow space for a numerical display of integrals 8 Click the center mouse button above the right end of any displayed integral This adjusts the integral vertical scale 9 Enter ins x where x is the value you wish to assign to the sum of the integrals The value entered affects only printed output not the trace of the integral 10 Enter dpirn The text window displays a list of integral amplitudes The sum of the integrals is normalized to the value of the parameter ins Baseline Correction Almost all of the operations performed on spectra assume a good baseline Line lists integrations resolution measurements 2D volume integrations etc all measure intensities from zero and do not perform any baseline adjustments If the baseline in your spectrum is not good you should first perform a baseline correction operation before performing further data reduction Two types of baseline correction are provided linear and non linear The dc command turns on a linear baseline correction using the beginning and end of the displayed spectrum to define a straight line to be used for baseline correction The result is to calculate a zero order baseline correction parameter 1v1 and a first order baseline correction parameter t 1t The cdc command turns off this correction The results of the dc or cdc co
341. isplay limits to left half of screen Position cursor at nearest line Select normalized intensity mode Adjust vertical scale to limit noise level Recall display parameter set Set display limits to right half of screen Set reference line Save display parameters as a set Set frequency referencing for proton spectra Calculate offset frequency for given nucleus and ppm Split difference between two cursors Adjust threshold for peak printout Reference spectrum to TMS Adjust vertical scale Adjust vertical scale in powers of two Adjust vertical scale of carbon spectra Adjust vertical scale of proton spectra Adjust display to given width d1ll lt pos lt noise_mult gt gt lt number_lines scale gt dpf lt lt noll gt lt pos gt lt noise_mult gt lt leader gt lt length gt gt dres lt lt freq lt fractional_height gt gt gt linewidth digital_resolution dscale lt lt axis gt lt vertical_start gt lt display_start gt lt color gt gt setref lt nucleus gt rfl rfp Sreffrq refpos thadj lt maximum_peaks lt noise_mult lt llargl lt llarg2 gt gt gt gt Parameters aig ai nm axis h p k cutoff number in mm cutoff number in mm dmg ph av pwr pa rfl number in Hz rfp number in Hz th 0 to le9 in mm vp 200 to 200 in mm vs le 6 to 1e9 wysiwyg y n 244 Getting Started VNMR 6 1B Absolute intensity group 1D axis label for displ
342. isplayed as 3 and all other integral values are accordingly scaled Integral value scaling can be interactively set with the ds command The set int macro can also be used to adjust integral value scaling set int sets the value of an integral and is used in conjunction with the command d1i to scale integral values Normalized integral values can also be selected In this case ins represents the total number of nuclei The individual integral values will be scaled so that their sum is equal to ins The normalized mode may be selected by setting insref to not used The integral is scaled by ins and insref Two commands are closely related to dli e nli is equivalent to dli except that no screen display is produced e dlni normalizes the values from dli using the integral normalization scale parameter ins and then displays the list 01 999083 00 A1298 Getting Started VNMR6 1B 253 Chapter 9 Display Plotting and Printing The dpir command displays numerical integral values below the appropriate spectral regions using the integral blanking mode in which only every other integral is plotted The command dpirn shows the normalized integral values in an analogous fashion The pir command plots digital integral values below the spectrum using the integral blanking mode in which only every other integral is plotted The command pirn plots the normalized integral values in an analogous fashion 9 7 Plotting VNMR software allows plotting
343. it button in the Interactive 2D Peak Picking Main menu Button Description Box OR If labeled Box select two pairs of cursors box mode If labeled Cursor Cursor select one pair of cursors cursor mode Mark Mark peak cursor mode or volume box mode at current cursor location s Unmark Delete peak cursor mode or volume box mode at current cursor location s Expand OR If labeled Expand expand to area between cursors box mode Full If labeled Full display full area cursor mode Clear Delete peaks and volumes of peaks in the current display area Combine Combine peaks into a single peak Label Prompt for and label peak cursor mode or peaks box mode with 15 character label Comment Prompt for and label peak cursor mode or peaks box mode with 80 character comment Info Print information to text window about peak nearest the cursor Set Int Set volume scaling Return Display the Interactive 2D Peak Picking Main menu page 75 2D Peak Picking File Menu ll2d Program The 2D Peak Picking File menu part of the 112d program is activated by selecting the File button in the Interactive 2D Peak Picking Main menu Button Read Read Text Write Text Backup File Return Description Read in a binary peak file Read in a text peak file Write out a text peak file Prompt for a filename and copy current binary peak file to that file Display the Interactive 2D Peak Picking Main menu page
344. ities Even on a perfect spectrometer these distortions cannot always be avoided e The acquisition time of each FID may have been too short to allow for full decay of the signal leading to distortion in the Fourier transformed spectrum Both types of distortions can be solved using linear prediction This uses the good part of the FID to analyze for the frequencies that are present in the signal and then uses that information to extend the FID either in a reverse direction to fix the first few bad points or in a forward direction to eliminate truncation problems Following this process the new improved FID is then Fourier transformed in the usual way In VNMR linear prediction is incorporated directly into the Fourier transform routine so that normally one does not see the improved FID but merely the spectrum which results from Fourier transforming the linear predicted FID This is accomplished by setting proc 1p and then entering ft or wft as usual If you do wish to see the linear predicted FID it is possible to do so by entering ft noft which performs all the steps of the Fourier transform routine except the actual Fourier transformation You can now see the real points of the FID by setting 1p 0 rp 0 or see the imaginary points by setting lp 0 rp 90 Since linear prediction involves solving a series of equations for appropriate coefficients based on the actual FID it involves quite a number of
345. ition computer ADC Analog Plus filter array Bayes software Brickwall filter CDE depth indicator diffusion software digital signal processing DSP downsampling experiment FID 01 999083 00 A1298 Computer in NMR system console that controls the acquisition process Analog to digital converter Digitizes the analog signal from the probe Type of real time digital filter with similar characteristics to traditional analog filters but uses digital technology to obtain flatter passband and sharper cutoff in the stopband compared to the corresponding analog filter Set of data that are related so they can be treated as a single entity Optional software available from Varian that uses Bayesian probability theory to directly analyze 1D time domain data providing signal amplitude frequency and linewidth for all statistically significant resonances Type of real time digital filter with much sharper cutoff than the AnalogPlus digital filter Common Desktop Environment A UNIX windowing environment Device provided to position the sample accurately n Optional software available from Varian containing acquisition and analysis programs for the determination of diffusion constants using the pulsed gradie3nt echo method Capability of VNMR software to oversample the data apply a digital filter to the FID and then downsample the data Benefits of DSP include constant noise level across the spectrum impr
346. k on the Do button at this point unless you wish to acquire data immediately Clicking on Do after making a change is the equivalent of entering the go command in which acquisition begins but no further processing is performed Click on the Process button in the Custom Setup window The Process Setup window appears with the current values of the Fourier Number and Line Broadening To change the value displayed delete the number with the Back Space key type a new value and click the Set button When you are done click on the Close button to save any changes and exit Do not click on the Do button unless you wish to process the data immediately with the parameters you have chosen this feature lets you easily reprocess data already in the experiment Click on the Plot button in the Custom Setup window The Plot Setup window appears for customizing plot layouts Make the changes you want When you are done click on the Close button to save any changes and exit Do not click on the Do button unless you wish to plot the data immediately with the parameters you have chosen this feature lets you easily make additional plots of your processed data Exit the Custom Setup window by clicking on the upward pointing triangle at the bottom of the Custom button in the GLIDE user interface window Now that you have chosen all the parameters for acquisition processing and plotting click the Go button in the GLIDE user interface to initiate acquisit
347. l trace and the scale are duplicated with the inset spectrum After running inset you can shift the displayed spectrum expand it or even contract it with the left and right mouse buttons and the following menu notice that the labels change on some of the buttons according to the mode the program is in Box sc we Full sp wp plot ds Return Getting Started VNMR 6 1B 01 999083 00 A1298 9 5 Spectral Display and Plotting These buttons function as follows The first button is Box or Cursor depending on if you are in box or cursor mode Box Change to the box mode with two cursors Cursor Change to the cursor mode with one cursor The second button does not change labels sc we Interactively adjust start of the display and its width on the screen The third button is Expand or Full depending on if you are in the box or cursor mode Expand Expand the area between the cursors Full Display the full area The remaining buttons do not change labels sp wp Interactively adjust the starting frequency and width of frequencies displayed in the spectrum plot Plot the spectrum and if displayed the integral and the scale ds Return to the ds menu without erasing the display Return Return to the 1D Display Menu While working with the inset display the mouse buttons function as follows The left mouse button positions the cursor or pair of cursors In the sc wc mode the left button adjusts the starting position of the display In
348. lained earlier however one of the real advantage of DSP with significant oversampling is the ability to work at lower gain settings while maintaining full signal to noise This headroom afforded by DSP makes it is far less important to carefully adjust 01 999083 00 A1298 Getting Started VWMR6 1B 215 Chapter 7 Acquiring Data 216 the gain setting and fill the ADC Thus gain settings 6 to 10 or even 20 dB below ADC overflow are likely to give perfectly acceptable results Data Format Issues The output of inline and real time DSP is a normal FID without the distortion associated with the large frequency dependent phaseshift associated with some digital filters and with characteristics such as np that are identical to an FID obtained without DSP As such the output can be processed by any software VNMR or third party that can process standard VNMR FIDs Real time DSP FIDs are always in fixed point format 16 or 32 bit depending on the value of the parameter dp The output of inline DSP is also a normal FID that can be processed in standard ways If dp n the FID is in a 16 bit fixed point format however if dp y the FID is in 32 bit floating point format not 32 bit fixed point VNMR processes such FIDs transparently but some third party software may not be compatible with this mode Obtaining Good Baselines with Inline and Real time DSP The algorithms used by inline and real time DSP processing now
349. ld labeled Save As with the left mouse button and begin typing To enter text which will be printed along with parameters on the spectrum click in the box below the label Text One click positions the insertion point and cursor at that spot in the text Two clicks highlights the single word under the pointer Three clicks highlights the entire line Four clicks highlights the entire text In all cases highlighted text is deleted and replaced as soon as you type any character including the space bar Multiple line texts are supported 8 If your system has automatic insert and eject capability buttons for insert and eject appear in the window Getting Started VNMR 6 1B 01 999083 00 A1298 3 2 Using GLIDE e Ifa sample is currently in the magnet click on the Eject button to eject the sample Next insert your sample and click the Insert button to insert the sample into the magnet e Alternately if a sample changer is attached to your system enter the location of the sample in the sample tray using the field labeled Location e If you do not have the auto insert and eject feature on your spectrometer the Insert and Eject buttons are not displayed and you need to manually insert your sample 9 Click the Setup button to exit from the Experiment Setup window Acquisition does not begin at this point GLIDE is only setting up parameters Once you click Setup the Experiment Setup window disappears the Custom and Go buttons become
350. le interface UNITYINOVA and UNITYplus 500 600 or 750 systems Disconnect the cable from PROBE J5321 port on the TUNE INTERFACE panel Connect this cable to the PROBE J5311 port or the TH 9F J5301 port whichever was the original port Then disconnect the cable to the TUNE OUTPUT J5323 port and connect it to the OUTPUT port J5312 or J5302 as appropriate At this time the red indicator light should turn off 11 Repeat the steps above for each channel on the system For further information about probe installation and tuning on the UN YTNOVA and UNITYplus refer to the manual NMR Probes Installation Using the Graphical Probe Tuning Program qtune This section describes how to use the graphical probe tuning program qt une shown in Figure 23 for swept tune type NMR probe tuning qt une is available on UN YINOVA and UNITYplus systems qtune runs on the host computer and offers you an interactive tuning method that provides separate information for matching and resonant frequency This program is especially useful for tuning probes with complicated coil configurations such as imaging probes After the system is put into tune mode the reflected power from the probe passes through the directional coupler and is detected and digitized by the receiver circuitry Any power that the receiver detects is reflected power Taking one or more complex pair of data points at each frequency gives a data set that shows reflected power versus
351. le or the next file on the tape is read After running readbrut ape to read the data file it must be converted using the convertbru and sread commands for use with VNMR Getting Started VNMR 6 1B 01 999083 00 A1298 10 6 Magnetic Tape Operations Sharing a Tape on a Network A single tape can easily be shared between two or more computers provided the systems are installed according to the instructions on remote installation in the manual VNMR and Solaris Software Installation Files can be backed up or restored remotely over the network using the following UNIX commands e To read a tape catalog of a remote tape on a remote computer named lal600 rsh n 1al600 dd if dev rmt 0lb bs 20b tar tvfbB 20 e To read all files from the remote tape rsh n 1al1600 dd if dev rmt r0lb bs 20b tar xvfbB 20 e To read named files filel file2 from the remote tape rsh n 1al600 dd if dev rmt r0lb bs 20b tar xvfbB 20 filel file2 e To write named files filel file2 to the remote tape tar cvfb 20 filel file2 rsh 1al600 dd of dev rmt 01b obs 20b Unfortunately the slightest error in typing one of these rather complex commands can make it go wrong If you need to do this regularly you should make up several shellscripts to accomplish the task in a simpler fashion For more information refer to documentation on the UNIX tar command Moving Data to PCs and Macintoshes via Floppy Disk The 1 44 Mbyte flo
352. le on the back of the 5 Gauss Warning Sign shows the typical 5 gauss stray field for various magnet systems WARNING Keep metal objects outside the 10 gauss perimeter of the magnet The strong magnetic field surrounding the magnet attracts objects containing steel iron or other ferromagnetic materials which includes most ordinary tools electronic equipment compressed gas cylinders steel chairs and steel carts Unless restrained such objects can suddenly fly towards the magnet causing possible personal injury and extensive damage to the probe dewar and superconducting solenoid The greater the mass of the object the more the magnet attracts the object Only nonferromagnetic materials plastics aluminum wood nonmagnetic stainless steel etc should be used in the area around the magnet If an object is stuck to the magnet surface and cannot easily be removed by hand contact Varian service for assistance 01 999083 00 A1298 Getting Started VNMR 6 1B 17 SAFETY PRECAUTIONS Warning Notices continued 18 A table on the back of the 10 Gauss Warning Sign shows the typical 10 gauss stray field for various magnet systems WARNING Only qualified maintenance personnel shall remove equipment covers or make internal adjustments Dangerous high voltages that can kill or injure exist inside the instrument Before working inside a cabinet turn off the main system power switch located on the back of the console WARNING D
353. les 67 line drawings 272 linear prediction parameters 228 listing of last spin simulation 84 local Ethernet node 283 modes 232 numerical integral amplitudes 254 one or two cursors 231 output devices 92 parameter groups 112 Getting Started VNMR6 18B 303 Index parameter value 96 peak frequencies 246 plot jobs in queue 255 pulse sequence as a graph 189 pulse sequences 188 regression analysis results 87 remote directory on Ethernet 283 scale under spectrum or FID 246 second cursor 234 shim gradient parameters 136 simulated spectrum 85 spectra 243 spectra horizontally 78 spectral line frequencies and amplitudes 78 spectrum 159 225 231 spin simulation parameters 83 summed FID 155 synthetic spectrum 85 text file in current experiment 197 time for experiment 70 vertical scale 232 whitewashed FIDs 237 Display button 66 75 81 90 display button 85 display command 253 Display FID button 71 display monitor 44 display parameter set 243 display screen 27 Display Shimmap button 170 divide spectrum into regions with peaks 253 dla macro 85 dli command 253 dil command 246 dlni command 253 dlp parameter 193 dm parameter 190 194 195 dm2 parameter 191 dm3 parameter 191 dm4 parameter 191 dmf parameter 193 194 195 dmf2 parameter 193 dmf2adj macro 194 dmf3 parameter 193 dmf3adj macro 194 dmf4 parameter 193 dmf4adj macro 194 dmfadj macro 194 d
354. lfa delay before acquisition Acquisition time Completed transients First delay Second delay Decoupler high power with class C amplifier Decoupler low power with class C amplifier Decoupler mode Decoupler modulation frequency Decoupler modulation mode Power level for decoupler with linear amplifier Decoupler fine power Decoupler linear modulator power Tip angle resolution for WFG decoupling Decoupler sequence Filter bandwidth Gradients for X Y and Z axes Homodecoupling control for decoupler Number of data points Number of transients First pulse width Preacquisition delay PFG amplifiers on off control Pulse width 90 degree pulse width Receiver gating time preceding pulse Receiver gating time following pulse Pulse sequence name Steady state pulses Sample temperature Observe transmitter power level with linear amp Observe transmitter fine power Observe transmitter linear modulator power Variable temperature cutoff point 186 Getting Started VNMR 6 1B 01 999083 00 A1298 7 2 Setting Pulse Sequence Related Parameters Transmitter Receiver Figure 53 Acquisition Parameters for Standard Two Pulse Sequence Standard Two Pulse Parameters To allow the hardware to set up at the beginning of the experiment the parameter pad a preacquisition delay is used pad is usually set to 0 5 seconds The other principal use of this parameter is for kinetics experiments The part of the experiment
355. liasing of large peaks just outside the downsampled window dscoef does not need to be changed as downsamp is changed because dscoef is automatically adjusted by VNMR to give filter cutoffs that are the same regardless of the value of downsamp This is done by actually using dscoef downsamp 2 coefficients in the digital filter VNMR always rounds dscoef downsamp 2 to an odd number e dslsfrq is used to select a bandpass filter that is not centered about the transmitter frequency tof dslsfrq is specified in Hz and works much like lsfrq A positive value of dslsfrq selects a region upfield from the transmitter frequency and a negative value selects a downfield region Bandpass filters are used to select regions away from the transmitter frequency e dsfb specifies the digital filter bandwidth which is set to half of the downsampled spectral width by default If dsfb n the default value for the filter bandwidth is used A smaller value rejects frequencies at the edges of 01 999083 00 A1298 Getting Started VNMR6 1B 217 Chapter 7 Acquiring Data 218 the spectrum and a larger value aliases noise and signals at frequencies outside of sw 2 filtfile specifies the name of a file of finite impulse response FIR digital filter coefficients The file must be in the user s vnmrsys filtlib directory The filter coefficient file is a text file with one real filter coefficient per line Complex filters are not currently supported To use the d
356. like this bin csh b umount floppy eject 3 Runachmod 4755 on the two shell scripts and then create a floppy directory with 777 characteristics The user now uses mount floppy and eject floppy in place of the mount and eject commands to accomplish the otherwise forbidden tasks 10 7 Compressing Data 292 A number of data compression programs are available to reduce the space occupied by data on storage devices and to increase the throughput of data sent electronically The standard UNIX compress utility is a general purpose program that can compress any file typically by 40 to 50 percent The compressfid command is a more specialized program that is used to compress double precision VNMR FID data to single precision Compressing and Uncompressing FID Data Files If you enter compress witha file name e g compress mydata fid from UNIX the compress program replaces the file you specified with a compressed file and identifies it by adding a Z suffix e g mydata fid 2Z You can not do this on a directory so to make this work on data you must compress the FID file itself An easy way to accomplish this is to create a pair of macros The first macro saves the compressed FID svcf save compressed fid svf 1 shell compress 1 fid fid amp Getting Started VNMR 6 1B 01 999083 00 A1298 10 7 Compressing Data The second macro retrieves the compressed FID TOGE retrieve compressed fid
357. limitation 96 frequency related 183 hardware autoshim 145 integer truncation 96 01 999083 00 A1298 Index interactive parameter adjustment 159 line broadening 72 linear prediction 228 names 94 organization 107 phasing 224 plot list of values 261 Pulsed Field Gradient PFG module 196 resolution enhancement 72 retrieve from parameter file 279 rf channel related 109 selection 72 73 shim gradients 136 turned off 95 types 94 update old parameter characteristics 109 value display 96 value ranges 96 weighting 72 parameters parameters 262 Params button 78 80 85 paramvi macro 112 pards macro 217 Parent button 88 parent of a directory 88 parentheses 94 parfix macro 280 parlib directory 36 107 parlp macro 228 paros macro 212 Part Integral button 239 parversion parameter 280 password prompt 40 password selection 40 pathname defined 37 pathname to current experiment 277 PC platform 291 Peak button 74 75 peak frequencies 246 peak regions selection 77 Peaks button 78 peak to peak noise 246 pen and raster plotters 258 pen command 272 pen number 272 pen plotters 255 Performa PFG modules 24 Performance Meter program 50 Permanent menu 46 60 65 pfgon parameter 196 pfww command 237 PH button 79 ph command 225 PH mode 80 Phase button 71 73 225 234 235 239 240 phase command 225 Phase F2 button 73 phase parameters 225 phase rotation 223 226 233 phase s
358. ll within the desired spectral width The use of the os1sfrq parameter with inline DSP allows these artifacts to be removed by the digital filter before downsampling so that they are not present in the downsampled FID that is stored on the disk This technique is called frequency shifted or digital quadrature detection Frequency shifted quadrature detection is accomplished by moving t of to just outside the desired spectral width and then using oslsfrq to offset the digital filter center frequency by the same amount thus keeping the region of interest after digital filtering Frequency shifted quadrature detection is done in the inline DSP algorithm e If real time DSP is used dsp r oversamp is set to a multiple of 4 and downsampling of a factor of oversamp 4 is then done in real time DSP The remaining factor of 4 is then done in inline DSP during which frequency shifting by oslsfrq is also done This feature is available only on UN TYINOVA systems e If pure inline DSP is used dsp i filtering and frequency shifting is done in a single stage To Apply Frequency Shifted Quadrature Detection UNITYINOVA Systems 1 Turn DSP on by setting dsp to r or i 2 Setfsq y Getting Started VNMR 6 1B 01 999083 00 A1298 7 5 Applying Digital Filtering Doing these steps sets os lsfrqto 1 25 sw and offsets the transmitter frequency to toft toslsfrq Just before acquisition If a different value of os1sfrq is desired it ca
359. lock time constant The values for locktc are the same as for lockacqtc These parameters do not normally exist in the software The system uses the slowest value for lockacqtc 4 for Y TYINOVA or UNITYplus and 2 for UNITY or VXR S and the fastest value 1 on all systems for Locktc if the parameters do not exist To try other values you can create one of the parameters and give it a value by entering for example create lockacgtc integer global setlimit lockacqtc 4 1 1 global lockacqtc 1 You do not need to create both parameters 6 9 Adjusting Shims Shim coils are small magnetic fields used to cancel out errors in the static field In shimming the current to the shim coils is adjusted to make the magnetic field as homogeneous as possible Computer controlled digital to analog converters DACs regulate the room temperature shim coil currents Every time a new sample is introduced into the magnet or probe is changed it is necessary to readjust the shims Shim Gradients The shims are actually printed coils wrapped round a cylindrical form that encloses the NMR probe A coil or sum of coils whose field is aligned along the axis of the magnet is called a Z axial shim gradient Z1 Z2 Z3 etc Coils whose fields are aligned along the 01 999083 00 A1298 Getting Started VNMR 6 1B 135 Chapter 6 Preparing for an Experiment 136 other two orthogonal axes are called X and Y radial shim gradients X1 XY X2Y2 Y1 Y
360. low on a single transient When DSP and hence oversampling are activated two changes occur that affect the maximum signal seen by the ADC First the initial sampling occurs earlier in time The system may have acquired 10 points of an oversampled FID before it would have acquired a single point in a normal FID Thus any transient signals e g probe background pulse breakthrough that occur at the front of the FID are more likely to cause ADC overflow in an oversampled FID Second the analog filter bandwidth is now set to a larger value it may have gone from 2 5 kHz up to 50 kHz Any large out of band signal that was being filtered out by the analog filter appears at the ADC to be digitized and then to be subsequently filtered out by the digital filter Thus again ADC overflow may occur under conditions i e identical pulse width and gain where it did not occur when DSP was not used Even more subtly because of the digital filtering that occurs the output of the digital filter may actually have a value less than the maximum possible value even though the input to the digital filter did indeed exceed the ADC limit Thus you should not be surprised if you occasionally need a very slightly lower gain to avoid ADC overflow when using DSP and you should also not be surprised if you examine the output signal and do not see any evidence of ADC overflow despite having been told by the software that ADC overflow did occur As exp
361. lt option gt experimentl lt experiment2 lt experiment3 gt Table 6 Automated Calibration Macros Macros AC1S AC11S Autocalibration macros ACbackup Print copy of probe file after autocalibration ACreport Make backup of current problem file 98 Getting Started VNMR 6 1B 01 999083 00 A1298 5 4 Macro Automation Table 7 Automated Plotting Macros Macros pacosy plapt lt 13Cexp_number gt parstyle string Plot automatic COSY analysis Plot APT style spectra automatically plarray Plot arrayed 1D spectra plc lt pltmod gt Plot a carbon spectrum plcosy Plot COSY and NOESY type spectra automatically plh lt pltmod gt Plot proton spectrum plhet2dj Plot heteronuclear J resolved 2D spectra automatically plhom2dj Plot homonuclear J resolved 2D spectra automatically plhxcor Plot X H correlation 2D spectrum plot Plot spectra automatically plotid Plot simple non arrayed 1D spectra plp lt pltmod gt Plot phosphorus spectrum plcosy lt pos neg gt lt gt lt levels lt spacing lt exp1D gt gt gt plhet2dj lt pos neg gt lt gt lt levels lt spacing lt exp1D gt gt gt plhom2dj lt pos neg gt lt gt lt levels lt spacing lt exp1D gt gt gt plhxcor lt pos neg gt lt gt lt levels lt spacing lt exp1D_H lt exp1D_X gt gt gt gt Parameter Parameter style to plot Table 8 Automated Processing Macros Macros autostack c13p cleanexp lt
362. lue and the interlock parameter in is vw Low Speed High Speed Spinner Selection w Low speed spinner liquids style set to y spinning w High speed spinner solids style regulation is checked after _4 each transient Acquisition is aborted with an Figure 34 Spinner Control Window appropriate error message spinner Program if spinning goes out of regulation just as it does if lock is lost If in is set to w a warning is generated if the spin speed goes out of regulation however acquisition is not stopped If in is set to n spinning is checked and regulated before the first transient and not checked thereafter The spin parameter can also be set to n which indicates that no spin rate adjustment is to be done when acquisition begins The system will still attempt to regulate at the last entered spin rate but acquisition will not wait for regulation to occur If spin n and in y only lock loss causes acquisition to stop The in parameter can be set to handle both lock level and spinner speed errors For details see Lock Level and Spin Speed Error Handling on page 150 Using the Acquisition Window Applies to all systems configured for acquisition if the optional spin control hardware is installed This feature is not available on data stations 1 Ifthe Acquisition window is not open enter acqi in the input window then click on the Connect button in the window when it appears 2 Click on t
363. m 1 to 20 The default value is Not Active If the lfs option is selected ssorder is not used The quality of filtering with zfs diminishes rapidly as the solvent peak moves off the exact center of the digital filter It may be necessary to adjust lsfrq or sslsfrq to move the solvent peak to within 0 2 Hz of the center of the filter to obtain optimal solvent suppression The Ifs option is less sensitive to small offsets but typically removes or distorts peaks near to the solvent peak Interleave FIDs The i1 id command converts a multiple FID element into a single FID by interleaving the FIDs When invoked in an experiment of nf FIDs each of np points i1fid sorts the data into a single FID of np nf points that can then be transformed The interleaving takes the first complex point of each of the nf FIDs and places them in sequential order in the new FID It then takes the second complex point from each of the nf FIDs and appends them sequentially to the new FID This operation is repeated for all complex points Although ilfid adjusts np and nf it does not alter other parameters such as sw CAUTION Because ilfid alters the data irrevocably it is strongly recommended that you save the FID before using ilfid For further information on il fid including an example refer to the VWMR Command and Parameter Reference 01 999083 00 A1298 Getting Started VNMR6 1B 229 Chapter 8 Data Processing 230 Getting Started VNMR 6 1B 01 999
364. m criterion and lastly shim Z1C and Z2C with a medium to medium criterion User Defined Shim Methods for Autoshim The shim methods supplied with the system are based on a series of standard coil groupings however you may wish to perform an automatic shimming operation using other groups of shims than are provided For example you might wish to shim Z1 Z3 and ZA while holding Z2 fixed To allow this operation certain combinations of shims coils can be selected by constructing a 7 digit hexadecimal base 16 number based on the shim coil diagram in Table 19 To construct a method for this example first notice in the diagram that Z1 is represented by a 4 in the first digit on the far right and that Z4 and Z3 are represented by a 8 and 4 respectively in the second digit which gives a total of 12 or C in hexadecimal notation The rest of the digits are 0 because no other shimming is desired Thus the seven digit hexadecimal number representing Z1 Z3 and Z4 is 00000C4 This number is then prefixed by zm or tm the two are equivalent making szm00000C4 the method desired Some examples of user selected methods e stm0A30004 clm means shim Z1 X1 Y1 YZ Y3 with loose to medium criterion e szm0000108 cmm means shim ZIC and Z5 with medium to medium criterion To make it easier to modify the standard shim gradient combinations the hexadecimal code for each standard coil grouping is listed in the third column of Table 18
365. m number of pens to use plotter string Plotter device wcmax number in mm Maximum width of chart wc2max number in mm Maximum width of chart in second direction x0 number in mm X zero position of HP plotter or Postscript device y0 number in mm Y zero position of HP plotter or Postscript device Plotter Output 254 Plotting in a multiuser environment is controlled by pages Each plot produces a one page output on the selected plotter device note that on certain plotters such as the Zeta plotter one page might be physically several fanfold pages long Multiple commands which may in fact be separated by a long delay can produce one page A page is started by any one of the legal plotter commands It can be followed by any other plotter commands All these commands immediately calculate the appropriate plotter information which is then stored in an intermediate file or memory buffer in the case of Getting Started VNMR 6 1B 01 999083 00 A1298 9 7 Plotting raster graphics printers Finally each plot or group of plots is terminated by the page command page closes the current page and submits it to the appropriate plotter queue where it is sent to the plotter as soon as possible page also requests a new page on those plotters equipped with an automatic paper changer The UNIX command vnmrp1ot is installed as part of the VNMR system to plot files from inside VNMR commands The showplotq macro displays t
366. macro 222 sqsinebell macro 222 squared sinebell function 221 squared x axis scale 86 squared y axis scale 86 sread command 289 290 ss parameter 187 188 ssecho button 69 ssfilter parameter 228 sslsfrq parameter 228 229 ssntaps parameter 228 ssorder parameter 228 Stacked Plot button 80 standard 2 pulse experiment 69 Standard button 70 standard carbon experiment 67 standard coil groupings 142 standard decoupler pulse sequence 69 standard parameter sets 110 standard parameter sets for a nucleus 36 standard proton experiment 67 standard two pulse sequence 185 190 316 Getting Started VNMR 6 1B STARS software package 33 start button acqi 162 start of chart 232 start of FID 232 start of plot 232 starting criterion for shimming 140 starting Plot Designer 262 status concept 190 status line 45 status window 44 stdpar directory 36 107 108 111 145 stdshm macro 143 steady state pulses 188 steady state transients 187 STOP button acqi 162 stopping acquisition 202 jobs in plot queue 255 limNET server 286 streaming tape directory 89 string arguments 94 string parameters 94 stty command UNIX 97 su command VNMR 115 136 138 sub button 83 Subtract button 82 subtract spectrum from add subtract experiment 82 sulog file 208 Summed button acqi 155 Sun computers 23 25 superconducting magnet 25 svf command 138 277 svp command 138 278 svs command 138 278 sw paramete
367. mage and allow interactive adjustment Display the 2D Display Size Selection menu below Display the 2D Data Manipulation menu page 79 Display the 2D Data Processing menu page 73 Display the 2D Plotting menu page 80 Display the 2D Data Display Secondary menu page 80 2D Display Size Selection Menu The 2D Display Size Selection menu is activated by selecting the Size button in the 2D Data Display menu or by entering the command menu size_2D Button Left Center Right Full Screen Full with Traces Return Description Set display for left half of the screen page Set display for center of the screen page Set display for right half of the screen page Set display for full screen page Set display to use most of the screen page but leaving sufficient room at the top and left for traces and projections Display the 2D Data Display menu above 2D Data Manipulation Menu The 2D Data Manipulation menu is activated by selecting the Massage button in the 2D Data Display menu or by entering the command menu massage_2D Button DC f2 01 999083 00 A1298 Description Drift correct the 2D data set along the f2 axis Getting Started VNMR 6 1B 79 Chapter 4 Using the VNMR Menu System 80 Button Description DC f1 Drift correct the 2D data set along the f1 axis Foldt Perform a trigonal symmetrization for COSY COSYPS COSY3 DQCOSY Foldj Perform a symmetrization in J r
368. mand 293 computed data 281 computer acquisition 24 host 23 25 Host Acquisition Link 24 config macro 92 193 Configuration menu 92 configuration parameter file 36 Getting Started VYNMR 6 18 301 Index Configure button 91 configuring hardware 92 Connect button acqi 150 CONNECTED message 49 conpar file 36 console 23 CONSOLE shell window 48 construct a shim method 142 CONT message 45 CONTENTS file 38 continuous wave CW modulation 191 Contour button 79 contour plot 45 80 control temperature 196 Control d key combination 91 Control h key combination 97 Control n key combination 97 Control p key combination 97 Control U key combination 97 conventions used in manual 21 convert Bruker data 289 data between systems 286 multiple FID element into a single FID 229 VXR style FID file to VNMR 288 convert command 287 288 convertbru command 227 289 290 Copy button 91 copy command 276 copying directories 276 files 91 276 correct saved parameter sets 280 cosine transform 224 COSY analysis 82 COSY button 69 81 COSY correlation map 80 cosy macro 32 COSY with double quantum filter 70 COSYPS button 69 coupled spectra with NOE 190 cp command 277 282 cpos_cvt command 287 cr parameter 184 185 239 create directory 276 linear prediction parameters 228 new directory 88 new experiment 67 Create New button 67 88 credit cards caution 19 crf parameter 234 criterion for
369. manipulation of a single FID For arrayed 1D experiments or for 2D experiments a particular FID can be viewed by supplying the index number as an argument From the menu system this program is opened by selecting the button Display FID in the 1D Data Processing Menu The FID is left shifted by the number of complex data points specified by the parameter 1sfid The FID is also phase rotated zero order only by the number of degrees specified by the parameter phfid Table 34 lists commands and parameters associated with the interactive FID display Table 34 Interactive FID Display Commands and Parameters Commands df lt index gt df lt options gt Display a single FID dscale Display scale below spectrum or FID dscalex lt axis gt lt vertical_start gt lt display_start gt lt color gt gt Parameters axisf s m u n Axis label for FID displays and plots crf number in sec Current time domain cursor position deltaf number in sec Difference of two time domain cursors lsfid n number Number of complex points to left shift np FID phasing 10 to 100 in Control update region during interactive phasing phfid n 360 0 to 360 0 in deg Zero order phasing constant for np FID vf le 6 to 1e9 Vertical scale of FID vpf number in mm Current vertical position of FID vpfi number in mm Current vertical position of imaginary FID FID Display Menu Figure 66 shows a typical display with a FID a
370. max sc wc cr sp wp wc2max Move to cursor position along x and to the top of the chart along y move wcmax sc wc cr delta sp wp 20 Move to delta position along x and the bottom of the chart along y draw wcmax sc wc cr delta sp wp wc2max Move to delta position along x and the top of the chart along y Getting Started VNMR 6 1B 01 999083 00 A1298 9 10 User Controllable Line Drawing To draw a box on a plotter or a display use box lt plotter graphics gt xlmm x2mm ylmm y2mm lt nolimit gt lt EL 2 gt with the values for the left edge x1mm right edge x2mm bottom edge y 1mm and top edge y 2mm specified as arguments e g box 20 100 40 150 The location of the edges are given in plotter units mm on most plots and are scaled in mm for the graphics display If units are in Hz or ppm you can use the h zt omm command to convert to plotter units The keyword nolimit allows the box to extend outside the limits determined by the parameters sc wc sc2 and wc2 Table 45 summarizes the commands for line drawing by the user Table 45 User Controllable Line Drawing Commands Commands box Draw a box on a plotter or graphics display draw Draw line from current location to another location hztomm x_position lt xmm gt Convert location from Hz or ppm to plotter units move lt graphics plotter gt x y Move to an absolute location to start a line pen Select a pen or color fo
371. may not redistribute anything in the user library in any form to anyone outside your own organization without the express permission of the submitter Neither Varian Associates Inc nor the submitter makes any warranty or representation of any kind express or implied with respect the material found in the user library This material is distributed as is and you assume the entire risk as to the quality reliability and performance of any software you choose to use In no event shall Varian Associates Inc be liable for any consequential special incidental direct or indirect damages of any kind arising out of the use of software in the user library Use of any material in the user library shall constitute acceptance of these terms and conditions 38 Getting Started VNMR 6 1B 01 999083 00 A1298 Chapter 2 VNMR Basics Sections in this chapter e 2 1 Entering and Exiting VNMR this page e 2 2 Working with VNMR on the Host Computer page 41 You will find that you can work in VNMR through three different modes e GLIDE user interface e VNMR menu system Command mode These modes are generally interchangeable You can use whichever mode you want or even mix modes to accomplish your goals At times you will also use certain UNIX commands outside the VNMR programs for certain NMR tasks 2 1 Entering and Exiting VNMR In some cases the VNMR program is left running on the host computer at all times and when
372. me DSP is first installed on a system each user should enter dsp to check that real time DSP dsp r is set on the system From that point on the software automatically calculates oversampling factors and performs experiments using real time DSP in a manner totally transparent to the user To turn DSP off in a single experiment set oversamp n to turn DSP back on in that experiment set oversamp y To turn off DSP permanently for all future experiments until you decide to turn it back on again set dsp n Types of Real Time Digital Filters Two different digital filters are supplied with real time DSP The first type the AnalogPlus filter was designed to have similar characteristics to traditional analog filters while using digital technology to improve on the analog filter in every way The AnalogPlus digital filter is flatter in the passband the spectral region of interest than an analog filter and has sharper cutoff in the stopband the region outside the spectrum to be filtered out This gives better quantitation across more of the spectrum and reduced noise fold in compared with analog filters in addition to the improvement in S N from the removal of digitization noise 01 999083 00 A1298 Getting Started VNMVR6 1B 213 Chapter 7 Acquiring Data 214 When comparing AnalogPlus digital filters with analog filters see Figure 65 note that when using a real analog filter VNMR increases the filte
373. mg parameter 72 74 79 80 dmgf parameter 156 dmm parameter 191 194 195 dmm2 parameter 193 194 dmm3 parameter 193 194 dmm4 parameter 193 194 DMSO button 68 dn parameter 185 dn2 parameter 185 dn3 parameter 185 dnode command 282 285 dof parameter 152 185 dof2 parameter 185 dof3 parameter 185 done codes 208 DOS file system 291 304 Getting Started VNMR 6 1B double backslash character 197 double precision VNMR FID data 293 double quantum filtered COSY 70 down button 155 down arrow key 97 downsamp parameter 217 downsampling data 210 downsampling factor 217 dp output 87 dp parameter 216 293 dp cubic button 87 dp exp button 86 87 dpf command 246 dpir command 254 dpirn command 254 dp linear button 86 dp quad button 86 87 dps command 189 dpwr parameter 193 194 195 dpwr2 parameter 193 dpwr3 parameter 193 dpwr4 parameter 193 dpwrf parameter 193 dpwrf2 parameter 193 dpwrf3 parameter 193 dpwrm parameter 193 dpwrm2 parameter 193 dpwrm3 parameter 193 DQCOSY button 70 DraftMaster plotter 255 DraftPro plotter 255 draw box 273 draw command 272 draw line 272 dres command 247 dres parameter 194 dres2 parameter 194 dres3 parameter 194 dres4 parameter 194 drift correct 2D data set 79 drift correct spectrum 77 ds button 243 ds command 73 225 231 232 237 242 253 Dscale button 71 73 234 239 dscale
374. mmand is stored in the dcg parameter which can be queried dcg to determine whether drift correction is active If active dcg ifinactive dcg cdc The bc command turns on 1D and 2D baseline correction The 1D baseline correction uses spline or second to twentieth order polynomial fitting of predefined baseline regions bc defines every other integral that is those integrals that disappear when intmod partial as baseline and attempts to correct these points to zero A variety of parameters can be used to control the effect of the bc command For more information about the bc command refer to the entry for bc in the VNMR Command and Parameter Reference Getting Started VNMR 6 1B 01 999083 00 A1298 9 6 Integration Integral Reset Points The z command or the equivalent function key resets the integral to zero at the point marked by the displayed cursor z reset 1 reset2 allows the input of the reset points as part of the command instead of using the position of the cursor Reset points do not have to be entered in order The resets are stored as frequencies and will not change if the parameter fn is changed The command cz removes all such integral resets cz resetl1 reset2 clears specific integral resets For a list of integrals the 1iamp parameter stores the integral amplitudes at the integral resets points and the 1ifrq parameter stores the frequencies of integral reset points To display the values of Liamp en
375. mming 139 saturation 139 shimming on the 142 solvents 110 status 151 time constant control 135 LOCK button acqi 149 151 lock command 134 LOCK display 151 153 lock frequency 248 lock frequency acquisition window 134 lock frequency set 153 lock level display 43 lock level interlock 134 LOCK menu 151 lock receiver gain 157 lock_N primary file 206 lock_N secondary file 206 lockacqtc parameter 135 locked experiment 207 lockfreq parameter 152 183 184 248 lockgain parameter 130 150 152 154 lockphase parameter 152 154 lockpower parameter 130 150 152 154 locktc parameter 135 log file 37 208 278 logarithmic x axis scale 86 logarithmic y axis scale 86 login command UNIX 40 login directory 88 login macro 109 280 login prompt 40 logout command UNIX 41 loose shimming criterion 140 162 Lorentzian lineshapes 222 low rf band 184 low frequency suppression 228 Ip parameter 216 224 225 241 ls command VNMR 276 Isfid parameter 156 223 226 233 Isfrq parameter 227 229 lvl parameter 241 252 Lvl Tilt button 73 239 241 M M shimming criterion 140 Macintosh computer 291 maclib directory 34 70 98 macros automation 98 defined 32 93 keyboard execution 33 language 32 library directory 34 names 32 MAGICAL II language 32 MAGICAL II macro library 34 magnet 23 25 Getting Started VNMR6 18B 309 Index magnet quench warning 18 magnetic media caution 19
376. mmon Desktop Environment CDE or VNMR menus Recalling Data in CDE Before recalling data the VNMR command 1istenon must have previously been given once is sufficient for the procedure to work To recall data with the CDE FileManager do the following steps l 2 Change to the directory in which the data was stored Double click the icon for the desired data FID to load and process the data using processing parameters including the name of the processing macro which were stored with the data set The Open Windows FileManager cannot be used for this purpose Recalling Data Using VNMR Menus To recall and process data using VNMR menus do the following steps 1 2 Click on the Main Menu button in the Permanent menu If you are not already in the data directory click on the DATA button in the second level menu If you are already in the desired directory choose Files from the second level menu If you used the DATA button find the name of the directory containing the data you want to recall and highlight it by clicking on it with the left mouse button Click on Set Directory in the second level menu Find the name of the data file you wish to load highlight it and click the Load button in the second level menu to recall data and processing parameters including any processing macro names To process the data click on the Main Menu button in the top level menu and then click on the AutoProcess button in the
377. mouse arrow The parameter affected will be io if the integral is displayed or vp if the integral is not displayed Interactive Spectral Windowing Mode The sp wp button activates interactive spectral windowing mode No cursors will be displayed The left mouse button is used to adjust the starting frequency of the displayed spectrum Position the mouse arrow at some position and click the left mouse button A cursor will be displayed at the selected frequency Moving the mouse arrow to another position in the display and clicking the left mouse button will drag the cursor defined frequency to that new mouse arrow position The right mouse button is used to adjust the width of the displayed spectrum Position the mouse arrow over some spectral region and click the right mouse button A horizontal and a vertical cursor will intersect at the mouse arrow Moving the mouse arrow above or below the horizontal cursor will adjust width of the spectral display The start of the spectral display will also be adjusted so that the position of the displayed vertical cursor remains constant The further the mouse arrow is from the horizontal cursor the larger the size of the relative change Interactive Phasing Mode The Phase button starts the interactive phasing mode Any integral and cursors that are displayed along with the spectrum are removed Position the mouse arrow on a spectral region of interest toward the right side of the spectrum about h
378. mouse button and drag the cursor to highlight the words or characters to be cut or copied Press the Cut key to remove the highlighted words or characters Press the Paste key or mouse button 2 to paste the selected or cut words characters Table 4 summarizes the key actions described in this section Note that these key actions can be changed with the UNIX stt y command Table 4 Special Keys for VNMR Line Editing Key Left arrow Control H Control Left arrow Control Backspace Right arrow Control L Control Delete A Control P V Control N Delete Backspace Control mouse button 1 Move left one character without deleting Move cursor left to previous word Deletes all characters before cursor Move right one character Delete all characters following cursor Recall command previously entered Move to next line Delete one character Move cursor to position of pointer Control U Delete entire line Return Terminate end of one line of input End Moves cursor to end of line Cut Delete all selected characters Paste mouse button 2 Undo Paste characters that are selected or cut Undo previous paste of delete 01 999083 00 A1298 Getting Started VNMR 6 1B 97 Chapter 5 Using the Command Mode 5 4 Macro Automation Many experiments can be automated by using macros supplied with the system software by modifying system macros or by running user written macros Many system macros are available The majority were
379. ms gt Gradient Nucleus a If you have PFG click on Pfg H2 set pw to one half the 90 pulse found in step 2 and set d1 6 b If you have homospoil click on Homospoil H2 set pw to the 90 pulse p1 to the 180 pulse and d1 6 4 Enter gmapsys click on Set Params gt Go dssh and wait for acquisition to complete You should see two profile spectra 01 999083 00 A1298 Getting Started VNMR 6 1B 175 Chapter 6 Preparing for an Experiment 176 5 Map the shims Enter gmapsys and click on Shim Maps gt Automake Shimmap At the mapname prompt enter a file name Wait for acquisition to complete and the message to be displayed shimmap done 6 Perform shimming on z s Enter gmapsys and click on Autoshim on Z Wait for the acquisitions to complete and the message to be displayed Gradient Autoshimming on Z done N iterations 7 Enter acqi and adjust lock phase Shim only on low order nonspins x1 y1 xz yz etc Do not shim on z s z1 z2 etc 8 Perform shimming on z s Repeat step 6 9 Measure proton lineshape Turn on spinner if appropriate and enter acqi to make fine shim adjustment Shim on all shims as necessary General User Gradient Shimming For the general user gradient shimming can be run from outside gmapsys from any experiment Any one of the following methods is recommended for routine use e Click on Main Menu gt Setup gt Shim gt Gradient Autoshim on Z Parameters are retrieved fr
380. n be entered after fsqis setto y MERCURY VX and MERCURY Systems 1 Because only inline DSP is available set dsp i 2 Setfsq y Doing these steps sets os lsfrqto 1 25 sw and offsets the local oscillator from the transmitter by os 1sfrq when the transmitter frequency is set This occurs at the beginning of the pulse sequence or any time the transmitter frequency is set If a different value of os1lsfrq is desired it can be entered after fsq is setto y On systems other than UN TYTNOVA MERCURY VX and MERCURY inline DSP with oslsfrqcan be used 1 Setdsp i 2 Setoslsfrqto1 25 sw and move tof by the same amount To move tof you can add two statements to the relevant pulse sequences to shift the transmitter to the center of the spectrum tof at the beginning of the pulse sequence and then shift the transmitter to the position offset by os1sfrq for data acquisition For example status A obsoffset tof delay d1 obspulse pw oph last pulse in sequence obsoffset toftoslsfrq 3 Enter fsq y tosetoslsfrqa Setting Frequencies For pulse sequences that explicitly use a frequency other than tof during acquisition the appropriate frequencies need to be set in a similar fashion Frequency setting is automatically done on MERCURY VX and MERCURY To set frequencies on other systems add the pulse sequence statements and set oslsfrqto1 25 sw On UNITYINOVA you must also set fsq n Keep in mind th
381. n FID Spectrum Display Window acqi Program scsseeeeeteereeeeees 159 Figure 45 Spectrum Display Window with IPA acqi Program ecesseeeseeseeeeeeeseeeeeeeenes 160 Figure 46 SHIM Display Window acqi Program oe eeeseeesecseesseseceeeeceeeeaeeeeeeeseenaeeetseenes 161 Figure 47 Auto Mode Window acai Program oo ceeeessesseescsecseeseeseceeceseecsaeeaseeesesseeeneaeenes 162 Figure 48 Ultrasnmr Shim System Interface Controls and Display ceeeeeeseeeeeseeteeeeeeeees 165 Figure 49 Shimmap Plot oo eesecseeeesessecesecceseaeeeceesceseeseseecneeaeesecnecaseaesaecaeeeseeesaeceseneees 171 Figure 50 Curve Fit Plot jiiscnccdiaiseantianadeauin tie ae aiie poe e Daa eae ae ea te iiti 173 Figure 51 Display of Shim Adjustments for Each Iteration oo eeeeeeecseeseeseeeeeeeeesseeeeeeeeeenee 173 Figure 52 Positioning the Spectral Window 0 cesccseeseeeceseeseceeescesecaeeecesesaeeeseesaeseeeeeeenes 185 Figure 53 Acquisition Parameters for Standard Two Pulse Sequence o eseeseeeeeeseeeeeeeeeeeee 187 Figure 54 Graphical Pulse Sequence Display dps Program eeseeeseesseseeseceeeeeeceaeeeeeeeees 189 Figure 55 Display Properties Panel dps Program eeseesecescsseseesececseeseesecaeeeseecaeeeseeeees 189 Figure 56 Property Button Window dps Program o ecessssecescsseseeeececseeecesecaeeateecaeenseeeees 190 Figure 57 Logical Periods A B C in Standard Two Pulse Sequence o eeeeeeeeeeeseeeeeeeeeeeee 190 Fig
382. n Hz and ppm The d11 command displays line frequencies and intensities that are above a threshold defined by the parameter th The number of lines and a scaling factor for line amplitudes can be returned to the caller The list of line frequencies above th is stored by the 1lfrq parameter Frequency units are defined by the parameter axis Frequencies are stored in Hz and are not adjusted by parameters rf1 and rfp The argument noise_mult todll enables suppressing noise peaks The default value of noise_mul1t is 3 A smaller value results in more peaks a larger value results in fewer peaks and a value of 0 0 results in a line listing containing all peaks above th The list of line amplitudes above th is stored by the 1lamp parameter Amplitudes are stored as the actual data point value they are not scaled by vs The thadj command adjusts the threshold th to select peaks The syntax is thadj lt maximum_peaks lt noise_mult lt llargl lt llarg2 gt gt gt gt where the maximum_peaks specifies the maximum number of peaks desired above the threshold the default is wc 4 noise_mul1t is a noise multiplier used to calculate the minimum value for th from the size of the root mean square noise the default is 3 and llarg1 and 1llarg2 are arguments for the noise_mu1t and a keyword respectively sent to the n11 command used inside thadj The dpf command displays peak frequencies in units specified by the axis parameter on the graphics scr
383. n internal program criteria Getting Started VNMR 6 1B 01 999083 00 A1298 6 9 Adjusting Shims Table 19 Hexadecimal Codes for Shim Groups qrecalls an algorithm s internal parameters so that shimming starts quickly q is a background autoshim that keeps the magnetic field at an optimum during experiments of long duration Shimming is performed at the time wshim instructs Only the portion of the shim methods following the letter q is executed after the experiment s first increment Any shim method may follow q however the sz1 Z1 only and szq Z1 Z2 are the most effective Multiple shim methods may follow q but time effectiveness is reduced Methods may be entered into the shimmethods file using a text editor such as vi The macros newshm and st dshm provide an interactive method of defining shim methods Note that unlike normal text files which have unrestricted size the maximum text file size for a shim method is 128 characters The following examples show complete user defined shim methods szq cmm rn stz cmm ry zq cmm means shim Z1C Z2C with medium to medium criterion turn off spinner shim X Y XZ YZ Z1 with medium to medium criterion turn on spinner and then shim Z1C Z2C again with medium to medium criterion throughout d50 szq cmm d150 sza cmm means to sample every 0 5 seconds while shimming Z1C Z2C and then to sample every 1 5 seconds while shimming all Z gradients Use medium to medium criterion
384. n of mouse 42 center command 250 center of the screen page 78 79 centersw macro 185 chained experiments 201 CHAN switch 115 01 999083 00 A1298 Index change directory 37 275 filename 276 change bar 22 Change button 88 change macro 106 channel selection 25 channels rf 24 chart parameters 232 chemical shift scale 79 chemist style parameters 261 clear add subtract experiment 82 text file of current experiment 197 weighting parameters 72 74 Clear button 76 82 clicking a mouse button 42 Clock program 50 CLOSE button acqi 149 150 162 closed icons 51 closing a window 50 closing Plot Designer 271 coarse shim controls 163 coarse shim gradients 136 coefficients for digital filtering 210 212 coefficients for filter computation 217 color command 257 color for graphics screen 272 Color Map button 74 79 color printing 257 258 Color Selection window 258 combination experiments customizing 56 processing and plotting 57 Combine button 76 command line editing 97 command mode 93 commands arguments 93 94 defined 93 entry 94 help files 34 interactive 94 interspersed with parameters 94 names 93 sequential execution 94 types 93 Comment button 76 compare shim values in files 138 compiled sequences library 36 completed transients 188 complex data point 227 compress command UNIX 292 compress double precision FID data 293 compress FID files 292 293 compressfid com
385. n type au or use the Go Periodic Wft button in the Acquire Menu you are telling the computer When block size that is when bs transients are completed perform the action wft Now every 64 or whatever the value of bs is transients the FID is automatically transformed and the spectrum displayed on the screen Any command or macro can in fact be invoked to occur automatically e g wbos dfid display the FID after every bs transients If acquisition is started by go or ga wbs processing may still be set by using the wos command e g wos wft wbs processing may also be disabled by entering wbs stop Setting bs n before starting the acquisition disables this block size storage If bs n data are stored on disk only at the end of the experiment and if the experiment is aborted prior to termination data will be lost There are other times when automatic processing is desirable e When an FID is finished frequently you want it to be automatically transformed You can accomplish this with the wnt for when number of transients parameter e g wnt wft This particular action in fact is automatically performed by the ga command since it is so common e When more than one FID is being accumulated we may want to reserve one particular action to occur at the end of all of the FIDs We might be performing a 2D experiment and after all the data have been accumulated we want to perform a 2D transform for mul
386. nal and typing seqgen s2pul cor seqgen s2pul1 is functionally the same Lines of text containing command syntax examples of statements source code and similar material are often too long to fit the width of the page To show that a line of text had to be broken to fit into the manual the line is cut at a convenient point such 01 999083 00 A1298 Getting Started VNMR 6 1B 21 Introduction as at a comma near the right edge of the column a backslash is inserted at the cut and the line is continued as the next line of text This notation will be familiar to C programmers Note that the backslash is not part of the line and except for C source code should not be typed when entering the line e Because pressing the Return key is required at the end of almost every command or line of text you type on the keyboard use of the Return key will be mentioned only in cases where it is not used This convention avoids repeating the instruction press the Return key throughout most of this manual e Text with a change bar like this paragraph identifies material new to VNMR 6 1B that was not in the previous version of VNMR Refer to the VNMR 6 1B Release Notes for a description of new features to the software Other Manuals This manual should help you get started in learning how to work with Varian NMR spectrometer systems and software Other VNMR 6 1 manuals you should have include e Walkup NMR Using GLIDE e User Guide Liquids NUR
387. names always assume the existence of a default directory also called the current working directory This is the directory the user currently is in To display the path of the current working directory enter the command pwd The default directory is set with the change directory command cd lt directory gt where directory is the name of the new default directory for example entering cd export home steve vnmrsys changes the current working directory to the directory export home steve vnmrsys Entering cd alone sets the current working directory to the user s home directory the tilde symbol shorthand for the home directory of in UNIX does not work with VNMR commands By making the directory containing a file the current directory file name entry is simplified For example if the default directory is set to vnmr fid1ib the file names androl fidand vnmr fidlib androl fid are equivalent The defaultdir parameter holds the name of the default directory for the fi les menu system Chapter 4 Using the VNMR Menu System describes this menu 01 999083 00 A1298 Getting Started VWMR6 1B 275 Chapter 10 Storing Retrieving and Moving Data 276 Table 46 Directory and File Handling Commands and Parameters Commands cat filel lt file2 gt cd lt directory gt copy lt r gt from_file to_file cp lt r gt from_file to_file delete filel lt file2 gt dir lt string gt lf lt
388. nd GEMINI 2000 setting lock power to 0 Lockpower 0 means no lock pulses that is no lock The ZO field position parameter z 0 holds the current setting of the Z0 setting The limits of z0 are 2047 to 2047 in steps of 1 if the parameter shimset is set to 1 2 or 10 and 32767 to 32767 if shimset is set to 3 through 9 On MERCURY VX and MERCURY systems shimset is 10 On GEMINI 2000 systems shimset is 1 Zero is no current The readhw command reads into VNMR the current values of lock system parameters in the acquisition hardware To make VNMR set the lock values in the acquisition hardware use the set hw command Lock Control Methods A number of methods are available for controlling lock e Leave lock in the current state e Run an experiment unlocked e Use simple autolock e Use optimizing autolock e Perform full optimization of lock Each method is discussed in the following separate sections Additional sections discuss error handling and lock loop time constant control Leaving Lock in the Current State Using the Inout Window e Enter alock n If simple or optimized Autolock was previously selected lock is established upon insertion of the new sample If simple lock was previously selected the system only locks if the new sample has the same lock solvent Running an Experiment Unlocked Using the Input Window Applies to all systems except MERCURY VX MERCURY and GEMINI 2000 e Enter alock u Lock
389. nd a single vertical cursor Figure 66 Interactive FID Display df Program 01 999083 00 A1298 Getting Started VWMR6 1B 233 Chapter 9 Display Plotting and Printing 234 At the top of the display is the FID Display Menu with the following buttons note that the labels change on some of the buttons according to the mode the program is in Box Imaginary Full sf wf Dscale Phase Return These buttons function as follows The first button is Box or Cursor depending on if you are in the box or cursor mode Box Change to the box mode with two cursors Cursor Change to the cursor mode with one cursor The second button is Imaginary Zero Imag or No Imag depending on which mode you are in Imaginary Display the imaginary FID Zero Imag Display the imaginary FID as all zero No Imag Remove the imaginary FID display The third button is Expand or Full depending on if you are in the box or cursor mode Expand Expand the area between the cursors Full Display the full area The remaining buttons do not change labels sf wf Opens the interactive FID windowing mode see below Dscale Toggle the display of a time scale under the FID in units specified by the axisf parameter Phase Opens the interactive phasing mode Return Returns to the last menu active before entering the df display Controlling Cursors and FID Intensity The cursor is controlled by moving the mouse arrow and pressing the left button on the mouse Alternativ
390. nd data This button does not appear if gradient shimming is not running e Using the Input Window To start gradient shimming enter gmapshim This is the same as clicking on Gradient Autoshim on Z To stop gradient shimming before it completes enter gmapshim quit This is the same as clicking on Quit Gradient Shim e Automation Use wshim g within automation parameter sets applies only to UN YINOVA UNITYplus MERCURY VX or MERCURY systems See Fully Automatic Autoshim page 144 or the wshim entry in the VNMR Command and Parameter Reference Getting Started VNMR 6 1B 01 999083 00 A1298 6 9 Adjusting Shims Which Shims to Use on a Routine Basis The following suggestions should assist you in routine shimming especially on shim systems with a larger number of shim channels Establish and maintain lineshape Use Z to Z5 possibly Z6 X Y ZX ZY and possibly Z2X and Z2Y The effects of Z7 and Z8 and realistically Z6 are too small to see with the lineshape sample e Shim a new lineshape sample of different geometry Use Z to Z5 possibly Z6 X Y ZX ZY and possibly Z2X and Z2Y e Shim anew sample of the same geometry Use Z Z2 and maybe Z3 e Shim anew sample of different geometry Use Z to Z4 and possibly Z5 X Y ZX ZY e Shim for water suppression Start with a shim set that produces a good lineshape for the same sample geometry Next tweak Z and Z2 and then vary Z5 and Z7 to minimize
391. ned by fn 8 4 Phasing 224 Phasing spectra may be considered part of either data processing or data display we treat it here as part of data processing Table 32 lists spectral phasing software tools Table 32 Phasing Spectra Commands and Parametersn Commands aph lt args gt lt ok rp 1lp gt Automatic phase of rp and Ip aph0 lt args gt lt ok rp 1lp gt Automatic phase of zero order term aphx Perform optimized automatic phasing av Set absolute value mode in directly detected dimension ds lt index gt ds lt options gt Display a spectrum ph Set phased mode in directly detected dimension phase phase_change Change frequency independent phase rp pwr Set power mode in directly detected dimension Parameters lp 3600 to 3600 in degrees First order phase in directly detected dimension rp 360 to 360 in degrees Zero order phase in directly detected dimension Performing a complex Fourier transformation produces two sets of data referred to as the cosine and sine transforms or the real and imaginary channels respectively In almost all cases the absorption spectrum peaks in phase and the dispersion spectrum peaks out of phase do not coincide with the real and imaginary channels but must instead be produced from a linear combination of the two channels Phase Parameters The process of phasing a spectrum requires the determination of an angle 9 that can be used to mix t
392. ng Ethernet and limNET export rwxr xr x rwxr xr x If export home vnmr1 does not have execute or read access for the world set then the file export home vnmr1 vxr example is not accessible from limNET even if its file protection does allow world access Also no entry can be overwritten or erased even if the file protection would allow it A new file can be written only if the world has read write and execute access to the parent directory Read and execute access is required for each directory above the parent in the tree for example File to be written Required access export home vnmr1 limnet newfid 5 N A to be created Parent directories Required access export home vnmr1 limnet CWXIEWXEWX export home vnmrl rwxr xr x export home rwxr xr x export rwxr xr x rwxr xr x A good idea is to create a separate directory for limNET transfers so write access for the world can be limited to that subdirectory Error Messages from limNET The dnode and eaddr commands should never produce an error If one occurs contact the system administrator because the limNET software was probably not installed correctly The eread and ewrite commands can fail for a variety of reasons Some of the error messages that may appear are listed below in alphabetical order with an explanation of each message and the recommended action Can t open limNET service file The limNET server was never started Contact the system administrator Error
393. ng Experiment Text Files page 197 e 7 4 Performing Acquisition page 198 e 7 5 Applying Digital Filtering page 209 7 1 Setting Frequency Related Parameters With a spectrometer configured to perform the proper experiment and a sample in place spinning locked and shimmed you are ready to select parameters to acquire data There are two aspects to selecting parameters The first is the frequency related aspect setting the position and size of the spectral window The second is the pulse sequence related aspect The following section covers frequency related parameters Selecting pulse sequence related parameters are described in Setting Pulse Sequence Related Parameters on page 185 Frequency Setting Table 24 lists frequency related parameters and related commands Starting with VNMR version 4 3 the selection of frequencies for the observe channel and the decouplers is done differently from earlier versions of VNMR The mechanism of setting frequencies is essentially the same for example entering tn H1 selects the proton frequency But in earlier versions that resulted in s f rq being set to a value of the IH frequency taken from a nucleus table When a data acquisition was requested with the go command the value of s f rq was combined with information about the lock 1ock freq solvent and the small offset tof to generate the final frequency In the new scheme when tn H1 is entered the H frequency is aga
394. ng on np FID Full bandwidth of digital filter to yield a filtered FID Center of solvent suppressed region of spectrum Number of coefficients in the digital filter Order of polynomial to fit digitally filtered FID Starting point for linear prediction data ext in np dim Starting point for linear prediction calculation The parameter 1s fid is a constant used in left shifting the FID If 1sfidis set toa value other than n the FID is left shifted by 1s fid complex points before weighting or Fourier transformation is performed The value for 1sfid must lie between 0 and np 2 The parameter ph f idis a zero order FID phasing constant If ph f idis set to a value other than n the FID is phase rotated by phfid degrees before weighting or Fourier transformation is performed The tmove macro provides a method of setting the parameter 1 s f id position the right time cursor at the place that should be the start of the FID then enter tmove to adjust the parameter 1sfid Getting Started VNMR 6 1B 01 999083 00 A1298 8 5 Advanced Data Processing Frequency Shifting The parameter 1sfrq sets a frequency shift of spectral data in Hz with a negative value resulting in peaks being shifted upfield to the right and a positive value in peaks being shifted downfield to the left 1 s f rq operates in the time domain on complex FID data and thus must be entered before any Fourier transformation is performed Data Processing Methods
395. ng screen dfww Display FIDs in whitewash mode fidpar Add parameters for FID display in current experiment pfww Plot FIDs in whitewash mode plfid Plot FIDs dfs lt lt start gt lt finish gt lt step gt lt all imag gt lt color gt gt dfsax lt start gt lt finish gt lt step gt lt all imag gt lt color gt gt dfsanx lt start gt lt finish gt lt step gt lt all imag gt lt color gt gt dfsh lt lt start gt lt finish gt lt step gt lt all imag gt lt color gt gt dfshnx lt start gt lt finish gt lt step gt lt all imag gt lt color gt gt dfsnx lt start gt lt finish gt lt step gt lt all imag gt lt color gt gt dfww lt lt start gt lt finish gt lt step gt lt all imag gt lt color gt gt pfww lt lt start gt lt finish gt lt step gt lt all imag gt gt plfid lt lt start gt lt finish gt lt step gt lt all imag gt lt pen gt gt Parameters axisf s m u n Axis label for FID displays and plots crf number in sec Current time domain cursor position deltaf number in sec Difference of two time cursors dotflag n y Display FID as connected dots ho number in mm Horizontal offset lsfid n number Number of complex points to left shift np FID phfid n 360 to 360 in deg Zero order phasing for np FID sc 0 to wcmax in mm Start of chart sf 0 to at in sec Start of FID display vf le 6 to
396. ningsare used when failure to observe instructions or precautions could result in injury or death to humans or animals or significant property damage CAUTION Cautions are used when failure to observe instructions could result in serious damage to equipment or loss of data Warning Notices Observe the following precautions during installation operation maintenance and repair of the instrument Failure to comply with these warnings or with specific warnings elsewhere in Varian manuals violates safety standards of design manufacture and intended use of the instrument Varian assumes no liability for customer failure to comply with these precautions WARNING Persons with implanted or attached medical devices such as pacemakers and prosthetic parts must remain outside the 5 gauss perimeter of the magnet The superconducting magnet system generates strong magnetic fields that can affect operation of some cardiac pacemakers or harm implanted or attached devices such as prosthetic parts and metal blood vessel clips and clamps Pacemaker wearers should consult the user manual provided by the pacemaker manufacturer or contact the pacemaker manufacturer to determine the effect on a specific pacemaker Pacemaker wearers should also always notify their physician and discuss the health risks of being in proximity to magnetic fields Wearers of metal prosthetics and implants should contact their physician to determine if a danger exists A tab
397. nits 6 dB and the lock level changes by more than a factor of two Set lock gain as necessary 5 Ifthe SHIM display window is not open click the SHIM button from any Acquisition window to open it In the SHIM display window try a change of 4 or 4 in the setting for Z1C If the lock level goes up with one of these continue in that direction until the level is maximized it no longer increases but instead begins to fall At this time if you are fairly certain your shim values are close to correct you can click on the Z1C and Z2C the coarse controls for Z1 and Z2 buttons until the signal level is maximized 6 Change the setting for Z2C by 4 or 4 and continue in that direction until the level is maximized 7 Adjust Z1C for maximized lock level then adjust Z2C for the same Continue this iterative process until the lock level goes no higher If the lock level increases to 100 decrease lock gain and then continue to adjust Z1C and Z2C Lock power is adjusted by selecting z0 pwr gn ph from the SHIM menu Return to the shims by selecting this shim window from the same SHIM window 8 Adjust Z1 and Z2 the fine Z controls in the same way until the lock level is maximized In most cases this concludes the shimming however some times it is necessary to shim the other Z controls and the non spin shims This must not be undertaken in the same way as the procedure above suggests That is if you simply go through Z1 Z2 Z3 and
398. nt rtp lt file gt Retrieve parameters rts file lt status gt Retrieve shim coil settings rtv Retrieve individual parameters updatepars Update all parameter sets saved in a directory compressfid i indir o outdir f compressfid e exp_number o outdir f makefid file lt element_number gt lt format gt rtv lt file parl lt par2 gt gt lt variables gt Parameter parversion real value Version of parameter set Using rt rtp and rts to Retrieve Files The macro rt lt file gt retrieves FIDs stored in the FID file file fid into the current experiment e g rt vnmr fidlib fidld If file fid does not exist and the parameter file file par does exist rt retrieves the parameters only from file par If rt is entered without an argument it asks for a file name In that case the file name can be given without single quotes Retrieved data is placed into the current experiment Any data in that experiment is overwritten Remember that it is the FID that is retrieved and it must be transformed but if the data is stored after it is originally processed as previously recommended it is not necessary to rephase re reference or otherwise reprocess the data except as desired The macro rt p lt file gt retrieves all parameters from the parameter file file par if this file exists If not and if file fid exists rtp retrieves the parameters only from the FID file file fid If you only wish to retri
399. nts in the text window If the text is longer than what one window can hold cat pauses after the window has filled and waits for a keystroke from the operator to fill the window with more text The curexp parameter is useful when accessing text files generated by various commands curexp contains the full UNIX path to the currently active experiment For example cat curexpt fp out displays the contents of the fp out file in the current experiment directory 10 2 Storing Data As explained previously NMR data on the VNMR data system is acquired in a temporary disk file the known as an experiment and is identified by the file name exp where is an integer from 1 to 9999 e g exp1 or exp6 Data reside in an experiment indefinitely until another set of data is collected in the same experiment At some time however it is generally desirable to transfer the data to a more permanent file The data can be transferred to a file on a hard disk to a magnetic tape or even via a mechanism such as Ethernet to some remote data system Table 47 lists tools for storing data Table 47 Data Storage Commands and Parameters Commands autoname Create path for data storage svf lt file lt nolog gt lt arch gt gt Save FIDs in current experiment svp file Save parameters from current experiment svs file lt status gt Save shim coil settings writefid file lt element_number gt Write numeric text file using a FID element
400. nu page 85 Use Line List Use Mark Fit Results Show Fit Plot Add Sub Regression 1 Menu page 86 x linear x square x log dp linear dp quad dp exp next Rt Regression 2 Menu page 86 y linear y square y log dp linear dp quad dp exp Next Rt Regression 3 Menu page 86 dp linear dp quad dp cubic dp exp plot dp output Return Files Main Menu from File button in Main menu page 87 Set Directory File Info Tape Load Data Delete More Return Directory Menu page 88 Change Default Set Default Parent Home Nmr More Return Directory Secondary Menu page 88 NMR Create New Return Files Information Menu page 89 By Size By Date Return Files Tape Menu page 89 Directory Sizes Write Read All Return Files Data Menu page 90 Load Save FID Show Shims Load Shims SaveShims More Return Files Data Secondary Menu page 90 Load Params Save Params Return Files Secondary Menu page 90 Display Edit Copy Rename Return continued on next page 01 999083 00 A1298 Getting Started VNMR 6 1B 63 Chapter 4 Using the VNMR Menu System Table 3 VNMR Menu System Part 4 of 4 Secondary Main Menu from More bution in Main menu page 91 Write Pulse Sequence Configure UNIX Exit VNMR Return Pulse Sequence Entry Main Menu see VNMR User Programming Start Delay Pulse DecPulse Status Other Finish Show Seq Pulse Sequence Entry Delay Menu see VNMR User Programming D1 D2 D2 2 D3 MIX Allow Homospoil Return Pulse Sequence Entry Phases Menu
401. nu page 87 to retrieve or store data edit files etc More Display the Secondary Main menu page 91 for other less common choices including writing a pulse sequence opening a temporary UNIX shell and exiting VNMR Getting Started VNMR 6 1B 01 999083 00 A1298 4 6 Workspace Menu 4 6 Workspace Menu All data acquisition and data processing is done using a series of files known collectively as an experiment Experiments have names exp1 through exp 9 Of these all except exp5 can be used for general purpose experiments exp5 is used for the spectra add subtract mode At any one time you are joined with or connected to a particular experiment but you can create up to nine experiments and switch back and forth between experiments according to your needs Selecting Workspace from the Main menu displays the Workspace menu which enables you to display the current list of experiments switch to any experiment and create or delete experiment files exp1 is created by default and cannot be deleted You can also enter menu workspace to display the Workspace menu Button Description Library Display in the text window the size pulse sequence used and text of existing experiments Exp 2 Exp 3 Join experiment exp2 exp3 exp9 Create New Create a new experiment using the first available number Delete Delete an experiment prompting for user input 4 7 Setup Menus Selecting Setup in the Main menu activates th
402. o acquisition e eject Eject sample i insert Insert sample sample Submit change sample autoshim experiment acgqi lt par disconnect exit standby gt lt ret gt Parameters loc 0 1 to traymax Location of sample in tray traymax 0 9 50 100 Sample changer tray size 2000 spectrometers manual control is the only way to withdraw samples unless the optional spinner control board is installed in the system Solids probes do not support sample insertion and ejection To Eject a Sample Without a Sample Changer You should always eject first even if no sample is in the magnet to start airflow to carry the sample The ejection air is turned on and under computer control the sample if present rises back to the top of the upper barrel You can now remove the sample and replace it with another sample Using the Input Window Applies to all systems if the optional spin control hardware is installed e Enter e in the input window Using GLIDE Applies to all systems if the optional spin control hardware is installed 1 Ifthe GLIDE interactive window is not open open it entering glide in the input window or by clicking on the GLIDE button in the Main Menu 2 Click on Experiment amp Solvent gt Eject gt Close Using the Acquisition Window Applies to systems configured for acquisition if the optional spin control hardware is installed 1 Ifthe Acquisition window is not open enter acqi in the input
403. o if the lock frequency changes as a result of an Autolock operation frequencies for that acquisition will be off by the amount of that change Switching from chloroform to acetone requires a change in the lock frequency of about 5 ppm which can cause problems in precision work Changing lock frequency is only a problem when you select Autolock with 01 999083 00 A1298 Getting Started VNMR 6 1B 133 Chapter 6 Preparing for an Experiment the alock parameter It is not a problem for the lock experiment since by definition the lock experiment is complete once the autolock operation is completed Using GLIDE 1 Ifthe GLIDE interactive Chse LOCK FID LARGE window is not open enter glide in the input window or click on the GLIDE button in the Main Menu troi ACQUISITION Coarse 2 Click on the Setup icon 0 20 40 60 50 100 3 Choose an experiment and Oe fine solvent 0246 8 02 4 6 8 4 Click on the Setup button starting lock level current lock level 5 Click on the Custom icon 6 Click on the Acquire icon SHIM 2pwr gnph 7 Inthe Locking field click on Auto lockfreq ole _ l6 Do 64 ZO lock power and lock oi A gain are optimized ae CED CED CUD GED L Full Optimization kipi ED CD ED ES a a 356 Full optimization is the most jeans ED ED CD ED complete optimization of lock parameters A fuzzy logic auto cy J lock algorithm automates the r CD G Ge Gy
404. o not substitute parts or modify the instrument Any unauthorized modification could injure personnel or damage equipment and potentially terminate the warranty agreements and or service contract Written authorization approved by a Varian Associates Inc product manager is required to implement any changes to the hardware of a Varian NMR spectrometer Maintain safety features by referring system service to a Varian service office WARNING Do not operate in the presence of flammable gases or fumes Operation with flammable gases or fumes present creates the risk of injury or death from toxic fumes explosion or fire WARNING Leave area immediately in the event of a magnet quench If the magnet dewar should quench sudden appearance of gasses from the top of the dewar leave the area immediately Sudden release of helium or nitrogen gases can rapidly displace oxygen in an enclosed space creating a possibility of asphyxiation Do not return until the oxygen level returns to normal WARNING Avoid helium or nitrogen contact with any part of the body In contact with the body helium and nitrogen can cause an injury similar to a burn Never place your head over the helium and nitrogen exit tubes on top of the magnet If helium or nitrogen contacts the body seek immediate medical attention especially if the skin is blistered or the eyes are affected WARNING Do not look down the upper barrel Unless the probe is removed from the magne
405. o set sw downfieldppm upfieldppm sets the parameters sw and tof for the given spectral window set sw also does referencing The centersw macro moves the cursor to the center of the spectrum The minsw macro searches the spectrum for peaks sets new limits accordingly and then calls movesw to calculate a new transmitter offset tof and a new spectral width sw 7 2 Setting Pulse Sequence Related Parameters The second step in setting experimental parameters is the pulse sequence related aspect Table 25 lists pulse sequence related parameters and related commands and macros Most experiments will be acquired using a pulse sequence known as the standard two pulse or S2PUL The s2pul1 macro converts the current experiment to an experiment suitable for S2PUL Figure 53 shows the parameters relevant to this pulse sequence and to many other pulse sequences The pulse sequence name is stored in the parameter seqfil 01 999083 00 A1298 Getting Started VNMR 6 1B 185 Chapter 7 Acquiring Data Table 25 Acquisition Pulse Sequence Related Commands and Parameters Commands dmfadj lt tipangle_resolution gt dmf2adj lt tipangle_resolution gt dmf3adj lt tipangle_resolution gt dmf4adj lt tipangle_resolution gt dps lt file gt ernst tl_estimate lt 90_pulse_width gt hoult pl flip_angle lt 90_pulse_width gt pps lt file gt pw lt flip_angle lt pulse_width gt s2pul time lt lt hours gt minutes gt P
406. o that only every other integral region is displayed and the spectrum is automatically broken into integral regions 2 Optional Enter be A spline fit baseline correction is performed to produce the flattest possible baseline 3 Enter isadj The largest integral is adjusted to a reasonable size 4 Enter dli The text window displays a list of integral intensities Manual Method 1 Enter cz Any currently defined integral reset points are cleared 01 999083 00 A1298 Getting Started VWMR6 1B 251 Chapter 9 Display Plotting and Printing 252 2 Enter intmod partial The integral display mode is changed so that only every other integral region is displayed 3 Click on Next gt resets 4 Click the left button slightly to the left of the left most group of peaks This establishes the end of the first from the left end section of baseline You can position the mouse cursor anywhere vertically that seems most comfortable 5 Click the left button slightly to the right of the left most group of peaks This establishes the end of the first section of peaks 6 Repeat steps 4 and 5 for each group of peaks across the spectrum The reset points must alternately separate baseline and peaks If two peaks are adjacent to each other but you want a reset between them click the button t wice at the same place This establishes a baseline region of zero length Note that you can also add additional resets in th
407. ocessing Menu oo eee eeesecsecsseceeceseeseceseeeceseeeceeeeeeseseseaeeaeesaeenee 73 2D Processing Parameter Setup Menu o00 cece eeeececeseceeceseeeeeeeeeeseeseeeseesaeeaes 73 2D Interferogram Processing Menu 0 eceeeeesecesseceececeseeeneeceeceeneceeeeeneeesaeeeee 74 Interactive 2D Color Map Display Main Menu dconi Program 0 0 74 Interactive 2D Display Projection Menu dconi Program eee eee 75 Interactive 2D Peak Picking Main Menu ll2d Program eee eee 75 2D Peak Picking Automatic Menu l12d Program esesesesseeeeesrrerrererrereererern 75 2D Peak Picking Edit Menu l12d Program essseseseeeessererrererrsrerrsrrerrrreereresrn 76 2D Peak Picking File Menu ll2d Program 00 cece eeceeeseceeceeeeeeeeeeseeeeaeeenes 76 2D Peak Picking Display Menu l12d Program 000 eee eeeeceeeeeeeeeeeeeeeeenes 76 AIO Display Menus sonarer enera e EE EE EE AEE SE 77 ID Data Display Menu wicicciciscccscesssctecscdsscssacceunnas ceescetees actcbsecesscadaeceetscaveccuceeeis 77 1D Data Manipulation Menu ee eceeeesecescceseeceseeceeeceseeeneecneeeeaeceeneeeeeesaeeeee 77 1D Display Size Selection Menu eee eeceeeeeeeseeeseceeecaeceesaessaeeaeensensees 78 TD POTN Menu vases dss scscecscevedcsescosseceas aeee aa ie aa EE E E E EAEE 78 1D Data Display Secondary Menu ssessessesesseeesrssesrssesrrresrerrsseesrsesrrsresrrrrsreerese 78 6 Getting Started VNMR 6 1B 01 999083 00 A1298 Table of Con
408. ocessor Multitasking is like queuing in one respect you do not have to do or know anything special Issuing successive commands to initiate an acquisition a plot some printing and some data processing quickly causes four processes to become active simultaneously Just like queuing the rule is simple tell the system what you want to do whenever you wish If the operation you request requires queuing it is e queued If it can be accomplished immediately and involves multitasking that happens as well Multitasking has one limitation however In normal circumstances the system is not designed to perform multiple data processing operations simultaneously within a single copy of the VNMR software Thus while it is possible to have two or more terminals attached to a computer and several users performing a 2D transformation at the same time it is not possible for a single user to do multiple data processing tasks from a single terminal Concurrent processing operations are possible outside the VNMR program by using UNIX For example assume you have started a long 2D Fourier transformation FT in the VNMR program You are now free to open or re open a different window which puts you in communication with the UNIX operating system or with one of the many programs supplied with UNIX text editors compilers etc Thus you can edit a new pulse sequence or write a report on your most recent results while the Fourier transform proceeds It
409. ock level has proven to be a sufficient criterion Floppy Disk Use Every Ultraenmr Shims floppy should contain 83 system files and up to 62 user files The system files include 39 strength files st r 39 divider files div a gradient channel configuration file him a shim coil resistance file res a shim configuration file cfg andtwo shim files file0 dacand file1 dac file1 dac isto contain the shim values for the CHCI lineshape sample in one particular probe The 62 user files are the shim files 2 to 63 file dac A version of each of the system files is stored in the system PROM programmable read only memory If any system file is missing on the floppy disk the PROM version is used instead It is acceptable to use the PROM versions for the him res and cfg system files It is not acceptable to use the PROM versions for the div and str files because these files are set at the time of system installation and are magnet dependent Getting Started VNMR 6 1B 01 999083 00 A1298 6 11 Shimming Using the Ultraenmr Shim System The readultra macro reads shim set files for the Ultraenmr shim system from a floppy disk on a Sun workstation into VNMR e g entering readult ra 6 reads shim set file 6 Entering readultra with no argument reads all of the shim set files Before using readultra the floppy disk is expected to be mounted as pcfs on the Sun workstation For details refer to the descript
410. odify the string 01 999083 00 A1298 Getting Started VYNMR 6 18 261 Chapter 9 Display Plotting and Printing value of ap See the manual VVMR User Programming for information on the template argument e hpa fills in the blanks on the bottom of the preprinted chart paper available for Hewlett Packard 7475A and 7550A plotters The x0 and y0 parameters adjust the x zero and y zero positions in mm respectively of Hewlett Packard plotters and Postscript devices You can use hpa to adjust x0 and y0 so that the numbers that are filled in on the blank lines are in a pleasing position e pltext lt lt file gt lt x lt y lt width gt gt gt gt lt Sxn yn y_inc gt plots the text contents of a file on the plotter The default is the current experiment text file x and y are the coordinates in mm of the first line of text width is the maximum column text width in characters p1text uses a word wrap to make the text fit into the width specified 9 8 Plot Designer 262 Plot Designer allows you to see and design a plot before you print it It provides templates drawing tools and a text editor that give you the capability of positioning spectra parameters axes and other plot output on a page System Requirement Plot Designer is a Java based application You must have Solaris 2 6 or later installed in order to use Plot Designer The J ava Runtime Environment JRE for Solaris from Sun Microsystems provides an envir
411. of 1le6 For most other systems the lock frequency is equal to lockfreq except for UNITY and VXR S systems where it must be calculated from lockfreq setref can calculate the deuterium reference frequency based on the chemical shift of the 7H lock signal lock_shi ft which is extracted from the file vnmr solvents using the solvinfo command h2_ref lock_frequency 1 lock_shift le6 This is the frequency of the deuterium frequency standard 0 ppm at the current field strength Using the ratio of the absolute standard resonance frequencies for deuterium stdfrq_h2 and for the current nucleus stdfrq_tn the ref frq parameter can now be calculated directly vreffrq h2_ref stdfrq_tn stdfrq_h2 Now rf1 can be calculated as rfl sw 2 sfrq reffrq le6 rfp is set to 0 referencing on the frequency standard and refpos is set to 0 referencing active set ref returns the values of rf1 rfp reffrq and refpos to the calling macro The accuracy of the set ref macro is mostly limited by the accuracy of the chemical shift of the lock resonance line which may depend on the concentration and the chemical properties acidity basicity of the components in the sample But set ref should Getting Started VNMR 6 1B 01 999083 00 A1298 9 5 Spectral Display and Plotting normally be accurate enough for macros such as tmsref to find an actual reference line close to its predicted position setref assumes a locked sample
412. of the sample tube should not exceed 124 mm If you need to use less than 0 7 ml of solvent for any reason you can center the liquid volume in the cross hatched area This centers the sample in the receiver coil indicated by the center line symbol To Position a Sample Using the Sample Tray Alternatively if using the sample changer the sample tray itself can be used to set an appropriate depth for the bottom of the NMR tube This procedure if followed for all samples placed in the tray results in a very reproducible sample position and once shim settings have been determined for this length of sample there should be very little shimming necessary when changing samples even with a solvent change Getting Started VNMR 6 1B 01 999083 00 A1298 6 2 Ejecting and Inserting the Sample Place Flange Here I mi i Nes at ya Liquid Height for Best Resolution 1 SE ty 10 mm 5mm ee 3 1 ml 0 7 ml ie i Gee _ Center Liquid Volume jj 98 mm 106 mm lt on This Line AT 1 Maximum Sample oo iy mm 133 mm Depth w at _ Probe Bottom Figure 21 Sample Depth Indicator e Insert the NMR tube into the turbine and gently push the tube down through the turbine while holding the turbine tube combination in the other hand within location zero When the tube touches the bottom stop pushing down The sample is now properly positioned If too much pressure is applied
413. of this interface 3 1 Activating GLIDE When you open the GLIDE interface shown in Figure 18 the menu overlays the top of the VNMR window Figure 18 GLIDE User Interface Window After GLIDE has been activated the GLIDE button in the Permanent menu acts as a toggle allowing the GLIDE window to be moved into view or hidden behind other windows Opening GLIDE To open the GLIDE user interface window do one of the following actions e Click on the GLIDE button on the Main Menu e Enter the command glide in the VNMR input window Closing GLIDE To remove the GLIDE user interface window from the display but keep the program running click on the GLIDE button in the VNMR Permanent menu To bring back the GLIDE window click again on the GLIDE button or enter the command glide To close the GLIDE program so it no longer is running take one of the following actions e Click on the Exit button e Enter the command glide exit 01 999083 00 A1298 Getting Started VNMR 6 1B 53 Chapter 3 Using GLIDE You might be asked to confirm that you want to exit GLIDE Customizing the file glide_defaults described in the manual Walkup NMR Using GLIDE determines whether or not you see the confirmation window 3 2 Using GLIDE 54 The GLIDE interface makes obtaining spectra on the system extremely easy Each experiment accessed from the Setup button can be run in exactly the same manner Only three simple steps are required to
414. oil Gradient Type in the chapter on PFG modules operation in the manual User Guide Liquids NMR The system administrator must make a shimmap using homospoil before homospoil gradient shimming can be used Follow the procedure in Mapping the Shims page 169 At step 4 select tn as appropriate set tof on resonance and then find the 90 pulse If deuterium is used t pwr should be kept low with a 90 pulse greater than about 200 us Getting Started VNMR 6 1B 01 999083 00 A1298 6 12 Gradient Autoshimming At step 6 select either Homospoil H1 for proton parameters or Homospoil H2 for deuterium parameters as appropriate Homospoil gradients must be configured at this step use config or set gradtype nnh At step 7 further testing of the gradient shimming parameters for homospoil can be done as follows 1 Enter gmapsys and click on Set Params gt Go dssh 2 Using the 90 pulse from step 4 calibrate the 90 and 180 pulses to obtain an echo Enter df to display the FID You should see an echo forming in the middle of the FID 3 If needed adjust sw so that the gradient covers at least 10 of the spectral window Increase np to 512 to improve Hz point resolution However np should be adjusted so that at is not longer than the homospoil time limit 20 ms on standard UN YINOVA and UNITYplus and 200 ms with the automated deuterium gradient shimming module The acquisition time at should also be shorter than T gt Set
415. om VXR style system VNMR tape lt type gt lt option gt lt filel gt Read tapes from VXR style system UNIX tar lt options gt Create tape archives add or extract files UNIX The simplest technique to operate the tape unit is to use the interactive tape file handling menu described in File Menus on page 87 This menu lets you perform all relevant operations reading files from tape writing files to tape and listing a tape catalog The second method is to use the UNIX command t ar tape archive Run in a separate window from VNMR a tar backup can proceed completely as a separate process If you have many megabytes of data to back up there is no reason to tie up VNMR with this process Simply open a separate window and use tar A number of ways are available for reading from and writing to a streaming tape See the documentation of the UNIX tar mt and dd commands for some possibilities For example on systems using Solaris the following commands append files abc and xyz to an already used tape mt f dev rmt Olbn rew mt f dev rmt Olbn fsf 1 tar cvf dev rmt Olbn abc xyz mt f dev rmt Olbn rew If data is written onto a magnetic tape using a Sun or IBM RS 6000 computer and is then to be copied into a Silicon Graphics computer the byte order on the tape is reversed To read such a tape you must use the dev tapens device when using tar tar xvf dev tapens 01 999083 00 A1298 Getting Started VNMR6 1B 289 C
416. om the current mapname which is displayed at the start of shimming and the spinner is automatically turned off The curve fit and shim adjustments are not displayed The previous parameter set and data are retrieved when shimming is finished This button only functions after a shimmap is made e Enter gmapshim This performs the same action as clicking on Gradient Autoshim on Z e Within automation parameter sets use wshim g UN TYINOVA MERCURY VX UNITYplus and MERCURY only To stop gradient shimming before it is completed use one of the following methods e Click on Main Menu gt Setup gt Shim gt Quit Gradient Shim Quitting aborts the experiment and retrieves the previous parameter set and data e Enter gmapshim quit This performs the same action as Quit Gradient Shim e Abort the acquisition with aa and click on Cancel Cmd Then enter gmapshim quit to retrieve previous data set and parameters Suggestions for Improving Results Calibrate the 90 pulse and adjust t pwr pw and gain to optimize signal to noise Reduce gain if ADC overflow occurs which may appear as wings on the profile For solvents with long T set d1 to 3 to 5 times T4 or use a small flip angle for pw Stimulated echoes may otherwise result which may appear as excess noise or a beat pattern in the spectrum or as secondary echoes in the FID use df to observe this The phase encode delay d3 is arrayed to two values the first of which is
417. ommand Line Editing and Reentry press the up arrow key marked A or enter Control P hold down the Control key and then press the P key to recall your command Each time you press the up arrow key or enter Control P the previous line is recalled think of the P in Control P as standing for previous Depending upon how much you have been typing you may be able to go backwards in time several minutes or even several hours If you go back too far the down arrow key marked W or Control N moves to the next line For example pressing Control P Control P Control N moves back two lines and then down one line Once you have recalled a previous line you can edit the line with these keys Left arrow Move left one character alternate Control H Right arrow Move right one character alternate Control L Delete or Backspace Delete a character Control U Delete the entire line Insertion is accomplished by typing the desired character When the line is correct press Return as usual to enter the line The cursor does not have to be moved to the end of the line before you press Return Command line editing is also active on the current line that is before you have pressed Return for the first time If you notice an error in a line you are typing press left arrow or Control H to return to the error press Delete to erase the characters you do not want type in the correct characters and then press Return Press the left
418. on In the first mode you customize acquisition processing and plotting parameters displayed in the setup windows prior to initiating acquisition with the Go button By clicking the Close button in each setup window the setup window is closed and the parameter values are saved We will use this mode in the following steps In the second mode you also change parameters but by clicking on the Do button in each setup window you immediately acquire or reacquire data process the data with specified parameters or plot the data with the specified parameters Note that each setup window is separate and immediate clicking on Do in the Acquire Setup window only acquires clicking on Do the Process Setup window only processes and clicking on Do in the Plot Setup window only plots This allows you to easily explore the effect of changing parameters 2 Click on the Acquire Setup button in the Custom Setup window The Acquire Setup window is displayed with the Number of Scans set to 1024 0 if this item is not on 01 999083 00 A1298 Getting Started VNMR 6 1B 55 Chapter 3 Using GLIDE view use the scroll bar on the right side of the window to scroll it into view In this example change the number of scans from 1024 to 16 by clicking on the line at the end of the number and using the Back Space key to delete the current value Type in the new value of 16 When you are done click on the Close button to exit and save the change Do not clic
419. on htune Tune H channel on GEMINI 2000 qtune Graphical tuning tool on UN TYINOVA and UNITYplus sethw tune n Place GEMINI 2000 into tune mode su Submit setup experiment to acquisition tune Assign frequencies on UN TYTNOVA and UNITYplus tuneoff Turn off tuning mode on GEMINI 2000 go lt lt acqi gt lt nocheck gt lt nosafe gt gt tune freql lt freq2 freq3 freq4 gt tune chl freql lt chan2 freq2 gt 01 999083 00 A1298 Getting Started VNMR 6 1B 113 Chapter 6 Preparing for an Experiment Sample Changes In general if the probe is already tuned to the proper nucleus as is almost always the case for proton and carbon observation only a small amount is gained by tuning the probe to match your particular sample An exception to this rule occurs when switching from normal organic solvents to strongly ionic samples such as a water solution with 1M buffer If the probe is tuned for an organic solvent such as CDCl and a strongly ionic sample is then inserted you may find a lengthening in the 90 pulse width by a factor of two or three For single pulse experiments this detuning of the probe will cause an apparent deterioration of signal to noise since you will only be using a 30 pulse for example when you intended to use a 90 pulse but in many cases this effect will be small Quarter Wavelength Cable When a large change is made in the frequency of the observe nucleus on broadband
420. onfunctional dmf 10000 Decoupler modulation frequency 194 Getting Started VNMR 6 1B 01 999083 00 A1298 7 2 Setting Pulse Sequence Related Parameters e Homonuclear decoupling with class C amplifiers dm y homo y dmm c dhp n dlp 15 to 25 Decoupler mode on Homonuclear decoupling on Decoupler modulation mode is continuous wave Decoupler high power off Decoupler low power level range e Heteronuclear decoupling with class C amplifier dm y homo n dmm w dhp 70 dmf 9900 Decoupler mode on Homonuclear decoupling off WALTZ 16 decoupling Decoupler high power level Decoupler modulation frequency The following values are typical for decoupling on GEMINI 2000 systems e Homonuclear decoupling with linear amplifiers dm y dmm c dpwr 6 to 20 dlp 0 to 1023 Decoupler mode on Decoupler modulation mode is continuous wave Decoupler power level range Fine attenuator control range e Heteronuclear decoupling with linear amplifiers dm y dmm w dpwr 45 dmf 10000 d1lp 1023 Decoupler mode on WALTZ 16 decoupling Decoupler power level Decoupler modulation frequency Fine attenuator control e Homonuclear decoupling with class C amplifiers dm y d1lp 1500 to 2047 Decoupler mode on Homodecoupler power level range e Heteronuclear decoupling with class C amplifier dm y dmm w dhp 0 5 1 dmf 9900 Decoupler mode on WALTZ 16 decoupling Decoupler high power level D
421. onment in which you can run Java applications You can download the latest version of JRE for Solaris from the Sun Microsystems Web site at http www sun com solaris jre index html Starting Plot Designer Start the Plot Designer program by entering the macro jdesign or the command jplot setup in the VNMR input window This opens the Plot Designer window shown in Figure 72 File Orient Region Magnily Pi Main menu Tools Workspace Figure 72 Plot Designer Window Getting Started VNMR 6 1B 01 999083 00 A1298 9 8 Plot Designer Customizing the Plot Designer zj TEE al Window Background snow 4 You can easily change the size and appearance Border Color black of the Plot Designer window by doing the aura eiaa ae E following procedure k j R Grid Color blue 4 1 Click on Preferences in the main menu then Set Up to open the Window Plotter black amp white Preferences panel shown in Figure 73 Aes JE 2 To change an aspect of or property in EET RRE the Plot Designer window click on its corresponding button to open a pull Enap onia down menu Snap Spacing 0 5 inch See Table 41for a description of each N eea control Figure 74 is an example of the window Figure 73 Window without visible region borders and Preferences Panel without a grid Table 41 Window Preference Controls Control Function Background Changes the background color of the wind
422. ons when moving the sample e Moving the same sample up Z Z3 and Z5 need to become more positive e Shortening and centering moving up the sample Z2 and Z4 need to become much more positive The trends for Z and Z3 are mixed and more complex but they tend to become a little more negative It appears as if Z and Z3 are driven positive as the sample is pulled up but they are driven negative faster as the sample shortens When shimming a lineshape sample plan on the following changes starting from lineshape shims for a 700 uL sample at a depth 67 68 mm 700 uL to 600 uL move Z2 50 DAC units and move Z4 250 units 700 uL to 500 uL move Z2 200 units and Z4 600 units The Z2 and Z4 changes track well with sample volume but are relatively independent of tube depth It is therefore easiest when changing sample geometries to make the appropriate Z2 and Z4 corrections then adjust the more complex Z1 Z3 Z5 interactions as needed 01 999083 00 A1298 Getting Started VNMR 6 1B 147 Chapter 6 10 6 Preparing for an Experiment Using the Acquisition Window The Acquisition window also called the interactive acquisition window or acqi window provides many capabilities including e Turning sample spinning on and off e Adjusting lock e Selecting manual or automatic shimming and adjusting shim values if manual shimming is selected e Displaying the FID or spectra in real time e Changing parameter values interactively
423. ontains your annotations For arrayed experiments containing multiple FIDs svf saves all FIDs in a single file there is no special command to allow individual FIDs of the array to be saved svf also saves the data files def acquired with GLIDE If you place relevant information into the text file using the text command it will be far easier to return to the data at some future time and understand exactly which experiment is stored in that particular file The command writefid file lt element_number gt writes a text file using data from the selected FID element The default for element_number is 1 The command writes two values per line The first is the value from the X real channel and the second is the value from the Y imaginary channel The autoname command creates file names from information in text files and from the values of VNMR parameters It determines a path where data might be stored autoname can be used in nonautomated sessions to generate a path name it is used the same way that the aut oname parameter is used during automation Saving Parameters Parameters from the current experiment are saved by the macro svp lt file gt A file with the par suffix is created which contains the parameters and text If svp is entered without an argument you are prompted for a file name Unlike the svf macro svp reflects any changes made in parameters up to the moment of entering svp including acquisition paramete
424. or lock spin and the variable temperature VT status is displayed only if the vtt ype parameter is not 0 Color is used to identify status conditions e LOCKED is displayed in green if locked NOT LOCKED in yellow if not regulated and LOCK OFF in red if lock is off e SPIN where is the current spin rate for example SPIN 15 is displayed in green if spinning is regulated within 1 Hz from the requested value SPIN in yellow if not regulated and SPIN OFF in red if the spinner is off 01 999083 00 A1298 Getting Started VNMR 6 1B 151 Chapter 6 Preparing for an Experiment 152 e VT where is the current temperature in C is displayed in green if VT is regulated temperature is within 0 5 C from the requested value VT in yellow if the temperature is not regulated and VT OFF in red if VT is off The lower section of the LOCK display window contains controls for changing the values of the lock parameters z0 Lockpower Llockgain lockphase and spin optional on MERCURY and GEMINI 2000 The current value of each parameter is displayed as a number and as a slide control a horizontal bar with the slide at a position proportional to the value of the parameter The value of the parameter controlled by the slide control can be altered by dragging the mouse cursor across the slide control with the left button of the mouse held down If z0 is inactive then acqi shows a 1ock freq slider button array instead of showin
425. or Off If set to On a volume slider becomes available and a sound is generated that indicates how close the minimum reflection is to the center of the sweep window 01 999083 00 A1298 Getting Started VNMR 6 1B 117 Chapter 6 Preparing for an Experiment 118 CW mode Tune Display Show Control Panel reflection of 0 198 at 300 048 MHz Sweeping over a range of frequencies Tune Display Show Control Panel Minimum reflection 15 4 dB at 299 83 MHz Reflection at center 13 8 dB 300 05 MHz Figure 24 Minimal Display Mode for the Tune Display the lower the pitch of the sound the closer the minimum reflection is to the center The sound immediately stops if the response lacks a discernible minimum reflection or if CW mode is set To use the audio capability requires e An audio speaker on the Sun computer e The probe tuned well enough so that a clearly discernible minimum reflection exists in the signal A range of frequencies sent to the probe i e audio requires sweep mode rather than CW mode 5 Place a marker on the resonant frequency to which you want to tune the probe as follows this option is not available in minimal display a Inthe Tune Control Panel see Figure 25 click on the triangle next to one of the markers to open a pull down menu Figure 29 shows the Marker 1 menu For more detail on using markers see the To Use Cursors Grid and Markers on page 120 b In
426. or details about these windows under OpenWindows see the file openwin init Optional Windows In addition to the standard VNMR windows described above many other windows are possible some of which you will use so frequently that you may want to make them appear automatically when you enter VNMR Perhaps the most important optional windows from VNMR are the Acquisition window and the GLIDE user interface Many other options are available from the Workspace menu that pops up from the workspace including VNMR Online Shell Tools Clock and Performance Meter Getting Started VNMR 6 1B 01 999083 00 A1298 2 2 Working with VNMR on the Host Computer Acquisition Windows If the system is not just a stand alone workstation but is connected to a spectrometer the right side of the screen can be used for two optional acquisition windows e The Acquisition Status window displays information about the status of data acquisition Is data being acquired or is the system idle How many transients have been completed CT and what is the estimated completion time of the experiment What is the spinning speed What is the lock level The Acquisition Status window is strictly an output window Use of this window is described in Chapter 4 In the Acquisition window you have the ability to interact with the acquisition console On UN TYINOVA systems this window can be present at any time On other systems it can only be active CONNECTED when an
427. ore it to its original design by using this button Delete Removes text This option is not similar to Copy Deleted text is not stored in a buffer do not use Delete to cut and paste text Delete all Clears all text from the input area Copy Duplicates text Paste Inserts copied text in the input area Deleting a Region To delete a region from the workspace highlight the region then click Region Delete Click Region Delete All to remove all regions Note Regions removed with Delete All are not stored in a buffer and cannot be restored to the workspace Restoring a Deleted Region To restore a single region deleted from the workspace click Region Undelete Regions removed with Delete All cannot be restored with Undelete Clearing the Workspace To permanently remove all regions from the workspace click Delete All Remember if you remove all regions you cannot restore them with Undelete Customizing Objects in a Region You can change the size and color of objects in a region with the Item Preferences window shown in Figure 77 Click on Region Preferences to open this window You can also open the window by clicking on the Item Preferences tool described on page 265 01 999083 00 A1298 Getting Started VNMR6 1B 267 Chapter 9 Display Plotting and Printing Color Pop up Menu Item Preferencies a EJE Color RGB 208 15 103 moccasin Line Width Tuning needle Font Monospaced
428. ory h1 fid created by the svf macro fid procpar text The decomp program takes apart libraries brought over from a VXR style system It creates a subdirectory on the UNIX system using the name of the VXR style library and then it copies each entry in the VXR style library to a separate file in that subdirectory The next example uses the setup above with the convert command 1 The following commands are entered with the responses shown gt eread fidlib gemini fidlib 64 128 192 256 320 384 448 512 540 gt ls fidlib Fidlib 36 gt decomp fidlib 36 Loading fidlib apt 5 45 blocks Loading fidlib cl3 5 45 blocks Loading fidlib cosy 5 141 blocks Loading fidlib dept 5 144 blocks Loading fidlib hl1 5 23 blocks Loading fidlib hetcor 5 141 blocks gt ls fidlib apt 5 C1355 cosy 5 dept 5 h1 5 hetcor 5 gt 2 Atthis point any of the VXR style FIDs apt 5 c13 5 cosy 5 dept 5 and h1 5 can be converted into VNMR format using the VNMR convert command e g convert fidlib c13 5 Note that here the subdirectory fidlib is included as part of the convert command In normal operation the decomp program is not used with the actual VXR style FID files such as h1 5 If for some reason the actual data is to be examined using a separate program the decomp program would then be suitable 288 Getting Started VNMR 6 1B 01 999083 00 A1298 10 6 Magnetic Tape Operations Converting Bruker Data The command convertbru f
429. ossuseeesie taser un E e ree monte 121 Figure 31 Tune Calibration Window oo eeeeeesesessesereeesecneesceseesecaceecesesaeceseesaesaseeeeeeseeseesees 122 Figure 32 Help Pull Down Menu ou ecessseseseeesceeeeeesecneesceseesecaceeeesesaeceseeesaesaeeeeeesaeseeeees 124 Figure 33 Spin Information in LOCK Display acqi Program oe eeeseeesecseeeeeseeseeeeeeeeeeee 127 Figure 34 Spinner Control Window spinner Program oe eeeeeseeeeceecseeeeeecaeeeteeceaeeeeeeeees 128 Figure 35 Acqmeter Lock Displays acqmeter Program oe ee eeeseesceeeseeseesecseeeteeceaeeeseeeees 130 Figure 36 Lock Frequency Acquisition Window ccccesssssssescsecsseseesecseeeseecsaeeaseeenecseeeeeanenes 134 Figure 37 Acquisition Window acqi Program oo sceeeessesssescsecseeseesecaeeaceeeaesareecsecsaeeeeeeenes 149 Figure 38 Abbreviated Acquisition Window o cesssescesesseneeseceeceeeecesecaeceeesesaecaseeesacsaeetenenes 149 Figure 39 LOCK Display Window acqi Program eeceseccescsseseeeececsceseesecaeeeeeecaeeeseeeees 151 Figore 40 Finding Lock iisccasgntinia ani aeee aE EENS RE EEE SERENE 153 01 999083 00 A1298 Getting Started VNMR 6 1B 13 List of Figures Figure 41 Opening Style 1 FID Spectrum Display Window acqi Program seese 154 Figure 42 Style 2 FID Shimming Display in Real time acqi Program oo eeeeeeeeeeeee 155 Figure 43 Autoshim Method Editor Panel acqi Program oo eeeseecseeseeeeeecseeeeeeceaeeeeeeeees 158 Figure 44 Spectrum i
430. ou leave the FID spectrum display The current values of lockpower lockgain and lockphase parameters within acqi are used Autogain gain n can be used but it slows down the appearance of the first FID Getting Started VNMR 6 1B 01 999083 00 A1298 6 10 Using the Acquisition Window troi ACQUISITION Ea CLOSE LOCK FID SHIH Style 1 DC Correction On off Phase Cycle FF On Signal Avg OFF On V scale H scale FID Real Up Expand Spectrun Imaginary Doun Compress Envelope Medium Step Quick Shin Edit Start Autoshin 10 Hethod Shin Shin file Load Save Delete Renornalize Figure 42 Style 2 FID Shimming Display in Real time acqi Program FID Shimming Window Style 1 Figure 41 shows a typical Style 1 FID Spectrum display In the opening FID Spectrum display the FID is observed in a graphics window at the center of the display At the top of a FID display are a row of buttons CLOSE LOCK SHIM and LARGE These buttons were described on page 149 Below these buttons on the left are buttons labeled up and down These buttons adjust the number of bits of the ADC that are displayed for example 14116 bits means 14 bits of a 16 bit ADC make full scale on the display Near the center is a menu with choices FID and Spectrum The label of the currently active display is highlighted Selecting Spectrum in th
431. oved integral accuracy increased dynamic range and flatter baselines Reducing the number of data points in the FID to the number actually required for spectral analysis at the chosen spectral width Downsampling also called decimation is the final step in digital signal processing In VNMR a directory in which parameters and data are stored Free induction decay Signal observed from an experiment Getting Started VWMR6 1B 295 Glossary 296 Fourier transform FRED software GEMINI 2000 system GLIDE host computer IPA interactive parameter adjustment linear prediction lock macro MAGICAL MERCURY MERCURY VX NMR system administrator NMR system console OpenWindows oversampling Performa modules Getting Started VNMR 6 1B Converts time domain data FID into frequency domain spectrum Full Reduction of Entire Datasets Optional software package available from Varian that analyzes data by more advanced mathematical methods than are traditional in NMR analysis FRED extracts carbon connectivity information from data from INADEQUATE experiments Type of Varian NMR spectrometer system A VNMR user interface Sun workstation that controls the spectrometer system Window in which the values of up to five parameters can be changed by moving a horizontal slider with the mouse Uses information from the center of the FID to extend the FID either in a reverse direction to improve ea
432. ow Border Color Changes the color of the border surrounding the workspace Highlight Color When you double click on an object its color changes to indicate that it is highlighted This option controls the highlight color Grid Color Changes the color of the grid Plotter Allows you to choose a black and white or color plotter Border Shows on and hides off region borders Grid Shows on and hides off grid in the workspace Snap The grid has magnetic properties When snap is turned on the path of an object the center of its border automatically snaps to the grid whenever you draw or move the object or change its size or shape Turning off Snap demagnetizes the grid Snap Spacing Controls the amount of space on the grid to which an object snaps Spacing can be in inches centimeters or points 3 After you have entered all of your preferences click Apply to execute the changes 4 Click Close to exit the window Customizing a Plot You can add simple graphics and text to a plot and change its size and appearance by using the tools listed in Table 42 To use a drawing tool press and hold down the left mouse button and drag the cursor in the workspace 01 999083 00 A1298 Getting Started VNMR6 18 263 Chapter 9 Display Plotting and Printing 264 Plot Designer File Orient Region Magnify Preview Preferences Help 121110 9 8 7 6 5 4 3 2 1 OB pn STANDARD 1H OBSERVE exp sidih SAMPLE DEC amp VT
433. ow The value of ZO changes about 3500 coarse DAC units on a 500 MHz magnet about 4200 on a 600 MHz magnet when the lock solvent changes from CDCl to acetone d The other shim gradients are also no longer controlled through the Acquisition window Homospoil Z gradient produces approximately a 0 6 G cm field typically 99 of transverse magnetization is gone within 1 5 ms and signal recovery is 90 within 40 ms and is activated in the same manner as a spectrometer linked to Oxford room temperature shims 01 999083 00 A1298 Getting Started VNMR 6 1B 165 Chapter 6 Preparing for an Experiment 166 Shimming In the normal counts display mode each shim gradient has a coarse and a fine control The coarse control is 50 times more sensitive than the corresponding fine control All gradient DACs have a range of 32767 a knob twisted beyond this range will continue to turn but have no effect Each of the gradient DACs has an identical and a logical polarity For example a clockwise adjustment of Z2 moves an asymmetry to the right with Z2 coarse Z2C and Z2 fine moving asymmetries in the same direction Furthermore Z4 Z6 and Z8 also move asymmetries in the same direction as Z2 The even order axial shims Z2 ZA Z6 and Z8 may jerk the lock if large sudden changes are made the severity of the jerk decreases typically in the order Z4 Z8 Z2 and Z6 Within gradient families you also observe sensitivity differences with h
434. owing mode No cursors are displayed The left mouse button adjusts the starting time of the displayed FID Position the mouse arrow at some position click the left mouse button and a cursor is displayed at the selected time Moving the mouse arrow to another position in the display and clicking the left mouse button drags the cursor defined time to that new mouse arrow position The right mouse button adjusts the width of the displayed FID Position the mouse arrow over some spectral region click the right mouse button and a horizontal and a vertical cursor intersect at the mouse arrow Moving the mouse arrow above or below the horizontal cursor adjusts the width of the FID display The start of the FID display is also adjusted so that the position of the displayed vertical cursor remains constant The further the mouse arrow is moved from the horizontal cursor the larger the size of the relative change Interactive Phasing Mode The Phase button activates the interactive phasing mode 1 Position the mouse arrow on a FID region of interest about halfway vertically up the screen and click the left mouse button A horizontal cursor intersects at the mouse arrow and two vertical cursors are placed on either side of the mouse arrow A small region of FID is displayed in a different color if a color display is present only this spectral region is interactively updated 2 Move the mouse above or below the horizontal cursor but within the two v
435. p Secondary Menu page 70 DQCOSY HET2DJ INADQT HOM2DJ TOCSY 1D More 2D Return Applications Mode Menu page 70 Standard Imaging Return Acquire Menu from Acquire button in Main menu page 70 Show Time Go Go Wft Go Periodic Wft Automatic 1D Data Processing Menu from Process button in Main menu page 71 Display FID Select Params Adj Weighting Transform Weight Transform Interactive 1D FID Display Menu df program page 71 Box Imaginary Expand sfwf Dscale Phase Return 1D Processing Parameter Setup Menu page 72 No WT Resolve Broaden gt AV FN Small Normal Large Return Interactive Weighting Menu wti program page 72 next fid Ib sb sbs gf gfs awc return Interactive 1D Spectrum Display Menu ds program page 73 Box PartIntegral Full sp wp Mark Phase Next Return continued on next page 01 999083 00 A1298 Getting Started VNMR 6 1B 61 Chapter 4 Using the VNMR Menu System Table 3 VNMR Menu System Part 2 of 4 2D Data Processing Menu from Process button in Main Menu page 73 Select Params Adj Weighting Phase F2 Transform F2 Full Transform 2D Processing Parameter Setup Menu page 73 No WT Sinebell Pseudo gt PH FN Small Normal Large Return 2D Interferogram Processing Menu page 74 Color Map Adj Weighting F1 Transform Reprocess Interactive Weighting Menu wti program page 72 next fid Ib sb sbs gf gfs awc return Interactive 2D Color Map Display Main Menu dconi program page 74 Box T
436. p_number command removes the lock from the specified experiment and joins the experiment Note that unlock fails if the lock is still active or if the lock was placed on the experiment by the remote host Acquisition Information Information about acquisition is saved at several locations If Acqproc is active the UNIX command Acqst at displays the current state of the acquisition process e An ASCI log file of acquisition activity in vnmr acqqueue MasterLog This file is not available on UN YINOVA systems e An ASCII log file is also kept in user vnmrsys expn acqfil log for acquisitions and in user vnmrsys expn acqfil sulog for experiment setup Each of these log files will reset themselves to empty at 100 Kbytes so that the entire disk structure is not log jammed The expact ive command determines if the current experiment has an active acquisition The results are displayed on line 3 Acquisition Status Codes Whenever wbs wnt wexp or werr processing occurs the acquisition condition that initiated the processing is available from the parameter acqstatus This acquisition condition is represented by two numbers a done code and an error code The done code is set in acqstatus 1 and the error code is set in acqstatus 2 Macros can take different action depending on the acquisition condition As an example a werr macro could specify special processing if the maximum number of transients is accumulated The a
437. parameter 196 tip angle resolution 194 tlt parameter 241 252 tmove macro 226 TMS line 248 TMS referencing 110 tmsref macro 248 249 tn parameter 68 183 185 TOCSY button 70 tof parameter 152 183 184 185 total correlation 2D 70 tpwr parameter 190 tpwrf parameter 191 193 tpwrm parameter 191 193 Trace button 74 Trace label 156 Transform button 71 Transform F2 button 73 transformed spectrum storage 31 transients completed 49 transmitter attenuation 191 fine power control 191 offset 184 power 190 transmitter nucleus parameter 68 traymax parameter 106 tree structure file system 34 trigonal symmetrization 80 tune command 115 TUNE INTERFACE unit 25 115 tuneoff macro 124 125 126 tuning gain knob 25 tuning meter 25 01 999083 00 A1298 Index tuning rods 25 tuning selector switch 25 two spin system 83 U Ultrasnmr shim system II 24 Ultraenmr Shims 164 168 floppy disk use 166 interface box 164 power down 167 power on 167 shimming 166 umount command UNIX 291 uncompress command UNIX 293 unit command 95 UNITYplus spectrometer decoupler modes 190 linear modulators 193 lock frequency 184 probe tuning 115 UNIX convert file from VXR style 286 file security 284 file system 34 floppy disk as a file system 291 printing utilities 271 shell 91 system administrator 36 UNIX button 91 unix_vxr command 286 unix2dos command UNIX 291 unlock command 207 20
438. parameters and can be somewhat 01 999083 00 A1298 Getting Started VNMR6 1B 227 Chapter 8 Data Processing tricky to optimize if not optimized properly or if the data are not amenable the analysis may simply fail just like any least squares fit process may fail to converge The parameters required for linear prediction do not exist in standard parameter sets but can be created with the macro addpar 1p and displayed with dglp the macro parlp functions the same as addpar 1p Refer to Table 33 for a list of linear prediction parameters Each parameter is described in detail in the manual VNMR Command and Parameter Reference For more complex problems linear prediction can even be run in a iterative fashion first extending backward then forward and perhaps again backward Users desiring more information on the algorithm implemented in the software and on linear prediction in general are referred to H Barkhuijsen R de Beer W M M J Bov e and D van Ormondt J Magn Reson 61 465 481 1985 Solvent Subtraction Filtering Numerous solvent suppression pulse sequences exist that reduce the signal from a large solvent peak to a level where the desired resonances can be observed Often however experimental solvent suppression does not entirely eliminate an unwanted solvent peak Digital filtering of the data can further suppress or eliminate a solvent peak VNMR incorporates two algorithms for solvent subtraction by
439. pdated phasing 20 will cause only 20 of the screen to be updated phasing 70 will cause 70 of the screen to be updated The value of phasing can vary between 10 and 100 Continue this process until the peak or peaks in the update region are properly phased Now move the mouse arrow to another region of the spectrum near the left edge of the display outside the vertical cursors and click the left mouse button again The frequency independent phase correction made so far will first be applied to the entire spectrum A new horizontal cursor will be displayed at the mouse arrow and two new vertical cursors will Getting Started VNMR 6 1B 01 999083 00 A1298 9 4 Interactive Spectrum Display be displayed on either side of the mouse arrows The mouse will now control the first order or frequency dependent phase parameter 1p Clicking the left or right button above or below the horizontal cursor will now increase or decrease 1p and will also change rp so that the phase at the center of the previous region bracketed by the vertical cursors will be held constant This process eliminates or substantially reduces the necessity to iteratively adjust the two parameters rp and 1p As with the zero order correction the left button acts as a coarse adjust and the right button as a fine Each time the mouse arrow is moved outside of the two vertical cursors and the mouse button is clicked a new update region is defined below the mouse arrow an
440. peaks in the spectrum by adding phase_change to the current value of rp then removing any excess in rp more than 360 Autophase Algorithm The automatic phasing algorithms aph and aphO have been enhanced in several ways e Weighting parameters no longer affect the algorithms e Spectra with very low signal to noise can be phased e In vivo spectra can be phased These spectra are very difficult for most autophasing algorithms e Spectra with inverted lines can be phased Such spectra includes DEPT experiments or selectively inverted lines obtained with shaped pulses This type of phasing is difficult for traditional autophasing algorithms which cannot distinguish when a line is inverted and when a line is normal An autophasing algorithm uses many rules that are used in a manual phasing procedure First it finds the peak areas Then it estimates the correct phase for each peak An initial guess of the first order phasing parameter 1p is made based on the estimated phases of two normal peaks The peaks are categorized into three classes normal inverted and bad The peaks in the normal and inverted group will be used to find the optimal values for the phasing parameters 1p and rp A final check is made to determine whether autophasing was successful or unsuccessful Algorithms are complicated but fairly intelligent The key point of an algorithm is to use a set of fuzzy rules to estimate the correct phase for each peak The u
441. pend on the shimset configuration For the shim set on the Ultrasnmr shim system set allshims is active only if hardware to software shim communication is enabled setallshims is not available on GEMINI 2000 Methods of Shimming Depending on the system homogeneity adjustments can be made on the spectrometer by a number of manual and automatic methods e Direct keyboard entry e Retrieving previous shim values e Manual emulation mode e Interactive autoshim e Background autoshim e Fully automatic autoshim e Hardware Z1 autoshim e Gradient autoshim Each method is described below Table 16 lists the commands and parameters described for shimming For a general discussion about shimming refer to the manual System Administration Shimming using the Ultraenmr shims system is covered separately in Shimming Using the Ultrasnmr Shim System on page 164 Keyboard Entry Shim values can be entered by hand Such parameter changes are active or not active according to the setting of the Load parameter Getting Started VNMR 6 1B 01 999083 00 A1298 6 9 Adjusting Shims Table 16 Homogeneity Adjustment Commands and Parameters Commands acqi Open the Acquisition window dgs Display shim amp automation parameter group diffshims shimfilel shimfile2 Compare two sets of shims VNMR diffshims shimfilel shimfile2 Compare two sets of shims UNIX dshim lt file gt dshim method help Display a shim method
442. per barrel with your hand for a second to properly seat the sample To Change a Sample With a Sample Changer Only if the sample changer is disabled by setting t raymax 0 or loc 0 perhaps during daytime walk up operation should you work with samples as described above e Ifasample changer is in use and a sample is ejected using GLIDE the e macro or the Acquisition window the changer no longer has any way of knowing which sample is in the magnet When the next sample is loaded by the sample changer it will place the current sample in location zero e Ifasample is changed manually using the button on the magnet leg the sample changer will still think the previous sample is present and will return the sample in the magnet to that location when it is activated The following procedures change only one sample at a time on a sample changer Refer to the chapter on sample changers in User Guide Liquids NMR for automated changing of multiple samples Using the Inout Window 1 Place the samples you want to insert in the sample tray 2 Enter loc n change in the input window where n is the location on the tray where you want the sample to be taken e g to remove the sample in location 5 enter loc 5 change The change macro removes the sample currently in the probe and places it in the last position used by the changer or if none had been previously specified the sample is placed in the location 0 The sample changer arm then picks up
443. periment 3 exp3 when you leave the spectrometer you will not be able remotely to join exp3 when you log on from a remote terminal because that experiment is locked If that is the experiment in which acquisition is progressing you will be unable to affect that acquisition The preferable solution to this problem is to use the jexp 01 999083 00 A1298 Getting Started VWMR6 18 207 Chapter 7 Acquiring Data 208 command e g jexp2 at the time you leave the spectrometer to join an experiment in which acquisition is neither proceeding nor queued If you forget to do this there is a less desirable solution that can be executed remotely 1 From UNIX enter ps ef Listed are the processes that are running with the process number shown in the first column of the listing 2 Look for the process that begins Vnmr mforeground and note the process number belonging to that process 3 Enter kill 3 where is the process number from the previous step The kill 3 command causes the version of VNMR running on the spectrometer to act as if someone sitting there had typed exit that is in an orderly fashion it saves all its data and parameters and then exits kill 9 which is more common does not do this and is not the proper procedure 4 After the spectrometer version of VNMR has exited you can start VNMR from your terminal and enter any experiment you choose If the lock is inactive the unlock ex
444. pled spectral width by an analog anti aliasing filter Table 29 summarizes the commands and parameters associated with DSP Control of DSP The value of parameter dsp specifies the type of DSP for data acquisition i for inline DSP r for real time DSP or n for none As a global parameter dsp affects DSP operation in all experiments and should be thought of as an hardware configuration parameter because if DSP hardware is available such as on the UN YINOVA that hardware is generally the method of choice Normally DSP works quite invisibly to the user Regardless of whether dsp is set to i or r the oversampling factor the parameter oversamp is automatically set to the maximum allowed value whenever sw is entered Thus after the user enters sw at and Getting Started VNMR 6 1B 01 999083 00 A1298 7 5 Applying Digital Filtering Table 29 Digital Filtering Commands and Parameters Commands addpar downsamp oversamp digfilt exp_number lt option gt movedssw moveossw pards paros Parameters at number in seconds def_osfilt a b downsamp number n dscoef number ds fb n number in Hz dslsfrq number in Hz dsp i r n filtfile file fsq n y np number oscoef number osfilt a b osfb n number in Hz oslsfrq number in Hz oversamp n number sw number in Hz Add DSP parameters to the current experiment Write digitally filtered FIDs
445. pling performed by the system is contained in the parameter oversamp which is normally calculated by the software to be the maximum possible for any given spectral width You can change oversamp to smaller values only if you want to but since the maximum benefit of DSP is only obtained with the maximum possible oversampling there is little reason to do so For Brickwall filters which use more coefficients than AnalogPlus filters some difference appears in the steepness of the filter as a function of the oversamp parameter At oversamp set from 2 through 7 the cutoff is the steepest as oversamp increases the Getting Started VNMR 6 1B 01 999083 00 A1298 7 5 Applying Digital Filtering filter becomes slightly less steep and approaches Analogplus filters at oversamp 50 Thus if you want the flattest in the passband and sharpest in the stopband possible filter and if you are not operating at low gain where oversampling is important to S N you may wish to use minimum oversampling oversamp set from 2 through 7 Brickwall filters at oversampling factors of 20 to 40 make a nice compromise filter with better amplitude flatness than Analogplus and better baselines than Brickwall set at lower oversampling factors Real Time DSP Details Real time DSP is not compatible with pulse sequences that use explicit acquisition to acquire less than the full number of data points np ina single acquire statement e g solids sequences such as br24
446. ppropriate test in the macro would be if acqstatus 2 200 then do special processing e g dp y au endif Getting Started VNMR 6 1B 01 999083 00 A1298 7 5 Applying Digital Filtering The acquisition codes and their meanings are listed in the description of the acqstatus parameter in the VVMR Command and Parameter Reference VNMR Error Messages The errlog command displays a list of the most recent VNMR error messages in the text window The global parameter errloglen controls the number of lines displayed If errloglen is not defined errlog displays 10 lines by default Noise Level Analysis The command noise lt excess_noise lt last_noise lt block_number gt gt gt measures the noise level of a FID Using pw 0 so that no real signal is accumulated you can acquire one or more transients Usually about np 40 96 is sufficient noise then performs a statistical analysis of the noise informing you about noise level dc level etc for each channel This measurement can be repeated at various settings of gain various settings of fb etc for a full system diagnosis If the excess_noise and Llast_noise arguments are included they are used to calculate the noise figure the first input argument is the excess noise and the second is the last measured mean square noise A third input argument can specify the block number the default is 1 The following arguments further define FID noise level measurement e r1 returns
447. ppy disk drive found on most SPARCstation computers provides a convenient way not only to store data but also to move data particularly text files between the Sun PC and Macintosh platforms The Sun command fdformat formats a 1 44 Mbyte floppy disk and allows it to be addressed as dev rfd0 a raw device The floppy now acts like a tape and can be written to with the tar or bar commands This method is ideal for open access type instruments and provides a convenient way to share files between remote coworkers If you insert a floppy disk in the drive and format it using fdformat d a DOS file system is installed on the floppy disk You can make the floppy known to the system by mounting the file provided no programs are running If volmgt is not running you can mount the file by logging in as root then entering mount F pcfs dev disketteO pcfs Now you can copy files to the pcfs directory For text files you would enter unix2dos Suntextfile DOStext file which performs the necessary text conversion At this point after you enter the command umount pcfs followed by the command eject floppy to remove the disk from the drive you can take it directly to a PC and read the files especially the text files The only catch in all of this is that you have to be root to run these commands Mac operating systems earlier than 7 5 To read this disk on a Macintosh use one of the standard Mac to PC connectivity programs With most o
448. priate cable from the receiver J5303 or J5103 to the Q TUNE J5403 connector e Enter tn n su where n is the nucleus to be tuned e g tn H1 2 Inthe VNMR input window enter qtune gain power where gain and power are appropriate gain and power values Typical entries are qtune 20 65 for UNTYTNOVA and UNITYplus and qtune 0 15 for MERCURY VX Generally you want as low a gain value as possible with as high a power value as possible If qtune is entered without arguments the default values of 50 for gain and 60 for power are used The Tune Display and Tune Control windows open similar to Figure 23 The Tune Display is centered on the resonant frequency of the current experiment s frq To change the gain and power values click Exit in the Tune Control Panel and reenter the q une command with more appropriate values 3 In the Display field select Full or Minimal e Full display shows the network analyzer like graph as shown in Figure 23 e Minimal display simplifies the tune display by showing numerical values instead of the graph as shown in Figure 24 When sweeping over a range of frequencies the minimal display shows minimum reflected power and center frequency When in CW mode the minimal display shows the average reflected power and the current frequency Several display controls on the Tune Control Panel are disabled in minimal display mode including cursors grid and markers 4 Inthe Audio field select On
449. r 185 187 212 217 swept tune type NMR probe tuning 116 switchable probe caution 193 symmetrization in 2D inadequate 80 symmetrization in J resolved 2D spectra 80 synchronizing commands with experiment submission 201 synchronous decoupler mode 191 syshelppath parameter 70 system messages 45 system requirement for Plot Designer 262 systemmenulibpath parameter 70 T T shimming criterion 140 T1 Analysis button 81 T data set 81 T of deuterated lock solvent 130 T1 Proc button 81 T value 81 T2 Analysis button 81 T gt data set 81 T2 Proc button 81 T value 81 tape archive 289 tape command 290 tape operations on a network 291 tape parameter 89 tar command UNIX 289 291 293 01 999083 00 A1298 tcl directory 47 Tcl version of dg window 47 temp command 195 temp parameter 31 196 temperature control window 196 temperature cutoff point 196 template loading a Plot Design 264 terminal acquisition 207 tests directory 107 108 text command 32 94 197 278 text files 37 278 editor 197 format 286 plotting 262 printing 271 text window 271 uncover or conceal 65 textvi command 197 Th button 73 239 th parameter 78 thadj macro 246 ThinkJet printer 255 third rf channel parameters 109 three spin system 83 thumbwheel switches 184 tight shimming criterion 140 162 time macro 189 time to run an experiment 189 time domain data 227 time shared decoupling 191 tin
450. r MERCURY systems Style 2 provides shimming on either the FID or the Spectrum Figure 42 shows FID shimming selected The Style 2 shim button area is arranged to accommodate the number of shims in the installed shim set Selecting a shim button with the left mouse button decreases the shim value by the amount shown on the Fine Step Coarse Step button Clicking on the button with the right mouse button increases the value by the same amount while clicking on it with the middle mouse button toggles the Fine Step Coarse Step between fine and coarse The sizes of the coarse and fine steps are selected by clicking the left or right mouse button on the Fine Step Coarse Step button Other ranges besides coarse and fine can be created by editing the file SHOME acqirc Shim values can also be typed directly into the fields where they are displayed you need to press Return to download the entered value Select a shim to be included in Quick Shim by holding the shift key down while clicking any of the three mouse buttons on the desired shim button Doing the same action a second time deselects the button The buttons thus selected are displayed highlighted The shims selected this way are optimized when Quick Shim is active and the Start Autoshim button is clicked Autoshimming with a predefined method is also possible First a method must have been created and saved as described in Editing Autoshim Methods below Then select Method Shim s
451. r bandwidth fb by 10 compared with half the spectrum width in order to provide better filter flatness across the spectral region of interest This increase however causes significant noise to fold in to the spectrum With the AnalogPlus digital filter however the filter bandwidth the 3 dB point is set to exactly sw 2 to ensure the best possible S N across the spectrum CTT TSC COCA FOCCCNRCL COCO REST Pitt sw 2 Figure 65 Digital Filters Compared to Analog Filters The second type of digital filter provided the Brickwall filter has much sharper cutoff characteristics as implied by its name than the AnalogPlus filter and is flatter even closer to the edges of the spectrum This enhanced filtering may come at the expense of baseline performance however Users working with simple spectra such as of organic compounds should not notice this at all but for work with high dynamic range spectra or spectra of proteins the baselines obtainable with the Brickwall filter may not be as good as the baselines obtained with the AnalogPlus digital filter The global parameter def_osfilt specifies whether the digital filter you normally prefer is a AnalogPlus or b Brickwall Once you set def_osfilt you need not change it again You can set a local parameter in each experiment osfilt to a or b to run a specific type of digital filter in that experiment without changing your default choice The amount of oversam
452. r button of the mouse The vertical scale changes to bring the peaks to the location where you clicked the mouse arrow 12 Reverse this process by moving the mouse down towards the baseline directly under the same group of peaks and click the center button again 13 If your system is set up for a plotter plot the spectrum by clicking on Return gt Plot gt Plot gt Scale gt Params gt Page 4 4 Permanent Menu The Permanent menu is always available on the upper row of menu system To make a choice move the mouse cursor over the button label with the action desired and click press down and release the left mouse button Unlike all other menus the function keys on the keyboard can t be used to make selections on this menu The following choices are standard on the Permanent menu Button Description Abort Acq Abort terminate an experiment acquisition currently in progress Cancel Cmd Cancel the currently active command and all commands pending after that one regardless of whether the commands were initiated through the keyboard a mouse button or by some other means GLIDE Activates the GLIDE user interface window After GLIDE is activated clicking on the GLIDE button toggles the GLIDE user interface so it is alternately hidden actually placed in the back of other windows and displayed brought to the front of other windows Main Menu Display the Main menu on the lower row of buttons page 66 Help Display
453. r drawing box lt plotter graphics gt xlmm x2mm ylmm y2mm lt nolimit gt lt rl r2 gt draw lt graphics plotter gt lt xor normal gt x y pen lt graphics plotter gt lt xor normal gt pen color 01 999083 00 A1298 Getting Started VNMR6 1B 273 Chapter 9 Display Plotting and Printing 274 Getting Started VNMR 6 1B 01 999083 00 A1298 Chapter 10 Storing Retrieving and Moving Data Sections in this chapter e 10 1 Working with Directories and Files this page e 10 2 Storing Data page 277 e 10 3 Retrieving Data page 279 e 10 4 Transferring Data Using Ethernet and limNET page 281 e 10 5 Converting Data Between Systems page 286 e 10 6 Magnetic Tape Operations page 289 e 10 7 Compressing Data page 292 If you wish you can do virtually all file and directory operations should through a series of interactive menus in the main menu system These menus are accessible through the File button in the Main Menu or by entering the files command Chapter 4 Using the VNMR Menu System provides a complete description of the menus 10 1 Working with Directories and Files Typical operations with directories and files are saving and retrieving data copying files deleting and renaming files and examining the contents of directories and files This section covers the tools available for these operations Table 46 lists these tools Default Directory File
454. r row of buttons click on the following buttons File gt Set Directory gt Parent The graphics window shows a list of directories entries with a slash as last character and files if any The status window at the top of the screen shows the pathname of the directory you are in currently 3 Click as many times as necessary on the Parent button until the message Directory now appears in the status window 4 Click the mouse on vnmr so it turns to inverse video then click on Change You are now in the vnmr directory Getting Started VNMR 6 1B 01 999083 00 A1298 4 4 Permanent Menu 5 Click the mouse on fid1lib so it turns to inverse video then click on Change You are now in the idlib directory 6 Click the mouse on the fid1d fid so it turns to inverse video and then click on Return gt Load gt Process gt Transform A spectrum appears in the graphics window 7 Click on Next gt Dscale A scale appears under the spectrum 8 Move the mouse arrow to about 4 ppm and click the eft mouse button The vertical line cursor moves to the point you clicked 9 Move the mouse arrow to about 0 5 ppm and click the right button A second vertical line appears at the point you clicked 10 Click on Expand An expansion of the region between the vertical cursors fills the window 11 Move the mouse arrow above the group of peaks near 3 4 ppm and about halfway up the graphics window Click the cente
455. r the command login followed by your user name e g Login vnmr1 2 Ifyou are using the CDE interface enter your password in the password window and press the Return key Otherwise ifa password prompt is displayed enter your password Password userpassword For security your password is not displayed on the screen as you type it If you make a mistake in typing your user name or password the message Login incorrect appears and you are not given access to the system In this case you must reenter your user name and password On systems using Solaris unless CDE is running if you attempt to log in and you do not yet have a password the system informs you that you do not have a password and instructs you to choose one New password Follow the directions on the screen The password must be at least six characters long and include at least two alphabetic characters and at least one numeric or special character amp etc After your login is accepted various system and user configuration files are read into memory to set up the system for you including automatically starting VNMR software and displaying the VNMR interface If you are configured as connected to a spectrometer and your system can perform acquisition the Acquisition Status window and the Acquisition window should open without any further action on your part Of course if you are configured as a data station only you are not connected to a spect
456. r3 performs a full recall of display parameter set setting current display parameters to those values e The r macro entered as r where ranges from to 9 e g r3 recalls most of display parameter set except phase parameters drift correction parameters integral reset parameters and reference parameters 01 999083 00 A1298 Getting Started VNMR6 1B 243 Chapter 9 Display Plotting and Printing Table 37 Spectral Display Commands and Parameters Commands ai center eri dlix dpf dres dscale dtext lt file x y gt lt xn yn inc gt f frset_number fr set_number full left nl lt height lt frequency gt gt nm noislm lt max_noise gt rset_number r set_number right rl lt frequency gt sset_number s set_number setref setoffset nucleus ppm offset split thadj tmsref tms_found vsadj lt height gt vsadj2 lt height gt factor vsadjc lt height gt vsadjh lt height lt do_not_ignore gt zoom width Select absolute intensity mode Set display limits for center of screen Clear reference line Display listed line frequencies and intensities Display peak frequencies over spectrum Measure linewidth and digital resolution Display scale below spectrum or FID Display a text file in the graphics window Set display parameters to full spectrum Full recall of a display parameter set Set display limits for a full screen Set d
457. race Proj Expand Redraw Plot Peak Return Interactive 2D Display Projection Menu dconi program page 75 Hproj max Hproj sum Vproj max Vproj sum Plot Cancel Interactive 2D Peak Picking Main Menu ll2d program page 75 Auto Edit File Display Return 2D Peak Picking Automatic Menu Il2d program page 75 Box Peak Volume Full Both Adjust Reset Return 2D Peak Picking Edit Menu lI2d program page 76 Box Mark Unmark Full Clear Combine Next Return 2D Peak Picking File Menu ll2d program page 76 Read Read Text Write Text Backup File Return 2D Peak Picking Display Menu ll2d program page 76 Hd Pk Hd Num Hd Box Hd Lbl Sh All Hd all Return 1D Data Display Menu from Display button in Main menu page 77 View Interactive Massage Size Reprocess Plot More 1D Data Manipulation Menu page 77 DC Region BC Autophase Adj VS AdjIS Adj WP Return 1D Display Size Selection Menu page 78 Left Center Right Full Screen Return 1D Plotting Menu page 78 Plot Scale HP Params Params All Params Peaks Page Return 1D Data Display Secondary Menu page 78 Lines Integrals Dssh Dssa AV Reference Return 2D Data Display Menu from Display button in Main menu page 79 Color Map Contour Image Size Massage Reprocess Plot More 2D Display Size Selection Menu page 79 Left Center Right FullScreen Full with Traces Return 2D Data Manipulation Menu page 79 DC f2 DC f1 Foldt Foldj Foldcc Rotate Normalize Return 2D Plotting Menu page 80 All Contour
458. ral with respect to the spectrum in units of millimeters Plotting The general rule of plotting is that what you see is what you get the data that is displayed on the screen or would be displayed on the screen if you type df or ds is what will be plotted on the page This rule applies not only to the FID or spectrum but to the positioning of each as well In other words if the parameters are set to plot the FID or spectrum on the left half of the plotted page then a display of the spectrum will similarly display the FID or spectrum on the left half of the screen Vertically as well full scale on the screen represents full scale on the plotter This relationship is used to adjust the vertical scale in ai mode since in that case vf or vs is not the height of the largest peak In nm mode this fact is also used in cases in which the largest peak is desired to be off scale An exception to the general rule of plotting is provided by the wy siwyg parameter If you would prefer to scale the image to the full window which should be easier to view set wysiwyg to n This setting scales the window but does not change the ratio of the image To return to the normal what you see is what you get display change wysiwyg to y Getting Started VNMR 6 1B 01 999083 00 A1298 9 2 Interactive FID Display 9 2 Interactive FID Display The df lt index gt command or the equivalent command dfid lt index gt enables interactive
459. rameter 227 Process button 66 81 process data 71 99 process ID 286 process number 208 01 999083 00 A1298 processed data storage 31 procpar directory 280 procpar file 37 278 programmable decoupling 194 Proj button 74 prosthetic parts warning 17 proton gradient autoshimming 168 proton spectrum plot 249 ps command UNIX 286 pscale command 249 Pseudo button 74 pseudo echo weighting 74 pseudo quadrature data 227 psg directory 36 psglib directory 36 pslabel parameter 45 ptext command 271 public socket 285 pulse breakthrough effects 188 Pulse Sequence Controller board 24 Pulse Sequence Entry Main menu 91 pulse sequence implementation 24 pulse sequence name 185 pulse sequence programming 91 pulse sequences graphical display 188 189 library 36 plotting 188 requested by the operator 45 S2PUL 185 set up using a macro 32 solvent suppression 228 pulse shape definitions 36 pulse transmitter 187 pulse width optimum 188 Pulsed Field Gradient PFG experiments 24 Pulsed Field Gradient PFG module 196 puttxt command 197 pw command 188 pw parameter 187 188 pw90 parameter 188 pwd command UNIX 37 275 pwr command 225 Q qtune command 116 quadrature detection 227 frequency shifted 218 QUALITY menu 162 quarter wavelength cable 114 question mark notation 96 queued operations 30 queueing experiments 200 quick transform 72 74 QuietJet Plus printer 255 quitting Plot
460. ray of offset values 185 attenuation 193 field strength 193 fine power level 193 frequency 95 high power caution 193 homonuclear control 191 mode 190 modulation 193 modulation mode 194 offset 185 01 999083 00 A1298 power 193 power level 193 programmable 194 sequence 194 status 190 time sharing 191 waveform generator 194 decoupler coil caution 125 def_osfilt parameter 214 Default button 88 default directory 275 default value of parameter 96 defaultdir parameter 88 275 delay period 187 delete experiment file 67 files and directories 87 Delete button 67 87 delete command 276 Delete key 97 delta parameter 185 239 deltaf parameter 234 DEPT analysis 81 DEPT button 68 81 DEPT pulse sequence 68 dept out file 82 depth indicator 102 detuning of the probe 114 deuterated lock solvent 130 deuterated solvents 101 deuterium decoupler channel 192 deuterium frequency 184 deuterium gradient shimming 168 deuterium rf 24 devicenames file 36 devices defined as active 92 devicetable file 271 df command 71 231 232 234 dfid command 233 dfrq parameter 152 183 dfrq2 parameter 183 dfrq3 parameter 183 dfrq4 parameter 183 dfsa command 237 dfsan command 237 dfsh command 237 dfshn command 237 dfsn command 237 dfww command 237 dg command 47 112 dg parameter 112 189 dg program 44 47 dgl macro 112 dgl parameter 112 dg2 macro 112 dg2 parameter 112 dglp command 11
461. re 4 CDE Toolbar assis Ascisisis detvseaptag eetere Ra aN Asad el decease aaa 28 Figure S Windows Menih sigirini aeons nonea aeeaiei paea raaa eN AE EELEE EEEE staan NE 29 Figure 6 FontSelect WINdOW sissesecsoseoss garregen estaa oasen isara Eea ea kei EE a E aea EGES 29 Fig re 7 Fil Striicttire Overview s s scssceiectcccen voce net osneuehlecstnciheh evkaatptatbecdaptocebenseetiessateetesbpaees 35 Figure 8 Remote Status Module ose esesseseesecceccesesseeeceeesaesesscceecseescssecaesaseesaecaseeeeesaeeees 43 Fisure 9 VNMR Display Screen cis isschicicieasilievicsctisictsgactiqiabeatatbiet diac cseheoteldeed aiestasoasase 44 Figure 10 Status Window and Input Window ou ce ceeseeseeceseceseeeeeeesecseeseesecnecaeeecsaecaeeeceeeeaeeees 45 Figure 11 Menu System Buttons oo cee cseseessssecececceseesceccesesaesecseceecncescsecaecaseeesaecaseseeseaeeees 46 Figure 12 Typical Parameter Display in dg Program 00 cic eceeseseeeesecseeseeseeeeceeeecaecaeeeeeeesaeeees 47 Figure 13 CONSOLE and VNMR Shell Windows eeeeeessessssececeeeesceaeeeeeecaeseeeceeesaeseeeeenes 48 Figure 14 GLIDE User Interface Window 00 es essseecesesseeeceeeseseescceecseescesecaecaseceeaecaseeeeenaeeees 49 Figure 15 Workspace Menu under OpenWindows sssecssscsseseeeeceeceeseesecaeceeeeeaecaeeeeeeeeaeeees 49 Figure 16 CDE Tool bats icccgessendicieens aigivien ates ceeded ae Aiden hl ei Be ee eee 50 Figure 17 Icons for Closed VNMR Windows ccsssssses
462. re _solvent argument that changes vsad jh actions to include the solvent line and to exclude only the TMS line The vsadj2 macro adjusts the vertical scale by powers of two as required for expansion plots The syntax is vsadj2 lt height gt scaling_factor The argument 01 999083 00 A1298 Getting Started VNMR6 1B 245 Chapter 9 Display Plotting and Printing 246 height is used the same as in vsadj scaling_factor returns the ratio of the new compared to the old value of vs to the user or the calling macro The noislm macro limits the noise present in a spectrum by reducing the vertical scale vs If the noise is smaller than the noise limit vs is left untouched The noise limit is in single root mean square noise size the peak to peak noise width of the noise band is about twice that value The noise is determined by taking the smallest value from four 5 regions at the left end of the spectrum Any filter cutoff at the end will decrease the apparent noise in the spectrum and therefore increase the noise limit in the central part of the spectrum Because of the particular algorithm used in this macro signals at the left end of the spectrum should not affect the result of nois1m An optional argument max_noise can be entered to noislm max_noise is the maximum root mean square size in mm of the noise the default is 2 Line Listings The n1 command moves displayed cursor to nearest line and displays its height and frequency i
463. re either long or all of identical height simple z1z2 shimming is usually sufficient e Ifsample height might vary the method al1zs has been found to be the most reliable at the expense of greater time spent in shimming This method shims first Z1 Z2 and ZA then Z1 Z2 and Z3 and finally Z1 and Z2 The standard parameter sets st dpar hl and stdpar cl13 have method set to z1z2 If you find that more shimming is routinely necessary in your applications simply recall those parameter sets change met hod to all1zs or another method of your own devising and save the parameter set overwriting the original parameter set Using the Input Window e Enter method file shim where file is the name of a file in the directory shimmethods e g method z1z2 shim Two shimmethods directories can exist A user can have a private copy of shimmethods ina personal shimmethods directory A system wide set of shim methods is also located in the vnmr shimmethods directory The user s private library is searched first for a given method If the method is not found in the user s directory then the directory vnmr shimmethods is searched Shimming methods can be used in succession or strung together For example entering method 1z12m shim shim would cause the method in the file 1z12m Z1 Z2 shimming to be used as indicated by its code twice in succession and entering method 1z12m shimmethod nsm shim shim shim would cause the first method to
464. reading Turn the observe coil matching rod for a minimum meter reading Adjust the TUNE knob if needed Switch back and forth between the observe coil tuning rod and the observe coil matching rod until you achieve an absolute minimum meter reading Once a minimum is obtained enter tuneoff If the tuning is far off it may be better to turn each rod past the minimum meter reading before turning the other rod 10 Return the two cables to their original positions and turn the meter switch to SPIN Decoupler Coil Tuning on MERCURY VX MERCURY BB GEMINI 2000 CAUTION Before tuning the decoupler coil check that air is flowing through the probe dewar and decoupler cooling line cooling both the sample and decoupler coil Excessive heat will damage the sample and the decoupler tuning capacitors During VT operation the probe dewar requires nitrogen for cooling For maximum power use at least 20 CFH or 9 5 LPM Join an appropriate experiment and then enter tn H1 su for IH or tn F19 su for 19 Move the proton probe cable from the IH connector 35102 on the magnet leg to the TUNE connector J5402 Move the proton cable in the rear of the magnet leg to the coaxial tuning jack labeled TUNE J5604 Enter btune Turn the meter switch to the TUNE position Adjust the TUNE control knob for a mid range reading 01 999083 00 A1298 Getting Started VNMR 6 1B 125 Chapter 6 Preparing for an Experiment 126 7 8 Tu
465. recommended that the user execute this macro on all older parameter sets before using the parameter set again updatepars overwrites parameters in the current experiment The corrections that are applied to the parameter sets are defined by the par fix macro When a parameter set is updated with updatepars or parfix the parameter parversion is set to 5 3 to indicate the version The updatepars macro uses the current experiment to process the parameter sets Therefore whichever experiment is chosen for running updatepars should not contain a valuable data set Getting Started VNMR 6 1B 01 999083 00 A1298 10 4 Transferring Data Using Ethernet and limNET User Written FID Files The makefid file lt element_number gt lt format gt command lets you introduce computed data into an experiment by creating a FID file To use this command you must give the name of a file with input as the first argument This file must contain numeric values two per line The first value is assigned to the X or real channel the second value on the line is assigned to the Y or imaginary channel The other two arguments can be entered in any order element_number is the number of the element or FID the default is the first element or FID and format is a string with the precision of the resulting FID file the default is 32 bit for double precision data Before using make fid read the description of it in the VNMR Command and Parameter Reference for furth
466. red for the parameter dpwr can be adjusted in the config program The parameters dpwr2 dpwr3 and dpwr4 set the decoupler power for the second third and fourth decoupler channels respectively These parameters can also have safety maximums adjusted in config dhp and dlp are nonfunctional on MERCURY VX MERCURY YNTYINOVA UNITY plus UNITY and VXR S systems with a linear amplifier on the decoupler channel If the system is configured with a fine attenuator on one or more of the decouplers the decoupler fine power level is controlled by the dpwr f dpwrf2 and dpwrf3 parameters for the first second and third decouplers respectively Decoupler fine attenuators are linear and span 60 dB on YNITYZNOVA and UNITYplus systems or 6 dB on UNITY and VXR S systems UNITYINOVA and UNITY gt plus systems are configured with linear modulators on all transmitters The linear modulator power of each transmitter is set by tpwrm dpwrm dpwrm2 and dpwrm3 or by tpwrf dpwrf dpwrf2 and dpwrf3 Decoupler Modes The dmf parameter controls the modulation of the first decoupler Amf 2 for the second decoupler dm 3 for the third decoupler and dmf 4 for the fourth decoupler using the optional WALTZ 16 decoupling After calibrating the decoupler field strength YH2 dmf 01 999083 00 A1298 Getting Started VNMR 6 1B 193 Chapter 7 Acquiring Data or dmf 2 to dmf 4 should be set to equal 4 yH7 27 or 1 pw90 In efficient mode decoupling dmf an
467. riment If the new center is too close to either of the system frequency limits the span is decreased to allow the new center to be accepted the message window will beep and an error message will appear If the specified center is past either frequency limit the message window will beep and an error message will appear To Adjust the Span The span is the sweep width in MHz used in the Tune Display 1 To decrease or increase the span to the next in the series 1 2 5 10 20 etc in the Span TanalGantra ll Panal field enter a value or click the or button z Exit Display Save v Help 7 Setting the span to less than 1000 Hz causes cener F Gla 75 45 Moe EN the message window to beep and an error message to appear i Setting the span to more than maximum id Off O span causes the message window to beep at cue eni and an error message to appear Marker 1 J C13 75 455 MHz Marker 2 Off MHz Setting the span to a value beyond the P Marker 3 Off MHz maximum or minimum frequencies causes the span to decrease the message window Scale dB Linear to beep and user warnings to appear Max 0 00 cB EE 2 Inthe Span field click on the triangle to Step 5 00 gici Sse open the Span pull down menu see Figure Smoothing Off 1 2 3 4 5 27 Line width mamas e Select Last Span to return to the Calibrate Q calculation Off On previous span value e Select Maximum Sp
468. ring argument containing the same options as used with the UNIX 1s command Creating and Manipulating Files Files are typically created by data storage activities such as saving files FIDs or parameters If a file is no longer needed the delete filel lt file2 gt command removes a file from the file system The rm filel lt file2 gt command also remove files but delete is preferred because it is safer rm functions like the powerful UNIX command of the same name and can inadvertently delete important files without warning even for experienced users The rename old_name new_name command changes the name of a file By providing different directory paths as arguments rename can also be used to move a file from one directory to another The mv old_name new_name command works the same as the rename command To make a copy of a file enter the VNMR command copy old_name new_name with the name of the file you want to copy as the first argument and the new name as the second argument Include different directory paths for each file if you want to both copy the Getting Started VNMR 6 1B 01 999083 00 A1298 10 2 Storing Data file and at the same time move it to another directory The command cp old_name new_name works the same as the VNMR copy command To display the contents of one or more text files use cat filel lt file2 gt The cat command places the text of each file in the order given by the argume
469. rinted The plotter configuration is stored in global variables for each user Therefore each user can have their own plotter definition but all foreground and background tasks for one user will share the same information There is one exception to this rule If a plotter configuration command is placed within a macro command which is executed in background it will only be valid during and within the execution of that background task This is in fact true for any one of the global parameters Color Printing The color program allows you to change the colors on the VNMR display screen and color print to raster plotters and pen plotters Starting the Color Program To start the program enter color on the VNMR command line A color selection window shown in Figure 68 opens The default window is for General or 1D phase color selection for the graphics window Display To change to other color selection windows click on the buttons near the top of the VNMR Color Selection window to display the 2D Phase 2D Absolute Value and Image color selection windows e The General window has buttons along the left side that list the areas of the graphics window for which you can set colors background spectrum integral fid imaginary scale parameter cursor and threshold To the right of each button is the color currently assigned for that area of the graphics window 01 999083 00 A1298 Getting Started VWMR6 1B 257 Chapter 9 Displ
470. rlock is disengaged When the high power interlock disengages one of the two red lights previously displayed at the front of the interlock board turns off It is perfectly normal for the other red light to stay on all the time 6 12 Gradient Autoshimming Gradient autoshimming provides rapid automatic adjustment of room temperature shims It is a very reliable way to set high order shims eliminating many hours previously spent on shimming Typical gradient autoshimming time is only a few minutes and all steps are done with a few clicks of a mouse button Gradient autoshimming is implemented for use with the axial gradients Z gradients For optimal gradient shimming a PFG amplifier and probe are recommended for their fast recovery performance However if a PFG amplifier and probe are not available gradient autoshimming can be performed using the homospoil gradients Z1 room temperature shim coil For more details on how to set up homospoil gradients refer to Homospoil Gradient Type in the chapter on PFG modules operation in the manual User Guide Liquids NMR Gradient autoshimming methods support shimming on a wide variety of samples with different volumes and solvents For aqueous samples water protons provide sufficient signal for shimming For deuterated solvents gradient shimming can be performed if there is sufficient deuterium signal Deuterium gradient shimming is feasible on most samples where the lock solvent is a single
471. rly point in the FID or in a forward direction to eliminate truncation problems Following this process the FID is then Fourier transformed in the usual way e Circuitry that compensates for long term changes in the superconducting magnet field Single command that duplicates any series of commands macros and parameters enterable on the keyboard MAGnetic Instrument Control and Analysis Language Macro language built into VNMR Type of Varian NMR spectrometer system MERCURY with upgraded acquisition computer running VxWorks Special user with name vnmr 1 who is the only user with permission to change files found in the top VNMR system directory vnmr1 is also a regular user of VNMR with permission to run NMR experiments process data etc Main unit of NMR spectrometer housed in one to four cabinets UNIX windowing environment Acquiring data with larger spectral width using a larger number of data points as compared to acquisition without digital signal processing DSP Oversampling the data is the first step in performing DSP Optional pulsed field gradient PFG modules for high resolution liquids experiments 01 999083 00 A1298 remote status module root shims Solaris STARS software SunOS UNITY system UNITYINOVA system UNITYplus system UNITY series systems user library VNMR vnmrt Vnmrl VnmrSGl VXR S VXR style systems workspace 01 999083 00 A1298 Glossary Small case
472. rn the decoupler coil tuning control to obtain a minimum tuning meter reading Adjust the TUNE knob as needed Once a minimum is obtained enter tuneoff Return the two cables to their original positions and turn the meter switch to SPIN Proton Observe Decoupler Coil Tuning on H 3C GEMINI 2000 1 iD ae 8 Join an appropriate experiment and enter tn H1 su Move the proton cable from the IH connector J5102 on the magnet leg to the TUNE input connector J5402 also on the magnet leg Move the proton cable in the rear of the magnet leg from the IH connector J5602 to the TUNE connector J5604 Enter htune Turn the meter switch to the TUNE position Adjust the TUNE control knob for a mid range reading Turn the proton coil tuning rod for a minimum meter reading Adjust the TUNE knob if needed Once a minimum is obtained enter tuneof f Return the two cables to their original positions and turn the meter switch to SPIN Carbon Observe Coil Tunning on H 3C GEMINI 2000 l 2 pa OO AOD Or oA Join an appropriate experiment and enter tn C13 su Move the cable from the 13C connector J5302 to the TUNE connector J5402 Move the cable from the 3C connector J5603 on the rear of the magnet leg to the TUNE connector J5604 just above it Enter ctune Turn the meter switch to the TUNE position Adjust the TUNE control knob for a mid range reading Turn the C coil tuning rod until the meter reaches
473. ro estimates the acquisition time for the experiment using the parameters d1 d2 d3 mix null at ni swl ni2 and sw2 in the current experiment By entering a requested time in the format t ime lt hours gt minutes the macro can recalculate nt so that the total acquisition time is approximately the requested time Similarly the expt ime command estimates the experiment time for the current seqfil using the parameters in the current experiment expt ime can also estimate the experiment time of a specified file e g expt ime s2pul The dps command reproduces a graphical display of the pulse sequence complete with parameters as present in the dg display see Figure 54 Figure 54 Graphical Pulse Sequence Display dps Program This provides a quick and useful check of experimental conditions before beginning an experiment dps also displays shaped pulses in which the height of the pulse reflects the power levels spin lock transmitter gating observe transmitter power and other information The pps command plots the same display The button with the mouse face in the upper right corner opens the dps display control panel shown in Figure 55 This panel provides control of how the pulse sequence is displayed with timing power or phase information with or without parameter labels and values When you click on a segment off a pulse sequence with the middle mouse button the properties window displays information about
474. rol of the spinner and magnet homogeneity Each of the console units is controlled by the main processor which contains pulse sequence control information programmed in its memory The type of communication between the host computer and the acquisition computer is system dependent e UNITYTINOVA and MERCURY VX systems use Ethernet with control by an integrated chip on the acquisition computer board e MERCURY and GEMINI 2000 systems also use Ethernet but control is by a Ethernet board e UNITYplus and UNITY systems use a SCSI high speed link through a second computer in the acquisition unit known as Host Acquisition Link or HAL This computer provides a 2 MB memory into which data acquisition is performed Implementing the pulse sequence involves timing certain operations of the transmitter decoupler and receiver The transmitter produces a radio frequency at the frequency selected the parameter s f rq for the nucleus being observed In another section of the rf electronics another frequency in most instruments this is the proton frequency is sent to the decoupler In order to maintain long term electronic stability the instrument also generates a lock frequency that is normally set at the deuterium frequency A deuterated solvent is used in most cases although the spectrometer can be operated unlocked so that the deuterium rf can be locked onto the deuterium resonance of the solvent Up to eight rf channels are available on UN
475. rometer these windows will not be useful to you 3 If you want the Acquisition Status window to appear and it is not open enter the command acqstat in the input window to start it Alternatively move the mouse arrow over the workspace the background area not covered by any windows then press and hold down the right mouse button until a pop up menu appears Continue to hold down the right mouse button while moving the mouse downward to highlight Acquisition Status the first entry on the pop up menu then release the mouse button Or if CDE is installed click on the button above the VNMR icon in the tool bar then click on the Acqstat icon 4 If you want the Acquisition window to appear and it is not open enter the command acqi in the input window to start it You must be connected to a spectrometer for this window to open To Exit VNMR CAUTION Use only the following procedure to exit VNMR and log out Any other method can cause lost or corrupted files 40 Getting Started VNMR 6 1B 01 999083 00 A1298 2 2 Working with VNMR on the Host Computer 1 With the VNMR interface displayed take one of the following actions e If CDE is installed click on the EX J button in the toolbar instead of following steps 1 through 5 to exit VNMR e Enter in the input window the command exit e Click on Main Menu More Exit VNMR If the Acquisition and Acquisition Status windows are present both should automatically quit
476. ronically match the sample and experiment desired For this purpose depending on the type of probe there may be tuning rods extending from the probe a tuning meter a tuning selector switch that chooses between tuning the observe and decouple channels of the probe and a tuning gain knob that controls the sensitivity of the tune signal used for tuning a channel e OnN TYINOVA and UNITYplus systems a digital display on the TUNE INTERFACE unit attached to the magnet leg or to the dual preamplifier shows reflected power Dual push button switches below the digital display activate the tuning circuit select the channel and set the sensitivity of the channel during the tune operation e On MERCURY VX MERCURY and GEMINI 2000 systems reflective power is shown in a needle micrometer indicator on the magnet leg An adjacent toggle switch on the magnet leg selects whether the meter displays reflective power for tuning or the spinning rate For normal operation the switch is set for the spin rate UNITY and VXR S systems use a similar display to the MERCURY Chapter 6 Preparing for an Experiment describes probe tuning procedures For details about installing and tuning probes refer to the probe manual shipped with the probe 1 2 User Interface The host computer for the spectrometer includes a number of highly advanced concepts including multiple experiment capability multitasking windowing and automatic queuing The system ho
477. rs Saving Shim Coil Settings All shim coil settings except ZO are saved with the command svs file If the name of the file entered as an argument is a relative path svs looks for a shims subdirectory in the following order 1 Ifthe shims subdirectory exists in your VNMR user directory svs stores shim coil settings there 2 Ifthe shims subdirectory does not exist svs looks for a global parameter named shimspath If shimspath is present it is expected to contain the name of a directory If this directory exists svs saves the settings there if a new entry can be created 3 If step 2 does not work svs stores the shims in the vnmr shims directory provided you have write permission If the name of the file entered as an argument is an absolute path the file is saved directly Getting Started VNMR 6 1B 01 999083 00 A1298 10 3 Retrieving Data 10 3 Retrieving Data At times you need to recall stored data Table 48 lists tools for data retrieval The information in this section describes several methods for retrieving data in VNMR Table 48 Data Retrieval Commands and Parameters Commands compressfid lt indir gt outdir Compress double precision VNMR FID data compressfid Compress double precision VNMR FID data UNIX makefid Make a FID element using numeric text input parfix Update parameter sets rt lt file lt nolog gt gt Retrieve FIDs rtcomx lt file gt Retrieve Spinsight data into current experime
478. run each experiment on the list e Insert your sample e Choose the experiment and solvent via the Experiment Setup window e Click on the Go button GLIDE contains a nonfunctional icon box labeled GLIDE and six buttons Setup Custom Go Exit and Help For descriptions of each of these buttons refer to the Walkup NMR Using GLIDE manual Running a Standard Experiment A typical session with GLIDE is described in the following step by step procedure for running a 1D proton NMR in deuterochloroform 1 Ifthe GLIDE user interface is not displayed click the GLIDE button in the Permanent menu 2 Inthe GLIDE user interface click on Setup The Experiment Setup window appears on the screen 3 Using the right mouse button click on the menu button labeled Experiment A menu with a list of available experiments is displayed 4 Scroll through the experiment list by holding down the right mouse button and dragging the pointer through the choices Release the right mouse button when the Proton 1D option is highlighted 5 Using the right mouse button click on the menu button labeled Solvent A menu with a list of available solvents pops up 6 Scroll through the solvent list by holding down the right mouse button and moving the pointer through the choices Release the right mouse button when the CDCI3 option is highlighted 7 Ifyou want to enter a file name for saving the data or enter text for your sample click on the fie
479. running Acqi Button Under normal circumstances on a spectrometer when you start VNMR an Acqi button appears in the Main Menu Abort Aca Cancel Cmd GLIDE Main Menu Help Flip Resize Acqi However this button does not appear if VNMR is immediately started after an installation before the system is configured if a user s boot up macro has been changed to keep acqi from starting or on systems configured as data stations If you do not see the Acqi button Getting Started VNMR 6 1B 01 999083 00 A1298 6 10 Using the Acquisition Window and your system has been configured as a spectrometer enter acqi standby to display the button Enterin i termgacg troi ACQUISITION without arguments on CLOSE LOCK FID SHIM LARGE a command line starts SAMPLE HASSE the acqi program and if no acquisition is in progress displays an Acquisition window Figure 37 Acquisition Window acqi Program shown in Figure 37 Note The disconnected Acquisition window which initially appeared after the command acqi was entered no longer exists It has been replaced by the Acqi button in the Main Menu On all systems except UN TYINOVA if you start an acquisition and then click on the Acqi button the window does not appear UNITY m on INOVA E troi ACQUISITION systems if you start an CLOSE SHIN LARCE acquisition and then click on the Acqi button an abbreviated selection of buttons similar to
480. s Criterion Meaning Recommended Usage Borb Bad No decent starting shim values available Lorl Loose Extreme change in sample height Morm Medium Typical sample change Tort Tight Resolution desired above average Eore Excellent Resolution desired less than 0 2 Hz A full criterion consists of two letters for example L gt M indicates a loose starting criterion the shims are expected to be far from their desired values and a medium ending criterion end with normal shim quality Tight and excellent are only used for extremely high resolution where the beginning resolution is very nearly that desired Thus if you suspect that the resolution is poor and want to improve it rapidly but not spend the time necessary to get excellent resolution you might specify the starting and ending points as L gt M In the interactive Autoshim mode these criteria are specified on a pull down menu after clicking the auto button in the SHIM display The time of automatic shimming is a function of these criteria Therefore try to make an informed choice in light of the resolution needed and in particular for FID shimming the choice of acquisition time at specified in the parameter table An acquisition time of 2 seconds gives a limiting digital resolution of 0 5 Hz a resolution that would be inconsistent with shimming to a tight criterion In the interactive shimming mode using acqi only the most important criteria are accessible to the user L
481. s 1 to 5 Return Display the Main menu page 66 Automatic COSY Analysis Menu The Automatic COSY Analysis menu is activated by selecting COSY in the Analyze menu or by entering the command menu auto2D Button 2D Line List Find Correlations Plot Correlations Redisplay Return Description Perform a 2D line listing and display the peaks with the dconi program if dconi was active prior to selecting this button Perform an automatic 2D COSY analysis The analysis uses the information from the last 2D line listing which must be performed first Display the result on the screen Perform an automatic 2D COSY analysis using the information from the last 2D line listing and plot the results on the plotter A contour plot is not plotted by this button but the 2D Plotting menu page 80 will be displayed to allow a selection of additional items to be added to the plot typically just a contour plot Display a normal 2D contour map and allow for interactive adjustment Display the 2D Data Display menu page 79 Add Subtract Menu The Add Subtract menu is activated by selecting Add Sub in the Analyze menu or by entering the command menu addsub Button Description Clear Interactive Mode Add Spectrum Subtract Minimum Clear the add subtract experiment exp5 Display the Interactive Add Subtract menu below taking the currently active spectrum as one input and a spectrum that has
482. s 241 Interactive Zero and First Order Base Correction Mode eeeeeeeeeeees 241 Setting the Integral Value oo ceseesecseeeeceeceseceseeseeeeeeeeeeeesesenseaeeeaeeaee 242 Setting the Reference Position cece ceseeseceeceseceseeeeeeeeeeeeeeeeseseneeaeeeaeeaee 242 Interactive Inset Display sicciiscccsceiei ces acai ceei cas secceentes Gees ceioteesaheciavcelaveaeaaieiess 242 95 Spectral Display and Plott gu sic scccescescacesissscucvesnsnevsesseevecssenssesvcebeasuscwen sheen rest 243 Display Parameters sicvsesccusccsvastusasessichyacsusssstusceaassbsdacsautesbancsvncesasnubasesneedacseaes 243 Vertical Scale Adj stM nt 255 sisciceistesscesesjassdemeveeiaes caecnancrestackstssesencust Ee 245 Line Listings ccsicssstsesdtvcesdeansevstesaansesszedancatuncstabcapaassvacsoubevoastedusessendesasesacesanesbasas 246 Lame Resolution vessis sits eset ected seh Seve cs aebevtanvies seee ee aE REEE EEE COE AET EEE EESE 247 BROMCLOMCIT onr e O E E E O 247 Spectral PIONS srcciaie senna E E SEES 249 Display Wants ssscesscsdecdscvsussosdeccdacandescessteeocecesspeosdesdevacetscasescoediodssestweevscaicsrsseoeede 250 OOS Ime ration senica isa sie sla ee ee eet eee nee 250 Displaying Integrals Step by Step 00 eee eee ceesee cee ceseceeeseeeceeeeeeeeeeeeeeeeees 250 Baseline CorectiOnl sasc s ssiscsseesdsnscssxetacesbussscascanns i rereana e E Eea Ee iras a E ra EE Eoi 252 Integral Res t POMS sersrsscirosrsorcra Sebeones sbsabeandvbawdeh dee ss
483. s Pos Only Image All Params Params Page Return 2D Data Display Secondary Menu page 80 Stacked Plot F2 Mode PH Reference Analyze Return continued on next page 62 Getting Started VNMR 6 1B 01 999083 00 A1298 4 1 Working With Menus Table 3 VNMR Menu System Part 3 of 4 Analyze Menu from Analyze button in Main menu page 81 Exponential DEPT COSY Add Sub Simulation Deconvolution Regrs Exponential Analysis Menu page 81 T1 Proc T1 Analysis T2 Proc T2 Analysis Plot Print Return Automatic DEPT Analysis Menu page 81 Process Display Plot Edit Printout Full Analysis Return Automatic COSY Analysis Menu page 82 2D Line List Find Correlations Plot Correlations Redisplay Return Add Subtract Menu page 82 Clear Interactive Mode Add Spectrum Subtract Minimum Interactive Add Subiract Menu addi program page 83 Box Select Expand spwp sub save return Spin Simulation Main Menu page 83 Spin System Show Params Set Params Simulate Original_Next Spin Simulation First Definition Menu page 83 AB ABC A2B ABCD A2BC A3B other return Spin Simulation Second Definition Menu page 84 ABCDE A2BCD A3BC A2B2C A3B2 A3B2C other return Spin Simulation Third Definition Menu page 84 AX AXY AX2 AXYZ AX2Y AX3 other return Spin Simulation Secondary Menu page 84 list params assign display iterate observe return main Spin Simulation Line Assignment Menu page 85 ll use ll use fitspec auto assign iterate return main Deconvolution Me
484. s go ga and au through other macros containing go ga and au or through the menu system from the Main Menu select the Acquire button Table 27 lists acquisition related command and parameters Initiating Acquisition The main macros to initiate acquisition are go ga and au e go acquires the data and performs no processing To run go from the menu system select the Go button in the Acquire menu e ga automatically performs a weighted Fourier transformation after the FID has been collected To run ga from the menu system select the Go Wft button in the Acquire menu au allows for totally automatic and flexible data processing at a number of times during the experiment To run au from the menu system select the Automatic button in the Acquire menu Each of these macros initiates the acquisition of one or more FIDs as determined by the acquisition parameters go ga and au also perform several additional functions prior to starting data acquisition e Each macro executes two user created macros if they exist The first is usergo a macro that allows the user to set up general conditions for the experiment The second is a macro whose name is formed by go_ followed by the name of the pulse sequence from seqfil to be used e g go_s2pul or go_dept This macro allows a user to set up experiment conditions suited to a particular sequence If there is insufficient free disk space for the complete 1D or 2D FID data set to be
485. s plotted it is desired to have parameters printed a scale plotted below the spectrum and peaks above 20 mm in height labeled as to frequency This can be done by typing pl pscale pap page th 20 printon dll printoff which is not too difficult if the spectrum is plotted once but what if a similar spectrum must be plotted 5 times or 500 times The answer is to create a macro command that executes the exact series of the listed commands and parameters The name of the macro can be any convenient name such as plc13 or plc or just c Whatever the name chosen by the user the system uses that name exactly like any other system command Macros are extensively used to set up the various special pulse sequence experiments that are available Thus if a conventional 13C spectrum has been acquired entering apt executes the macro apt that sets up an APT experiment Or starting with a conventional IH spectrum and typing cosy sets up a 2D COSY experiment Macro commands can simplify the most complex set of commands and parameters Macros on the system are written in a macro language called MAGICAL II for MAGnetics Instrument Control and Analysis Language II that is built into VNMR MAGICAL is an extremely powerful language that combines three essential elements Getting Started VNMR 6 1B 01 999083 00 A1298 1 4 Introduction to UNIX and VNMR Files e Programming language features like conditional statements e Direct access to key features
486. scribes how to prepare for an NMR experiment including preparing and inserting the sample tuning the probe spinning the sample optimizing lock and adjusting shims Chapter 7 Acquiring Data covers setting parameters using experiment text files performing acquisition and applying digital filtering Chapter 8 Data Processing describes weighting functions Fourier transformation phasing and advanced data processing Chapter 9 Display Plotting and Printing covers FID and spectra display plotting integration printing and user controllable line drawing Chapter 10 Storing Retrieving and Moving Data explains working with directories files and data including Ethernet magnetic tape and data compression The manual also contains a glossary covering common Varian NMR and VNMR terms Notational Conventions The following notational conventions are used throughout all VNMR manuals e Typewriter like characters identify VNMR and UNIX commands parameters directories and file names in the text of the manual For example The shutdown command is in the etc directory Typewriter like characters also show text displayed on the screen including the text echoed on the screen as you enter commands For example Self test completed successfully Text shown between angled brackets in a syntax entry is optional For example if the syntax is seqgen s2pul lt c gt entering the c suffix is optio
487. sdascsanjederaesenbesoasesnssepvasidanseaadecuatananas 134 Lock Level and Spin Speed Error Handling o0 eee eee cee ceseeeeeeseeeeeeeeees 134 Lock Loop Time Constant Control 00 eee eeesesecseessecnecesececeseeeeeeseeeeeeeeees 135 OF ACJUStING SHUG sser Hacschees tists tasttoteds eotttes decal higedsecvabevaelocs navies daesictgeeticagbote He 135 Shim Gradients oes cc stestcetsosessstevensevecscescasceia EE E E E E E 135 Methods of SHIMMING siseses i oneee es 136 Keyboard Entry sis ccciscesiie acid aie ei i EEE EEEE EEEE EEEE EE EEY 136 Saving and Retrieving Shim Values 0 0 0 cece eeeeceseeeeceeeeeeceeeeeeeeseeeeeeseeeaeeaee 137 Manual Emulation Shimming 00 0 0 eee eececeeeeeeeeeeeeeeeseeseeeaeecaesaecaesnaeeaees 138 Automated ShiMMing sss scisoiry sa eresia s ser Eee EEES E EEE E Ee ETE EEEE EE EEE i 139 Shimming Criteria for Autoshim sssesesseeeesssresesreresrrerrreererrsrrerenreresreeerrrereees 140 Shim Methods for Autoshim s esesseeeeeeresesesrsreresrtrrersesrresrsstsrererrrerrersrnreeeeee 140 User Defined Shim Methods for Autoshim cececeseeseeecseeneeseeseteeeeeeeaees 142 Interactive AUtOSHIN lt s cscssess deccesessssceeis suotescsepecsed i ee nne enea Ei EE EEEE ESk 143 Fully Automatic Autoshim eeeeeeeeeseesseeseessreserssrsseessrsseesressresresesseseeseeereeseet 144 Back sround Autos bind oossasieclc ssssndeseesizscocesnssacons csdesscossessocesedivsssecdvemscasesnesceres 145 Hardware Autoshimn lt
488. se 7 Test the parameters Enter gmapsys and click on Set Params gt Go dssh You should see two profile spectra If you don t check that the gradients are active and check pw tpwr and gain 8 To make a shimmap again enter gmapsys and click on Shim Maps gt Automake Shimmap Enter a mapname any string valid for a file name at the prompt Automake Shimmap first runs an experiment that calibrates gzwin and tof to set the spectral window Next it runs an experiment with the shims arrayed to map the shims and processes the experiment when done Coarse shims are used if present The parameters and data for the shimmap are stored in the file userdir gshimlib shimmaps mapname fid These parameters are retrieved the next time gradient shimming is run if the gradient shimming system menu is exited To begin shimming skip to Automated Shimming on page 172 Displaying the Shimmap After the shims are mapped display the shimmap by entering gmapsys and clicking on Display gt Display Shimmap The shimmap display is a multicolored plot of the shimmap with Z1 as 1 and Z2 as 2 and so on see Figure 49 The shimmap is specific to the probe used and can also be dependent on sample volume for small volumes The shimmap shows the actual field dependence of the shims except for a dc offset added for display purposes Good signal to noise in the shimmap is needed for the shimming to work well Poor signal to noise may r
489. se of these rules makes an algorithm less sensitive to the signal to noise ratio weighting parameters and the base line quality Fuzzy logic also makes it possible to do the classifications on the peaks The command aphb autophases Bruker data Refer to the VWMR Command and Parameter Reference for more information about this command Spectrum Display The displayed spectrum is calculated in one of three mutually exclusive modes e The phase sensitive mode is selected by the command ph In this mode the displayed spectrum is calculated using the phase parameters 1p and rp The absolute value mode is selected by the command av In this mode the displayed spectrum is calculated according to the equation absorption spectrum real channel imaginary channel 2 e The power mode is selected by the command pwr In this mode the displayed spectrum is the square of the displayed spectrum calculated in the absolute value mode Once a spectrum is displayed using the interactive display command ds the spectrum can be interactively phased by selecting the Phase button from the menu see Chapter 9 01 999083 00 A1298 Getting Started VWMR6 1B 225 Chapter 8 Data Processing Display Plotting and Printing for details Any integral and cursors displayed along with the spectrum are removed 8 5 Advanced Data Processing 226 This section covers advanced data processing including phase rotation frequency sh
490. se the windows as you want Standard Windows The VNMR display screen contains a number of windows At the top is the combined status input and menu system buttons windows These windows appear as three separate windows when in use but can move as a single unit on the screen In the middle of the screen is the graphics window Below that is the dg program If the system is configured to perform acquisition not just to be a stand alone workstation the right side of the screen often displays two other windows the Acquisition Status window and the Acquisition window Status Window On most systems the status window occupies the top two lines of the VNMR display as well as a three line scrollable window that appears below the top two lines Figure 10 shows how a typical status window might look Getting Started VNMR 6 1B 01 999083 00 A1298 2 2 Working with VNMR on the Host Computer Seq s2pul Exp 3 Index 1 Ip 70 1754 rp 64 1578 lt q gt Figure 10 Status Window and Input Window Each part of the status window displays important information about the system e The first line is a status line that informs the operator about the system action in progress Near the center of this line is the name of the pulse sequence requested by the operator Seq s2pul in Figure 10 The sequence name is stored in the pslabel parameter The status line continues with an indication of the current experiment number
491. seeeeeeneeeeenee 36 Paths and the Working Directory 0 0 eee cece ceseeseceeceeeceeeeeeeeeeeeeeeneesaeeneesaeeaee 37 User La Dt ary sc 2 S6e sesshevesa roen n nee E stces E TEE EO OTE EE EO EEEE EE 38 Chapter 2 NNMR Basics ssssnnnnnnnnonunnnrnnnnrnnnnnnnonnunnnnnnnnnnnnnnnnnnnnnnnnnnnnn nenne nnmnnn 39 2 1 Entering and Exiting VNMR ssssessessesseesrseesssreereserreserresrerrsrenseresserteseneestetsrentereeeses 39 ToS tart VNMR 24 Seis ci a A ee a 39 TO Exit VINMIR 3233 sah case seskoadescabsbovbes Saas t25 Seats n E ra EEE ER Ea Ea EEEE OSES 40 2 2 Working with VNMR on the Host Computer sssssseseseeseseessseereseesrsrrsreersreernsrerrsreresrees 41 MOUSE Device es sissccedcnsscecauscevusteanbstezslascsthecedaansasd cb raare sas EERE dere ena EE r NE ESEE 41 Mo se Buttons iesene teerien ae Gees vaseteulassisvbessmsesmsantveaiens sh EE E 42 Keyboard e aen aeea A E O E E E E 42 Remote Status Module 5 01 scccceccsssssssssessebscseneceseseneseeuscessessseocasnerbesestsoetoesesees 43 VNMR Display SCteeny sssssscsiscsissvecscssnisessscenst annoar a anisa a oair inepe iss 44 Standard WINdOWS ssesiiiisiesosioie sesaria oe oa AE aE rE EEEn aiek 44 Optional WINdOWS seeiis a A E A RE E 48 GNapter 3 USing GLIDE ane ee een eee Renee aiaa iasa eee 53 Sed Activating GLIDE Siera R E A E AE N E S 53 01 999083 00 A1298 Getting Started VNMR 6 1B 5 Table of Contents Opening GLIDE sisccccsccevcesticcsgienesHvscbiveguiseucetloubtspeegnamect
492. seeeeneeesees 84 Spin Simulation Secondary Menu 200 0 eeeeceeeeseeeeeeceseeeeecaeeeaeceeaecnaeeaeeneensees 84 Spin Simulation Line Assignment Menu 000 cee eceeeeecseeeeecseesaecsseeaeeneensees 85 Deconvolution Menu ccssesccsssesssscsssesseesessssesensrsensesnsesssscssseretesesesessossnrs 85 Regression LIMON aiscsciesessstssiesscuscassscais sespecndelsyensb casseysas sean se E EE 86 R6gression 2 Men ssicscciscissiessesnesnaeiols tives enee Eee EEEE NEE RE EEEE EEEE 86 Regressio 3 Men 2icsass 2easessdenneusecscessiesebdetdatsgzanceavenevinsouessnasesbsessnaeuadsdbetsdensnes 86 PDD File Menus sereceenroes eorne in een na E EET A RE 87 Files Main Menu sisisi eroici eto e aeee n e e EEEE aE E REEE 87 Dir ct ry Men senian a EE Ei iais 88 Directory Secondary Men sieisisersiorsseericissesussssnisesnsicsniisereroieresesseriisivesnseses siss 88 Files Information Menu s nsesessesesssseescressceoseseeseseeveseosereesostenoensvseeovsesscreenceessoses 89 Files Tape Menu sscsceesseg itevssevivssveveceevsativerestaesdondeansevasevecer E e E a iaeiaiai 89 Fil s D ta Menu cerinnacraois cninn iia 90 Files Data Secondary Menu seseesesesseeesssenerseeeeseerererseversrerersevenseeeereesererseeeessese 90 Files Secondary Ment sicccscscsvsstssestessstescscensctuecssesadeessceuceveanvseaseanssusavtessceuscseensees 90 413 Secondary Main MENU ccisesisarreenrecreniereess reinsi oesi Kee NS eie S riais 91 Pulse Sequence Entry
493. ser interface ACQ LOCK SPIN PFG RCVR The UN TYTNOVA and UNITYplus versions of the module are shown in Figure 8 From top to bottom a e the module contains the following indicators and n x displays Ov Ow e VT indicator displays the status of the variable a temperature unit ex e Digital readout displays the temperature from ve the VT controller e e Analog 0 to 100 meter displays the lock level e ACQ LOCK SPIN PFG and RCVR OVFL we indicators display the status of acquisition Sune xe lock spin pulsed field gradient and receiver overflow respectively e XMITR WFG 0 90 180 and 270 indicators for CHANNEL 1 display the status of the transmitter waveform generator and phase information for channel 1 The same display appears for up to three more rf channels Figure 8 Remote Status Module depending on the number of channels configured on the system e WFG The UNITY version of the remote status module displays the status of lock spin observe transmitter decouple transmitter acquisition and rf overload In addition the status for observe 90 observe 180 decouple 90 and decouple 180 phase shifts are shown The module also contains a lock level meter MERCURY VX MERCURY and GEMINI 2000 systems use a spin light and meter on the magnet leg If the light is off the sample is not spinning If the light is flashing the spin rate is not at the requested rate If the light is steady th
494. sesassevsssoasccanessipesesaes 278 103 Retieving Datasport E EEE Ea S a 279 Using rt rtp and rts to Retrieve Files 0 cseeeceeceseceeceseeeeeeseeeeeeetees 279 Using GLIDE to Retrieve Dato eee ceeseeseessececesececeaececeseeeeeneeeeeeetees 280 Using CDE File Manager to Retrieve Data oe ees ceeesecteceseeeeeeseeeeeeeeees 280 Correcting Saved Parameter Sets e eee ceessecseesseceecesececeseeeeeeseeeeeeeseeeeeeeees 280 User Written FID Biles ans sce cal ressorsa rieres etin EREE EEEE E aE 281 10 4 Transferring Data Using Ethernet and limNET 00 eee eeeeceeneeeeeeeceeeeeeeeaeens 281 Transferring Data Using Ethernet 0 00 00 ee ceseeceeeeeecnceeeeeeeseceeeaeeseeaeeaseeetaceaees 282 Transferring Data Using HMNET 0000 ceeeeeeeeeeeneeeeeeeesecneeaeesetaeeaeeeesaeeaees 282 ETS SS WPT KOS se Faso sos thse basehenpedots asedcvans E ea EEEE EEEE a a EAE 283 Initiating Transfers from a Remote Node ccc eeeecesssseeeeeeecneeeeseeseeaeeeeeseaees 284 Error Messages from limNET o0 ce eeeseeeeeceseeeeeeeeecceseeeeeseceeeseesesaesaeeeesaeeaees 285 10 5 Converting Data Between Systems 0 eee cseceseeseceseeseceeeeseceeeeeeeeeeeeeseneeaeeeas 286 Converting Text Files sissisota i upeasti seri si stie isisi 286 Converting Data Piles sisinio neesi in a ne n No KEE Eora EESE 287 Decomposing a Library ssicsiscsrsrisracerrit eati seuren Ee EEEE EE E EEEE EEEE EEEE E 287 Step by Step Example with limNET 000 ee cece ceeeeeeeeeeeeeeeseeen
495. sets button 73 resets button 239 241 Resize button 47 66 resolution enhancement 72 223 Getting Started VNMVR6 1B8 9313 Index resolution enhancement function 221 222 resolv command 222 Resolve button 72 Results button 85 resuming acquisition 202 retrieving compressed FIDs 293 FID data in files 279 parameters from parameter file 279 previous shim values 137 shim settings 279 Return button 69 Return key 22 46 97 rf channels 24 rfband parameter 184 rfchannel parameter 184 rfl parameter 247 rfp parameter 247 Right button 78 79 right button of mouse 42 right command 250 right half of the screen page 78 79 right mouse button 91 right phase 224 right arrow key 97 rl command 247 rm command 276 rmdir command 276 ROESY button 69 rofl parameter 188 rof2 parameter 187 188 216 room temperature shim coil currents 135 room temperature shims adjustment 168 root directory 34 37 root user 36 root mean square noise 246 Rotate button 80 rotate spectral data 80 rotating frame NOE 2D correlation 69 rp parameter 224 225 240 rsh command 282 rt command 279 287 rtcmx command 280 rtp command 109 279 rts command 138 279 rtv command 279 S s macro 243 S2PUL button 69 s2pul macro 185 S2PUL pulse sequence 185 sa command 202 safety precautions 17 19 sample ejection 103 150 height 102 145 insertion 25 103 105 150 position 102 preparation 101 spinnin
496. shell uncompress 1 fid fid rt 1 Because compress does not work on directories and because many files are often linked to one another it is useful to combine various data files into a single but separable file A simple mechanism to do this is to use the t ar command to write not to a tape but to a file e g tar cvf mydata fid tar mydata fid This creates a new file mydata fid tar that is just a single file Compress this file by entering compress mydata fid tan The filemydata fid tar Z is created To reverse the process uncompress the file by entering uncompress mydata fid tar tar xvf mydata fid tar This extracts files from the compressed file and makes it back into a directory Performing this process on the entire vnmr directory for example creates a single file of 5 4 MB compared to 11 9 MB for the complete directory a 55 percent compression This is an excellent way to cut down on disk and tape usage Compressing Digitally Filtered FID Files Compressing digitally filtered DSP FID files creates two potential problems e DSP can produce a significantly higher dynamic range depending on the amount of oversampling and larger absolute numeric values than the equivalent FIDs acquired without DSP e Inline DSP produces FIDs in floating point format Because the UNIX compression of standard FIDs using compress or gzip largely relies on removing leading zeroes in those parts of the FID containing small numbers
497. shim system enable control of the shims from the Acquisition window as described in section Shimming Using the Ultrasnmr Shim System on page 164 CAUTION Do not spin the sample during gradient shimming Spinning may cause motion artifacts Mapping the Shims Mapping the shims is necessary after installing a new probe 90 H O is recommended for first time shimming on IH and 1 H 0 99 D 0 is recommended for 7H 1 Insert a sample and find lock 2 Stop sample spinning spin 0 Disable sample changer control loc n 3 Adjust lock power lock gain and lock phase Make coarse shim adjustments on Z1 Z2 X1 and Y1 01 999083 00 A1298 Getting Started VNMR 6 1B 169 Chapter 6 Preparing for an Experiment 170 4 Use s2pul to find the 90 pulse for tn H1 or tn 1k as appropriate 5 Enter gmapsys to display the Gradient Shimming System menu Standard parameters are retrieved from gmapz par the first time gmapsys is entered or if a shimmap was previously made parameters are retrieved from the current shimmap If desired enter gmapz to retrieve standard parameters from gmapz par 6 To set parameters for a particular gradient and nucleus enter gmapsys and click on Set Params gt Gradient Nucleus and then click on the appropriate button Pfg H1 Pfg H2 Homospoil H1 or Homospoil H2 Next set pw as follows e For PFG set pw to the 90 pulse or less e For homospoil set pw to 90 pulse and p1 to 180 pul
498. shimming 141 criterion values for Autoshim 140 crl command 248 cross polarization pulse sequence 69 CT message 49 ct parameter 96 188 202 ctext command 197 ctune macro 124 126 curexp parameter 277 current directory 87 88 current experiment number 45 current plane 45 302 Getting Started VNMR 6 1B current working directory 275 currently active experiment 277 cursor 41 Cursor button 71 73 74 75 76 83 234 239 243 cursor movement 234 cursor position 184 cursors 27 59 customizing experiments 55 customizing the menu system 64 cutoff parameter 245 cutoff steepness 214 cz command 241 253 D d suffix 95 di parameter 187 188 d2 parameter 187 D20 button 68 D2PUL button 69 data analysis tools 81 Data button 87 data compression 292 data directory 37 data files format 287 data processing methods 227 data recall in CDE 58 using VNMR menus 58 data station and acquisition 148 data storage files location 37 data storage for experiments 31 date of acquisition 200 date parameter 200 DC button 77 dc command 252 dc level 223 DC f1 button 80 DC f2 button 79 dcg parameter 252 dcrmv parameter 223 dd command 289 dd command UNIX 290 decaying exponential function 221 decimation 210 decomp command 287 288 deconvolution 222 Deconvolution button 81 Deconvolution menu 85 deconvolution starting point 85 decoupled spectrum without NOE 190 decoupler ar
499. sition another nucleus another pulse sequence another sample and then process the first while the second is being acquired Of course this routine can be extended to more than two data sets in fact up to nine To simultaneously work with two different sets of data such as processing one set and acquiring another you use two or more experiments For example first enter go to acquire data in exp1 Next join exp2 by entering jexp2 and starting another experiment Then enter jexp1 to rejoin exp1 and process and plot the first spectrum exp1 while the second exp2 is being acquired To follow the second experiment with a third even though the second is still being acquired join exp3 by entering jexp3 select parameters and start another experiment Since an acquisition is in progress this experiment exp 3 is queued up behind the second just as for other forms of queuing previously discussed Now you can go back to exp1 process more then enter jexp2 to look at that data either when it finishes or before and so on If the text command is used to annotate sufficiently each experiment the explib command enables us to juggle all these functions with ease MAGICAL II Macro Language A macro is a single command that duplicates any series of commands and parameters enterable on the keyboard Routinely used in daily operation a macro is not a necessary function of the system but is extremely useful Suppose every time a spectrum i
500. ss the data a text file e text describes the sample or experiment a text file with your annotations e log contains the acquisition log a text file FIDs have certain implications because directories are not copied or otherwise manipulated by UNIX in the same way as simple files but require special commands Paths and the Working Directory In UNIX the path for a file or directory is a list of directories that lie between the top level of a file system the root directory and the file or directory To build a path list the successive directory names in order starting with the symbol for the root directory with each subdirectory separated by a and the name of the file or directory as the last entry For example the path to the global file in the lower right of Figure 7 is export home vnmrl vnmrsys global Naming a file or directory this way is called an absolute path because every file and directory has a single unique path To avoid the need to type in a long path to reach a file UNIX provides the concept of the working directory The working directory is the current directory you are in To show the name of this directory at any time enter the UNIX command pwd print working directory and the absolute path is displayed To change to another directory enter the command cd change directory with the path of the directory you want to be in 01 999083 00 A1298 Getting Started VNMR 6 1B 37 Chapter 1
501. st deactivate z0 If z0 is inactive then the system uses the lock frequency to find the lock signal If z0 is active the system uses z0 To activate z0 enter zO y to deactivate z0 enter z0 n lkof Parameter On N YINOVA systems only a new global parameter 1kof has been added to track changes in the lock frequency resulting from changes in the solvent and minor changes caused by the magnet drifting The current lock frequency is the sum of the system global parameter lockfreg and 1kof The units for lock freq remain MHz The units for 1kof are Hz analogous to sfrq and tof or dfrq and dof lkof affects two components of the system autolock on the console and acqi on the host computer When either acqi disconnects or an experiment completes VNMR changes 1kof to reflect the new lock frequency in the console if zO is inactive Getting Started VNMR 6 1B 01 999083 00 A1298 6 10 Using the Acquisition Window Using sethw to Set Lock Frequency On only UN TYINOVA and MERCURY VX and MERCURY systems the lock frequency can be set with the set hw command To set the lock hardware type the following command sethw lockfregq lt lockfreq value gt The units for the lock frequency are in megahertz Be aware that go lock shim su and related commands reset the lock frequency in the console to the current value of the lockfreq parameter On YINOVA systems only this value is offset by the value of 1kof if that parameter
502. stems only Press the CHAN buttons until the readout is the number of the rf channel you want to tune Start with channel 1 This turns on the tuning function for the channel The TUNE INTERFACE display should shows a number and the red indicator light should not flash If the light flashes check the connector to the cable for an improper connection 01 999083 00 A1298 Getting Started VNMR 6 1B 115 Chapter 6 Preparing for an Experiment 116 5 Press the ATTEN buttons until the readout is 6 7 or 8 6 If necessary insert the appropriate sticks into the probe Refer to the probe installation manual as to which sticks are needed to tune to the desired nucleus 7 Tune the probe As the probe gets closer to being tuned the number on the TUNE INTERFACE display will decrease 8 Press the ATTEN button until the readout is 8 to increase the tuning level sensitivity Continue tuning until the number displayed on the TUNE INTERFACE display is as close to zero as possible 9 Disconnect the tuning function by pressing the CHAN buttons until the readout is 0 During normal spectrometer operation CHAN must be set to 0 or acquisition will not be allowed 10 Reconnect the rf cables to their original position as follows e UNTYTNOVA and UNITY plus 200 300 or 400 systems Disconnect the cable from PROBE J5321 port on the TUNE INTERFACE panel Connect the cable to the H Band CM or the B Band CM port at the rear of the magnet conso
503. sub spectra save Save the result spectrum in the add sub experiment and return to the last menu Return Return to the last menu without saving the result Spin Simulation Main Menu The Spin Simulation Main menu is the first of six menus covering almost the entire analysis of spin simulation The Spin Simulation Main menu is activated by selecting Simulation in the Analyze menu or by entering the command menu spins Button Description Spin System Display the Spin Simulation First Definition menu below to select a spin system Show Params Display parameters and allow for changes Set Params Set spin simulation parameters sminf smaxf slw svs and niter from the current display Simulate Perform a spin simulation using the current parameters Original Fourier transform and display the experimental spectrum Next Display the Spin Simulation Secondary menu page 84 Spin Simulation First Definition Menu The Spin Simulation First Definition menu is activated by selecting the Spin System button in the Spin Simulation Main menu or by entering menu spins1 Button Description AB Select two spin system AB ABC Select three spin system ABC A2B Select three spin system A2B 01 999083 00 A1298 Getting Started VNMR 6 1B 83 Chapter 4 Using the VNMR Menu System 84 Button Description ABCD Select four spin system ABCD A2BC Select four spin system A2BC A3B Select four spin system A3B Other Display Spin
504. systems such as switching from 13C to ISN an additional change is made in the quarter wavelength cable a coiled cable located on the system as follows e Attached to the preamplifier housing for 500 600 and 750 MHz systems e Attached to the inside of the left magnet leg on the MERCURY VX MERCURY and GEMINI 2000 e Attached to the inner face of the magnet console interface unit as part of the observe circuitry on other systems The quarter wavelength cable is not changed for each nucleus but only for broad ranges of frequencies for example 40 to 80 MHz usually covering a factor of two an octave in frequency An incorrect cable does not typically affect signal to noise but may have a profound effect on the 90 pulse length To Tune Probes on amp v NOVA and UNITY plus Probes on N YINOVA and UNITYplus systems can be tuned through the TUNE INTERFACE panel or the graphical probe tuning program qtune Using the TUNE INTERFACE Panel Probes can be tuned using a special panel called the TUNE INTERFACE shown in TUNE INTERFACE Figure 22 The panel is located either on the magnet console interface or on the dual preamplifier assembly The panel contains the following displays readouts and ports e At the top of the panel is the TUNE INTERFACE display a rectangular liquid crystal display that shows a numerical value two ways as a digital readout in the center of the display and as an analog representation along the
505. t does not react with the sample and available in deuterated form The instrument can be run unlocked that is without locking onto the deuterium of a deuterated solvent but resolution is better with a deuterium lock especially for lengthy accumulations Probably the most commonly used solvents are deuterated acetone chloroform methylene chloride and DMSO Sample Height Experimentation and calculation show that the liquid column length must be at least three times the length of the observe coil to minimize end effects This suggests a column length 01 999083 00 A1298 Getting Started VNMR 6 1B 101 Chapter 6 Preparing for an Experiment 102 of close to 5 cm for a standard broadband or switchable probe and about 4 cm for a H 19F probe Solvent volumes of 0 6 ml in a 5 mm tube and 3 1 ml in a 10 mm tube are adequate for removing the end effects Reduction of sample volume to attain higher concentration usually fails because the increased signal is found around the base of the NMR resonance not within the narrow portion of the signal In fact a well shimmed 0 4 ml sample will be lower in sensitivity than the same solution diluted to 0 6 ml and also shimmed well The questionable gain in sensitivity is further degraded by the longer time it will take to shim the system Small variations of sample height that would be insignificant in a 0 6 to 0 8 ml sample can be dominant when the sample is only 0 4 ml in volume For best results an
506. t never look down the upper barrel You could be injured by the sample tube as it ejects pneumatically from the probe WARNING Do not exceed the boiling or freezing point of a sample during variable temperature experiments A sample tube subjected to a change in temperature can build up excessive pressure which can break the sample tube glass and cause injury by flying glass and toxic materials To avoid this hazard establish the freezing and boiling point of a sample before doing a variable temperature experiment Getting Started VNMR 6 1B 01 999083 00 A1298 SAFETY PRECAUTIONS Warning Notices continued WARNING Support the magnet and prevent it from tipping over The magnet dewar has a high center of gravity and could tip over in an earthquake or after being struck by a large object injuring personnel and causing sudden dangerous release of nitrogen and helium gasses from the dewar Therefore the magnet must be supported by at least one of two methods with ropes suspended from the ceiling or with the antivibration legs bolted to the floor Refer to the Installation Planning Manual for details WARNING Do not remove the relief valves on the vent tubes The relief valves prevent air from entering the nitrogen and helium vent tubes Air that enters the magnet contains moisture that can freeze causing blockage of the vent tubes and possibly extensive damage to the magnet It could also cause a sudden dangerous release of ni
507. t to start airflow to carry the sample 2 Insert the sample by placing it in the top of the upper barrel 3 Enter i in the VNMR input window Using GLIDE Applies to all systems if the optional spin control hardware is installed 1 Ifthe GLIDE interactive window is not open open it entering glide in the input window or by clicking on the GLIDE button in the Main Menu 2 Click on Experiment amp Solvent gt Eject 3 Insert the sample 4 Click on Insert gt Close Using the Acquisition Window Applies to all systems configured for acquisition if the optional spin control hardware is installed 1 Perform a sample ejection even if no sample is in the magnet to start airflow to carry the sample 2 Insert the sample by placing it in the top of the upper barrel 3 Ifthe Acquisition window is not open enter acqi in the input window then click on the Connect button in the window when it appears 4 Inthe SAMPLE menu click on insert Manual Ejection Applies to systems without spin control hardware Used only in emergencies on other systems 1 Press the black button on the top of the left leg of the magnet 2 Insert the sample by placing it in the top of the upper barrel to start airflow 01 999083 00 A1298 Getting Started VNMR 6 1B 105 Chapter 6 Preparing for an Experiment 3 Slowly release the black button to slowly drop the sample When the button is completely released close off the top of the up
508. t the most reliable in an open access environment with users of differing skill levels nor is it applicable to fully automated operation using a sample changer Automated Shimming Like locking shimming can be done manually as already described Automated shimming is often preferred however It can be initiated the following ways e Interactive Autoshim Opening the Acquisition window and clicking on the auto button in the SHIM display described on page 143 e Background Autoshim Entering method file shim e g if the file is z1z2 enter method z1z2 shim in the input window described on page 145 This method is analogous to using the Lock command for full optimization of lock parameters e Fully automatic Autoshim Setting the parameter wshim analogous to alock at the beginning of an acquisition or series of acquisitions described on page 144 e Hardware Autoshim Setting the parameter hdwshim described on page 145 Available only on YNTYZNOVA systems or UNITY and VXR S systems with the Z1 shimming hardware This method is analogous to hardware simple Autolock No matter how the automated shimming is initiated except hardware Z1 Autoshim it is controlled by two aspects of the shimming process each aspect is discussed in detail in subsequence sections e Quality or criterion for shimming The quality of the field homogeneity when the automated shimming is started must be given and the quality of the homo
509. t the plot into the region Click Preview All to import plots into multiple regions You can also import a plot into a region by doing the following procedure 1 2 3 4 Click on Region Edit to open the Region Editor Draw a region Press the right mouse button to open the plot menu window ae i PAP Choose a command to import into the Region Editor Commands are stored in the vnmruser templates plot menu file or Svnmrsystem user_templates plot menu file You can edit both of these files to add or delete commands In the menu file the command is indicated by two lines the first line is the label of the command that appears in the plot menu window the second line is the command itself In Figure 76 the label p1 identifies the command line p1 pscale The label PAP identifies the pap command Editing a Plot To edit a plot do the following procedure l 2 3 Highlight a region Click Region Edit to open the Region Editor window Enter a command such as p1 or pscale in the text input area Use the buttons listed in Table 43 to edit text Exit Region Editor by clicking Close Getting Started VNMR 6 1B 01 999083 00 A1298 9 8 Plot Designer l pscale Label ele Command x menu 6 lines 23 characters Figure 76 menu File Table 43 Region Editor Buttons Button Function Restore Applies the original template to a region If you opened a template and made changes to it you can rest
510. t to Not Used e The zfs and lfs options are both turned off if ssfilter is set to Not Used The characteristics of the low pass digital filter used with the lfs and zfs options can be modified by changing the parameters ssfilter sslsfrq and ssntaps e The value of ssfilter specifies the full bandwidth of the low pass filter applied to the original FID to yield a filtered FID Its default value is 100 Hz e The value of sslsfrq specifies the location of the center of the solvent suppressed region of the spectrum Setting ss1sfrq to a non zero value shifts the solvent suppressed region by sslsfrq Hz Setting sslsfrqto n the default value solvent suppresses a region centered about the transmitter frequency 228 Getting Started VNMR 6 1B 01 999083 00 A1298 8 5 Advanced Data Processing e The value of ssntaps specifies the number of taps coefficients used for the digital filter The default value is 121 but the value can range from 1 to np 4 The more taps in a filter the flatter the passband response and the steeper the transition from passband to stopband giving a more rectangular filter For the lfs low frequency suppression option the default is suitable For the zfs zero frequency suppression option a value between 3 and 21 usually works better Additionally if the zfs option is selected the parameter ssorder specifies the order of the polynomial used to fit the digitally filtered FID The order can range fro
511. t ype tells the PFG hardware which channel is on For further information about PFG related parameters refer to the manual User Guide Liquids NMR Getting Started VNMR 6 1B 01 999083 00 A1298 7 3 Creating and Editing Experiment Text Files 7 3 Creating and Editing Experiment Text Files Each experiment has associated with it a file consisting of a block of text that describes the sample Table 26 lists commands for working with experiment text files Table 26 Experiment Text File Commands Commands atext string Append string to the current experiment text file ctext Clear the text of the current experiment edit file Edit a file with user selectable editor gettxt file Get a text file from a another file puttxt file Put a text file into another file text lt string gt lt str_var gt Display text or set new text for current experiment textvi Edit text file of current experiment Creating and Editing a Text File To enter text into the current experiment use text text_string For example the command text 24 Sep 1997 places the following line of text into the file 24 Sep 1997 To place more than one line of text in the text file insert either a double backslash or abackslash n n into the string to denote a new line For example entering the command text 30 Menthol in CDCL3 SW Probe 24 Sep 1997 sets the following three lines of text into the file 30 Menthol in CDCL3 SW Probe 24 S
512. tatus window can be changed using the Acqstatus Setup window which is shown in Figure 64 Open this window by clicking the right mouse button anywhere inside the Acquisition Status window and selecting Properties To quit the Acquisition Status window click on the horizontal bar at the top of the window with the right mouse button and select Quit from the popup menu Alternatively to close the window to an icon click on the inverted triangle in the upper left of the window with the left mouse button When you want to view the acquisition status window again reopen the window by double clicking the icon with the left mouse button Receiver Gain Low gain in multiline high dynamic range samples can cause a number of problems including intermodulation distortions lower sensitivity and extra lines in the spectrum Too high a gain on the other hand can cause receiver overload and consequent baseline distortion Autogain capability allows the observe channel to be set optimally for detecting and digitizing NMR signals from a wide variety of samples 01 999083 00 A1298 Getting Started VYNMR 6 18 205 Chapter 7 Acquiring Data 206 The parameter gain sets receiver gain with gain 60 representing the highest possible actual Geometry 399x184 666 1 22 receiver gain and gain 0 the lowest On MERCURY VX and Host Computer manuals MERCURY systems gain range is 0 to 38 dB step size for gain is 2 Acqstatus Setup Title manuals ACQ
513. ted If file retrieval is a regular mode of operation consider putting 1istenon in your local Login macro Do the following steps to retrieve data with CDE 1 Start the CDE File Manager by using the CDE toolbar 2 Goto the desired directory and double click on the desired parameter FID or shim file After you have selected the desired FID file it is processed and displayed def files files acquired with GLIDE are retrieved into GLIDE Using the Menu System 1 Follow steps 1 to 4 above for listing parameter sets using the menu system When the parameter set entries for the subdirectory you want are on view as shown in step 4 highlight the parameter file you want and click on Return 2 Click on Load Using the Inout Window Enter the command rtp lt directory gt where directory is the name of the directory containing the parameters set e g to recall the standard proton parameters enter rtp vnmr stdpar H1 Note that adding the par suffix is optional when using rtp After bringing parameters into the current experiment with rtp or similar macros such as rt rtv and convert the macro fixpar is automatically executed This macro takes the following actions e Updates old parameter characteristics and reconciles parameter differences due to the hardware present on the spectrometer e Sets the file parameter and calls the fixpar3rf fixpar4rf and fixpar5rf macros to check for the existence of all acquisi
514. ted VNMR 6 1B 129 Chapter 6 Preparing for an Experiment For the high speed spinner probes e g MAS the following safety measures have been implemented to prevent rotor and stator damage The air flow selected from the spinner window is ramped to the new value at a safe rate e If the spinner speed drops to zero and the spin setting is nonzero the air flow will be shut off This measure prevents spinner runaway if the tachometer fails e If for some reason the spinning speed cannot be reached the air flow will be shut off This measure prevents the continued spinning of a crashed rotor with more air flow 6 8 Optimizing Lock 130 Under computer control the lock system maintains the frequency stability of the spectrometer as the static field generated by the superconducting magnet drifts slowly with time or changes due to external interference Locking makes the resonance field of the deuterium in the deuterated solvent coincide with the lock frequency The lock level can be viewed using the Acquisition F si400 Acqmeter window or the Acqmeter window e To view the lock level in the Acquisition window enter acqi in the input window click on the Connect button in the window when it appears and then click on the LOCK button The LOCK display appears LOCK 43 18 e To view the lock level with the Acqmeter f si400 Acqmeter window enter acqmeter in the input window or Acqmeter in a UNIX shell A
515. tem A Tune Calibration window is available for calibrating the tune system using a shorting load an open load no device attached and a 50 ohm load To calibrate the tune system 1 Set up the system for tuning UNITYTNOVA UNITY plus Leave the switch set to observe mode MERCURY VX Connect the following e Connect the appropriate cable from the probe J5102 or J5302 to the TUNE J5402 connector on the inside of the magnet leg e Connect the appropriate cable from the transmitter J5602 or J5603 to the TUNE J5604 connector e Connect the appropriate cable from the receiver J5303 or J5103 to the Short Test Bae Q TUNE J5403 connector e Enter tn n su where n is the nucleus to be tuned e g tn H1 Tune Calibration Restore Backup Restore Sys Backup Correction Off On Power gt Accept Close Click the Calibrate button on the Tune Control Panel The Tune Calibration window opens see Figure 31 Figure 31 Tune Calibration Window Getting Started VNMR 6 1B 01 999083 00 A1298 6 6 Tuning the Probe You must run the calibration tests in the following order e Short Test e Open Test e 50 Ohm Test The test buttons are only available in this order The program stores only correction coefficients in files Therefore you will not be able to view old calibration sweeps after the experiments are finished 3 Inthe Correction field select Off or On to disable or enable cal
516. tents 2D Data Display Menu os svisccsdeiscisdesaes bles de labebsskcthia ies stevedadeaassavetaveenacdeneebescentees 79 2D Display Size Selection Menu 000 sees cee eseesecesceseceeeeeceeeeeeeeeeeseseeesaeeenes 79 2D Data Manipulation Menu sssseeseseeseseereseeresrsresrsrresrrreseeresrrresrersrenrrrsereresee 79 2D Plotin Menu seinere ecean E E E E E E GT 80 2D Data Display Secondary Menu ssesessesesseeeeeseesrseresrsrssreresreesreersreserreseeresee 80 A Analyze MENIS iccssesscisast sense teseesicgscs capsussececgutsscestoasussgcngvauaseadagicousedtasase osc EE Eie 81 Analyze Menu pinnone E E hee RE EE 81 Exponential Analysis Menu oo ee eeeceecsceceecseesseceaeeaeceeeeseceeeeseeeeeeeeseneeaeteaes 81 Automatic DEPT Analysis Menu eee cee ceeeseceseeseceeeeeceeeeeeeeeeeeseneeaeeenes 81 Automatic COSY Analysis Menu oo eee cceceeessecssceeeceeeeseceeeeseeeeeeeeseeeeaeeenes 82 Add Subtract Menu oscisisccsssessiansevszesnts roeier e EES EE EE EREE E EEEE E 82 Interactive Add Subtract Menu addi Program ssseesessereseererrsrrersrrererreererrern 83 Spin Simulation Main Menu ssesesssessesereesseeresreresreerresreresrertssreresrerenresenreeeeresee 83 Spin Simulation First Definition Menu ssessesesssseseserereersreeresreresrsrrsresrsresreerese 83 Spin Simulation Second Definition Menu ssesssseeeesereeereerssrerrsrsrrsreerereereerese 84 Spin Simulation Third Definition Menu eee eee eceeeesecseeesecseessecn
517. ter display liamp Frequencies are stored in Hz and are not adjusted by the reference parameters rf1 and rfp Integral Regions The region command divides a spectrum up into regions containing peaks A variety of parameters can be used to control the effect of the region command see the VVMR Command and Parameter Reference for details Integral Display and Plotting Display and plotting of the integral trace is independent of the values of the integrals The height of the trace is controlled by the parameter is and can be interactively adjusted with the ds command Also the macro isadj height adjusts the integral height so that largest integral fits the paper or is he ight mm tall if an argument is provided for example isadj 100 The command d1i displays a list of integral values at the integral reset points The frequency units of the reset points are defined by the parameter axis The reset points are stored as Hz and are not referenced to rf1 and rfp The amplitudes are stored as actual values they are not scaled The integral values are scaled by the parameters ins and insref and the Fourier number Typically ins is set to the number of nuclei in a given region For example if a region represented a single methyl group the following procedure would scale the integral values of that region 1 Set ins 3 2 Set insref to the Fourier number scaled values of that integral 3 Enter dli The integral value of that region is d
518. ter you create multiple window panes only one pane can be worked on at a time You can activate other panes by double clicking in them with the left mouse button If two panes represent two separate experiments double clicking in either pane automatically joins the appropriate experiment Whatever activity was running in the panes is remembered and restarted Creating Multiple Windows To create multiple windows do the following procedure Getting Started VNMR 6 1B 01 999083 00 A1298 1 3 Advanced Features 1 Click Main Menu More Windows The windows menu opens as shown in Figure 5 Abort Acq Cancel Cmd GLIDE Main Menu Help Flip Resize Select Fonts 1 Row 2 Rows 3 Rows 1 Column 2 Columns 3 Columns Return Figure 5 Windows Menu 2 Select the number of rows and columns of panes that you want to appear in the graphics window Selecting Fonts To select fonts for each window do the following procedure 1 Click Main Menu gt More gt Windows 2 Click on the Select Fonts button to open the FontSelect window shown in Figure 6 I FontSelect lel eel ae ES i ee ee mere Close Figure 6 FontSelect Window 3 Click on the corresponding buttons to choose the font Name Family Weight Slant Height and Width Exit the window by clicking Close Multiple Window Commands The multiple window environment is controlled by the following commands e setgrid sets the number of rows and col
519. th an index number as an argument the desired FID number in a multi FID experiment is selected otherwise the current index is used Button Description Box OR If labeled Box select two cursors go to the box mode Cursor If labeled Cursor select one cursor go to the cursor mode Imaginary OR Zero Imag OR No Imag Expand OR Full sf wf Dscale Phase Return 01 999083 00 A1298 If labeled Imaginary display the imaginary FID If labeled Zero Imag display the imaginary FID as all zero If labeled No Imag remove the imaginary FID display If labeled Expand expand to area between cursors box mode If labeled Full display full area cursor mode Adjust the start and width of the displayed FID Toggle the display of a time scale Enter the interactive phasing mode Return to last menu active before entering the df program Getting Started VNMR 6 1B 71 Chapter 4 Using the VNMR Menu System 1D Processing Parameter Setup Menu Parameters can be set up to the standard values with one of the buttons on the 1D Processing Parameter Setup menu or they can be typed in and observed e g type fn 8000 After parameter selection return to the 1D Data Processing menu with the Return button The 1D Processing Parameter Setup menu is activated by selecting Select Params in the 1D Data Processing menu or by entering the command menu procpar_1D Button Description No WT Clear all weighting param
520. th of the peak shows the accuracy of the impedance matching of the probe coil to the transmitter and receiver The horizontal location of the dip shows the frequency at which little power is reflected The goal of probe tuning is to increase the depth of the peak matching while centering the dip at the desired frequency 8 After the probe is tuned click Exit You are ready to begin the experiment To Select a Center Frequency The center frequency is the resonant frequency to which the probe is to be tuned A list of center frequencies appears in the Center pull down menu in the Tune Control Panel see Figure 26 This list of frequencies is read from the VNMR nuctable file Note that any frequency you type into the field will not be read until you press Return This applies to all text entry fields 1 Inthe Center field click on the triangle to open the pull down menu then select a frequency that equals or is close to the frequency you want 2 Adjust the frequency by typing a new value in the Center field or by clicking the and buttons The or buttons decrease or increase the value by the width of one span If the center frequency is either typed in or changed by the or button user is displayed next to the frequency If the typed value happens to correspond to a nuclear frequency in the pull down menu that nucleus is displayed 01 999083 00 A1298 Getting Started VNMR6 1B 119 Chapter 6 Preparing for an Expe
521. that is repeated is a sequence starting with a delay d1 then a pulse p1 followed by a delay d2 and another pulse pw After dead times rof2 with receiver off and alfa with receiver on np data points are acquired over a period of at seconds This process is repeated ss nt times with the data actually acquired only during the nt number of transients and not during the first ss steady state transients The alfa delay before acquisition consists of a variable part equal to the parameter alfa and a fixed part equal to 1 bet a fb The value of bet a depends on the type of audio filter in the system and cannot be set by the user but is selected in config for the UNITYINOVA UNITYplus UNITY and VXR S systems Because the total delay before acquisition is the sum of alfa and 1 beta fb it is possible to shorten the delay beyond normal values by setting al fa negative Refer to the description of al fa in the VNMR Command and Parameter Reference for the procedure fb is the filter bandwidth in Hz used to set the audio filters which prevent noise of higher frequency than the spectral limits from folding in to the spectrum The standard value of fb is 10 more than half of the spectral width sw The fb parameter is automatically changed whenever the spectral width sw is changed and thus is normally not a user entered parameter After sw has been change fb may be changed to a different value The parameter np is generally
522. the Gaussian function exp t gfs gf 2 e sb is a sinebell constant in seconds A positive value applies a sinebell of the form sin t p 2 sb A negative value applies a squared sinebell function of the form sin2 t p 2 sb e sbs isa sinebell shift constant in seconds It allows shifting the origin of the sinebell function according to the formula sin t sbs p 2 sb Again the square of this function is applied if sb is negative e awc is an additive weighting constant that adds the constant awc to each value of the weighting function It is applied after the sinebell and exponential function but before the Gaussian function All these weighting functions can be applied simultaneously to the data That is one does not first apply a decreasing exponential function then apply a convolution difference function etc Instead all weighting functions to be used are set and then are applied simultaneously as part of the wft command To remove a particular weighting function from use its value should be set to n for not used Its value is then displayed on the screen by dg as not used 01 999083 00 A1298 Getting Started VWMR6 1B 221 Chapter 8 Data Processing 222 Table 31 Weighting and Fourier Transform Commands Macros and Parameters Commands ft Fourier transform 1D data resolv lt a b gt Set resolution enhancement parameters wft Weight and transform 1D data wti lt element_numbe Interactiv
523. the menu select the resonant frequency to which you are tuning the probe A marker corresponding to the selected frequency appears in the Tune Display window 6 Inthe Tune Control Panel type values as appropriate in the Span Scale and other fields on the Tune Control Panel Using the dB scale usually facilitates probe tuning See the To Adjust the Span on page 120 7 Adjust the tune and match capacitors while watching the Tune Display window Use the match capacitor to increase the depth of the dip as much as possible Use the tune capacitor to center the dip on the marker created in step 5 Getting Started VNMR 6 1B 01 999083 00 A1298 Exit Display Save ete Center 23 H1 300 050224 Span 6 6 Tuning the Probe Tune Control Panel H2 46 059600 H3 320 047397 He3 228 564113 Help 7 MHz Cursor Lig 44 156355 fo On Marker Liz 116 603793 TE Be9 42 164581 Marker B10 32 241720 MHz Marker B11 96 265604 MHz C13 75 454856 Scale N14 21 672340 Max O N15 30 416302 i O17 40 675777 Step 5 19 282 298612 Smooth Ne21 23 683721 Na23 79 372883 Mg25 18 359318 Al27 78 183480 Si29 59 611190 P31 121 462138 bL T Figure 26 Pull Down Menu for Center Frequencies Figure 25 Tune Control Panel qtune Program The dip displayed in the Tune Display window shows where little power is reflected at the frequency being observed The dep
524. their standard positions 01 999083 00 A1298 Getting Started VNMR 6 1B 27 Chapter 1 Overview of Varian NMR 28 On the VnmrX version of VNMR the GLIDE user interface see Figure 3 is typically at the top of the screen Figure 3 GLIDE User Interface If the system is configured to perform acquisition not as a stand alone data station the right side of the screen often displays two other windows the Acquisition Status window and the Acquisition window Both windows are shown in Figure 2 If the system is running the Common Desktop Environment CDE the CDE toolbar which includes a custom tool to activate VNMR shown in Figure 4 is displayed on the bottom of the screen VNMR Tool a ie Two Three FOUr j ENT Figure 4 CDE Toolbar The part of the screen where no windows appear is called the workspace On a typical system the workspace contains artwork or a repeating design The default design is the Varian logo and name repeated in a grid over the background but the workspace can be customized locally Other objects that usually appear on the VNMR display screen include icons for closed windows Typically such icons for the console and VNMR appear on the opening screen Using Multiple Windows You can configure the graphics window into smaller panes dividing it into one two or three distinct graphical rows and or columns Each pane can be used independently of others Activating Window Panes Af
525. tical scale of the displayed spectrum to 500 mm It is not necessary to exit the display mode and enter a parameter entry mode to do this Each function key can cause a different change in the display Labels for the function keys are always displayed at the top of the display screen The action associated with each function key may be invoked by pressing the appropriate function key on the keyboard or by moving the mouse arrow to the appropriate label and clicking a mouse button Using function keys it is possible to take actions such as display one or two cursors to rapidly expand the region between two cursors to adjust the start and width of the displayed FID or spectrum and to return to the menu system Function keys that cause a change in display mode for example add a cursor to the display may also cause a reassignment of the mouse buttons In each case the mouse button will 01 999083 00 A1298 Getting Started VWMR6 1B 231 Chapter 9 Display Plotting and Printing 232 be changed with the name of the parameter it controls Until you have used the system for some time it is a good idea to look at the mouse labels before you click a mouse button to make sure you are changing the parameter you intend to change Display Parameters FID and spectral display is governed by a number of parameters The FID region displayed is determined by the plot parameters wf width of FID and sf start of FID Similarly
526. tidimensional NMR see the manual User Guide Liquids NMR For this we use the wexp for when experiment parameter e g wexp wft2d e When an acquisition error occurs some corrective action may be desirable You can accomplish this with the werr when error parameter e g werr react Analogous to wbs the commands wnt and wexp permit setting these automatic functions even after go or ga or to reset functions specified by the parameter wbs wnt and wexp and the au command Acquisition Status Window The Acquisition Status window normally appears automatically on Tj manuals ACQUISITION STATUS the screen when VNMR is started If SAUB lesius Kuaha i ipi USER EXP SAMPLE this window does not appear or if it FID CT DEC has been exited start it by entering Completion Time LOCK acqstat or by selecting Remaining Time level Acquisition Status from the Data Stored at Workspace menu SPINNER Actual Figure 63 shows a typical Acquisition Status window when first opened The display can contain Figure 63 Acquisition Status Window 19 fields of acquisition status acqstat Program information but all fields are not always displayed due to the hardware configuration of the system or the parameters set on the system Getting Started VNMR 6 1B 01 999083 00 A1298 7 4 Performing Acquisition Table 28 lists the possible fields with a description of each field Table 28 Fields in the Acquisi
527. tion Status Window acqstat Program Field Description STATUS Present status of acquisition The values displayed should be self explanatory e g Shimming with two exceptions Active means that the acquisition computer started but the console is not active yet and Inactive means that acqst at cannot communicate with the acquisition computer or that the acquisition computer is not executing QUEUED Number of experiments queued by multiple go commands USER Login name for owner of the experiment that is active EXP Number of the active experiment e g exp1 exp2 exp3 FID Number of the FID being acquired if in an arrayed experiment CT Number of completed transients DEC Decoupler state On Off Gated SAMPLE Sample number in magnet if in automation mode LOCK Lock status Off Regulated Not Regulated level Present lock level Completion Time Remaining Time Data Stored at Estimated time when experiment will complete Remaining time h m s until the experiment completes Last time that data was transferred to disk SPINNER Spinner status Off Regulated Not Regulated Actual Actual spinner speed Setting Requested spinner speed VT Variable temperature unit status Off Regulated or Not Regulated if VT is set as present and vtt ype 2 Actual Actual temperature if VT is set as present and vtt ype 2 Setting Requested temperature if VT is set as present and vtt ype 2 The look of the Acquisition S
528. tion Window acqi Program If you have connected acqi to the console and start an acquisition acqi is disconnected You can connect to acqi while acquisition proceeds 3 To shim during the acquisition click on the SHIM button The shim panel appears so you can perform shimming as usual The following features are not accessible from the SHIM window shown in Figure 62 during acquisition e The z0 pwr gn ph panel that lets you access the lock system from the shim panel e The autoshim panel e The lock gain slider adjustment You must use the same account that was used to start the acquisition Therefore if vnmr1 starts an acquisition only the acquisition process running as vnmr1 can connect to the console while the acquisition remains active If you log in as vnmr1 to the spectrometer on your X display terminal you can start acqi and it will connect to the console from the X display terminal Queueing Acquisitions Under many circumstances it is desirable to have the spectrometer perform more than one experiment on a single sample Each time you enter go ga or au the system first determines if an experiment is currently active If not the experiment you are submitting becomes active otherwise the new experiment is queued and waits for the current experiment and other previously queued experiments to complete before starting Note that you cannot queue acquisition commands go au etc from the same experiment dire
529. tion indication lock level 34 9 e In the remote status unit optional on systems other than 269 MERCURY VX MERCURY and zo _ 1 4 16 64 GEMINI 2000 or on the magnet zo g _ _ leg on the MERCURY VX lockpower E 4 16 64 MERCURY and GEMINI 2000 the spin rate is shown by the spin lockgain __ 1 EAr 21640 64 light E 120 3 lockphase i zaz 16 64 If light is off the sample is not spinning g 16 iy ale OD If light is blinking the sample is spinning but not at the last Figure 33 Spin Information in LOCK requested rate Display acqi Program If light is steady the spin rate is being regulated at the last requested rate On MERCURY and GEMINI 2000 systems without spinner control the spin rate is controlled by adjusting the needle valve on the magnet leg Spinning is indicated by a spin light and a needle valve on the magnet leg You can adjust spin rate from the input window or the Acquisition window Typical spin rates are 15 for 10 mm tubes and 20 26 for 5 mm tubes The Spinner Control window spinner program provides spin speed control experiment control and low speed or high speed spinner selection see Figure 34 Table 14 lists commands and parameters related to adjusting sample spinning Using the Inout Window The spin command regulates sample spinning according to the spin parameter note there is a spin command and a
530. tion parameters related to the third 01 999083 00 A1298 Getting Started VNMR 6 1B 109 Chapter 6 Preparing for an Experiment 110 fourth and fifth rf channels respectively if the channel exists on the system based on the value of the parameter numrfch Any parameters found to be absent are created characterized and initialized by the appropriate macro e Checks if a macro userfixpar exists If it does fixpar runs that macro This allows an easy mechanism to customize parameter sets The parameter file contains the file name of the parameter set returned by a rt or rtp macro This parameter is reset when the go command is issued e If the system is not in automation mode auto n file isresetto exp e If the system is in automation mode auto y file is set to the path of the directory where the data is stored To Recall Standard Parameter Sets The VNMR software offers several shortcuts if you only want to select standard parameter sets Once a nucleus and solvent are selected a parameter set is set up to do the experiment requested complete with positioning of the transmitter and decoupler and in the case of 1H and c approximate referencing to TMS Using GLIDE 1 Ifthe GLIDE interactive window is not open open it entering glide in the input window or by clicking on the GLIDE button in the Main Menu 2 Click on Setup 3 Using the right mouse button click on the triangle to the right of the Experiment
531. tive Autoshim mode is particularly useful to give the user a feel for the operation of Autoshim and the relative importance of the different gradients under different conditions such as different size samples or different sample heights Fully Automatic Autoshim In the fully automatic Autoshim mode the parameter wshim controls the automatic shimming activity wshim can specify no shimming shimming at the start of data acquisition etc Shimming in each case is initiated by some form of data acquisition whether by a command go ga au or a macro using one of these commands Using the Input Window e For shims on the lock signal set wshimto n e g or s where n indicates no automatic shimming is performed Even with wshim set to this value the shimming procedure specified by the parameter met hod can be activated by using the shim command e indicates automatic shimming is done for the experiment prior to data acquisition g indicates that automatic shimming using gradient shimming is done only at the beginning of the first experiment following the change of sample using the automatic sample changer The parameter met hod is ignored This value is available only in automation and is not used with the go ga or au commands See Gradient Autoshimming on page 168 on how to set up gradient shimming before using this method s indicates automatic shimming is done only at the beginning of the first experiment following the
532. tment of shims and parameters was discussed previously in this chapter e IPA selects interactive parameter adjustment in which the bottom panel displays up to five slide control and button combinations Figure 45 shows IPA selected with slide controls and button combinations for the parameter phfid on display Each slide control and button combination has a menu button on the left showing only the current selected value which serves as a label to identify which parameter is adjusted By clicking the right mouse button on this label a menu appears showing the parameters that can be adjusted by the current pulse sequence You can select any one of the parameters shown and the slide control and button combination will adjust the newly selected parameter This way when more than five parameters need to be adjusted any combination of five can be selected to show in the bottom window The 01 999083 00 A1298 Getting Started VNMR 6 1B 159 Chapter 6 Preparing for an Experiment 160 value of the parameter is displayed in a square bracket such as 10 0 to the right of the menu button If the pulse sequence is written with up500ts ACQUISITION multiple ipulse statements for oE LOCK SHIM LARGE Style 2 example and the same label is provided 3 16 bits FID Spectrum PANEL Shim IPA to the different i pulse statements a ZER T Single TlGrid OFF Trace G Bb down fid level 12 me single slide control is present
533. to make a copy of the file you marked You are asked for the name of new file Rename Start by marking one file in the files display and then click on this button to rename the file you marked You are asked for the new name of new file Return Display the Files Main menu page 87 4 13 Secondary Main Menu Selecting More in the Main menu activates the Secondary Main menu a series of additional choices that do not fall into one of the other main categories Of these the most important button will probably be Exit VNMR which you should routinely use when you are ready to terminate your session at your spectrometer or data station You can also activate the Secondary Main menu by entering menu main2 Button Description Write Pulse Sequence Display the Pulse Sequence Entry Main menu below to initiate menu driven pulse sequence generation Configure Display the Configuration menu page 92 to modify the system configuration such as selecting a plotter UNIX Open a temporary UNIX shell This shell becomes the active process superseding the VNMR software When finished use the right mouse button to select Quit or press Control d to terminate the process and display the Main menu page 66 Exit VNMR Exit the VNMR program returning to a UNIX shell All data in your temporary NMR files are saved Return Display the Main menu page 66 Pulse Sequence Entry Main Menu The Pulse Sequence Entry Main menu is typically entere
534. to your VNMR user directory which has your VNMR experiments maclib menulib etc More Display the Directory Secondary menu below Return Display the Files Main menu page 87 Directory Secondary Menu The Directory Secondary menu is activated by selecting the More button in the Directory menu or by entering files files_dir_2 Button Description VNMR Set the current directory to be the VNMR system directory Create New Show prompt New directory enter name and lt return gt then create directory with the name entered and set the current directory to be this new directory If done successfully the files display will have no entries because the new current directory just created is empty Return Display the Directory menu above 88 Getting Started VNMR 6 1B 01 999083 00 A1298 4 12 File Menus Files Information Menu The Files Information menu is activated by selecting the Files Info button in the Files Main menu or by entering files files_info Button Description By Size By Date Return Sorts the entries in the current directory by size Largest files are listed last For subdirectories the size of the entries in the subdirectory is included in figuring the size of the entry The resulting sorted list is displayed in the VNMR text window Sorts the entries in the current directory by the date each was last modified with entry most recently modified listed last Result
535. top of this curve The response of the lock level to changes in gradients is not as sensitive as in a non saturating case and therefore automatic shimming is not as reliable Nonsaturating lock power is easily checked by determining if the lock level changes by the proper factor of two upon a change of 6 dB in lock power Usually acetone d must have at least 8 to 15 dB less power than CDCl for example to remain non saturated 01 999083 00 A1298 Getting Started VNMR 6 1B 139 Chapter 6 Preparing for an Experiment 140 Shimming Criteria for Autoshim In all forms of automatic shimming whether interactive or noninteractive another concept the shimming criterion enters into the process Two aspects of Autoshim must in some way be specified by the user One is the resolution of the starting point good or bad If good only small changes need to be made to the shim settings to find the optimum if bad larger changes are necessary The second is how good must the final resolution be Clearly the better the desired resolution the smaller the steps that Autoshim must take as it approaches the maximum in order to find the absolute maximum to within a specified degree As shown in Table 17 for each there are five criterion values B bad L loose M medium T tight and E excellent The lower case letters are used when entering criterion values into a shim method discussed below Table 17 Permissible Shimming Criterion Value
536. tory 37 38 Workspace button 66 Workspace Menu 49 workspace part of screen 28 wp parameter 232 250 Write button 89 Write Pulse Sequence button 91 Write Text button 76 writefid command 278 wshim parameter 139 144 154 176 207 wtfile parameter 222 wti command 72 223 wysiwyg parameter 232 250 X X and Y radial shim gradients 136 X Window System 25 x0 parameter 262 x1 button acqi 156 xl parameter 136 X1 shim gradient 136 XL systems 281 x linear button 86 x log button 86 XPOLAR button 69 x square button 86 XY32 decoupling 194 Y yO parameter 262 y linear button 86 y log button 86 ypcat command UNIX 282 y square button 86 01 999083 00 A1298 Z Z axial shim gradient 135 z command 253 ZO field offset coil 136 ZO field position 132 z0 parameter 136 152 184 Z1 and Z2 adjustment 163 zl parameter 136 Z1 room temperature shim as a gradient 174 Z1 shim gradient 136 Z1 shimming hardware 146 zlc parameter 136 z2 parameter 136 Z2 shim gradient 136 z2c parameter 136 Z3 and Z4 adjustment 163 zero and first order baseline correction mode 241 zero filling 72 74 Zero Imag button 71 234 zero point of ADC 155 zero filling 224 zero frequency suppression 228 zero order baseline correction 241 252 zero order FID phasing constant 226 Zeta plotter 254 zfs zero frequency suppression 228 zoom macro 250 01 999083 00 A1298 Ind
537. tributed files similar to the system files found in the vnmr directory maclib psglib menu1ib etc Besides these directories at least two files in the vnmr directory are of interest conpar When the system is first installed or when changes are made the configuration parameter file conpar is modified to reflect the changes These parameters such as the spectrometer frequency are common to all users and hence placed in a system file devicenames A file listing possible choices for printers and plotter and identifying which of these devices are attached to your computer or to other Sun computers networked together via Ethernet NMR System Administrator and Other Users The export home directory contains one directory for each user who has been given permission to use the system user A user B etc in Figure 4 Every system is initialized with a special user named vnmr1 who is the NMR system administrator the owner of the VNMR software there is also a UNIX system administrator known by the standardized name root Thus vnmr1 is the only user with permission to change the files found in the vnmr directory In addition to being the NMR system administrator vnmr1 is also a regular user of VNMR with permission to run NMR experiments process data etc This capability is provided by the directory vnmrsys which is found within the vnmr1 directory and whose full name in UNIX terminology is export home vnmrl vnmrsys
538. trogen and helium gases from the dewar Except when transferring nitrogen or helium be certain that the relief valves are secured on the vent tubes WARNING On magnets with removable quench tubes keep the tubes in place except during helium servicing On Varian 200 and 300 MHz 54 mm magnets only the dewar includes removable helium vent tubes If the magnet dewar should quench sudden appearance of gases from the top of the dewar and the vent tubes are not in place the helium gas would be partially vented sideways possibly injuring the skin and eyes of personnel beside the magnet During helium servicing when the tubes must be removed follow carefully the instructions and safety precautions given in the manual Varian Magnet Installation and Maintenance Caution Notices Observe the following precautions during installation operation maintenance and repair of the instrument Failure to comply with these cautions or with specific cautions elsewhere in Varian manuals violates safety standards of design manufacture and intended use of the instrument Varian assumes no liability for customer failure to comply with these precautions CAUTION Keep magnetic media ATM and credit cards and watches outside the 5 gauss perimeter of the magnet The strong magnetic field surrounding a superconducting magnet can erase magnetic media such as floppy disks and tapes The field can also damage the strip of magnetic media found on credit cards
539. tton can be held down and the cursor will track any movement of the mouse arrow The parameter cr is updated by movement of this cursor Pressing the right mouse button will display a second cursor to the right of the original cursor Subsequent depression of the right mouse button or holding the right button down will cause this new cursor to move to the mouse arrow The parameter delta will be updated by movement of this second cursor This second cursor may not be moved to the left of the first cursor If both cursors are displayed depression of the left mouse button enables both cursors to be moved by the same amount That is the parameter cr is changed but the parameter delta is not changed The middle mouse button controls the spectral intensity Pressing this button causes the vertical scale of the spectrum parameter vs to be adjusted so that the spectral intensity at the position of the mouse arrow equals the vertical position of the mouse arrow If an optional integral is displayed when the middle mouse button is depressed the integral scale parameter is will be adjusted so that the integral intensity at the position of the mouse arrow equals the vertical position of the mouse arrow If the mouse arrow is positioned at 01 999083 00 A1298 Getting Started VNMR6 1B 239 Chapter 9 Display Plotting and Printing 240 the left edge of the display the vertical position of the display will be adjusted to the vertical position of the
540. ubmenu with more choices including these useful programs Shell Tool Allows you to interact with the UNIX operating system Many users find a Shell Tool window the fastest way to copy delete create and edit files do backups write macros change passwords monitor processes going on at the host computer and so on Clock Displays a clock that can be set many different ways for example as either analog or digital Click on the clockface with the right mouse button to open the Clock Properties menu that allows customization Performance Meter Gives you an indication of how hard the CPU of your computer is working and is useful as a monitor of what processes are going on in the background CDE Menu Programs can also be accessed from the CDE toolbar shown in Figure 16 aai s a cc _ Tagg ehh 5 6e68 3 3 coi amp 77 E fl 0 Figure 16 CDE Toolbar Closing and Opening Windows Each of the windows on the screen can be closed and changed to a small icon When closed each window changes to a small distinctive icon as shown in Figure 17 This can be useful when many windows are open and you would like more screen space To close a window on Vnmr move the mouse cursor to the line on the edge of the window and click the right mouse button until a popup menu appears Select Close from the menu
541. uch better method would be to recall a parameter set that describes exactly or at least approximately the experiment you wish to do That is the topic of this section how to set up an experiment using saved parameter sets including the standard parameters sets shipped with VNMR Table 11 summarizes the commands and parameters used in this section Table 11 Retrieving Parameter Sets Commands and Parameters Commands addpar Add selected parameters to the current experiment cd lt directory gt Change working directory dg lt template gt Display group of acquisition processing parameters dg1 Display group of display parameters dg2 Display group of 3rd 4th rf channel 3D parameters dglp Display group of linear prediction parameters dgs Display group of shim and automation parameters fixpar Correct parameter characteristics in experiment fixpar3rf Create parameters for third rf channel fixpar4rf Create parameters for fourth rf channel fixpar5rf Create parameters for fifth rf channel l1f lt directory gt List files in the current directory paramedit parameter lt tree gt Edit parameter and attributes with user set editor paramvi parameter lt tree gt Edit a parameter and attributes using vi editor rtp lt file gt Retrieve parameters setup lt nucleus lt solvent gt gt Set up parameters for basic experiments userfixpar Macro called by fixpar addpar lt 2d 3d 3rf 4d downsamp fid image 112d lp lt
542. um of the squares of both channels The history of the quality of the shimming as measured by the area under the FID envelope is displayed by the Quality Meter shown in Figure 42 The shim quality is calculated from the area in the FID envelope The large number at the bottom is the latest value of the shim quality arbitrarily scaled to a reasonable range Clicking the Renormalize button resets the scaling factor such that the next value displayed is 1000 The vertical scale of the graph is automatically adjusted to keep the most recent value in view Editing Autoshim Methods Autoshim Method Editor Clicking the Edit button on the Style 2 Waders File HELE shim control panel displays the Load Save Delete v Autoshim Method Editor shown in Nunber of Elesents 1 aE Figure 43 Current Element 1 An autoshim method consists of a series of autoshim elements Each element of at ae x the method optimizes the values of a Z YA i evz selected group of shims The elements ANS 29 ea a are executed in order to obtain the final 220 24 Yz Y3 shim values The number of elements in 25 the user s method is selected in the E entirety Elements field The user edits one Bad Bad element at a time the Current Element Loose Loose field selects which one is currently being changed Execel lent Execel lent Within a particular element the user selects which shim coils to optimize
543. umns in the graphics windows e fontselect opens the FontSelect window that enables you to define fonts for the panes e jwin is called at each double click of the left mouse button inside a pane This macro records the activity in a current window and then restarts the activity in the selected window including a jexp command if necessary jwin calls setwin to activate the selected window The global parameters curwin and mapwin maintain information about the panes 1 3 Advanced Features The data system incorporates many advanced operating features including queuing multitasking multi FID experiments multidata sets MAGICAL II macro language and optional specialized software 01 999083 00 A1298 Getting Started VNMR 6 1B 29 Chapter 1 Overview of Varian NMR 30 Queuing Virtually all operations on the data system are queued that is you are free to ask the system to perform any action at any time even in circumstances in which that action cannot possibly occur immediately For example suppose you give the system a command to plot a spectrum and that plot starts You do not need to wait for that plot to finish but instead can proceed to set up a second plot and issue the command to perform that plot as well Because the first plot is still occurring the system queues up your request and performs it when the resources needed to perform the task in this case the plotter are free As far as you are concerned the plot is now
544. un can be initialized by retrieving the shim values from the earlier run When a shim set is retrieved whether from a shims directory or from a data set only the shim parameter values have been changed The actual shim currents are only altered if Load y and su shim go ga or au is entered If load n each of these programs begins with the actual shim currents and not those specified by the parameters in the current experiment Also if load y the Acquisition window does not return shims Execute the 1istenon macro Activate CDE Start the file manager from the tool bar and go to the directory that contains the file you want to retrieve Use the mouse to double click on the file name Manual Emulation Shimming The most familiar method of homogeneity adjustment to many users is the manual emulation mode which is accessed with the Acquisition window For the procedures in using this mode see FID Spectrum Shimming Windows on page 154 In this mode the mouse is used to interactively select and display different combinations of four or five shim controls that can be used to manually adjust the homogeneity while Getting Started VNMR 6 1B 01 999083 00 A1298 6 9 Adjusting Shims observing a lock level real time FID display or real time spectrum display on the screen For small amounts of touch up shimming this method may prove to be the fastest short of simply retrieving old values however it is certainly no
545. unlock not work you can enter this command from VNMR as a workaround shell rm f userdirt lock_n primary where n is the number of the experiment In entering the she 11 command do not use a wildcard character such as a question mark or an asterisk for the experiment You should also not build this command into a macro because this would defeat experiment locking completely There are definitely many instances in which a lock file exists for good reasons Remote Acquisition Beginning with VnmrS version 4 1 control of acquisition is possible from a remote computer terminal or terminal emulator Use of VNMR software from these devices is discussed in the manual System Administration and the user is referred there for further information on operation of VNMR itself remotely All data acquisition commands are supported The only acquisition related feature missing from remote operation with a terminal is the Abort Acq button because the row of buttons containing that button is missing from the terminal environment The equivalent keyboard command aa is functional Prior to the release of VnmrxX 4 3 remote interactive shimming using acqi was not supported although remote computer shimming could be accomplished by using the parameters wshim and method as part of a go Remote interactive shimming using acqi is fully supported in VnmrX 4 3 and later From a remote Sun computer you can use the remote Acqst at command which was described
546. ure 34 From this window the spinner can be started or stopped and experiment control of spinning can be turned off That way if an experiment you just joined has the spin parameter set to a value other than the current spinning speed and you forget to set spin to n and type go the spin speed will not be changed On the N YINOVA system high speed solids style sample spinning and low speed liquids style sample spinning are both under computer control The spinner program can be used to select these spinner types 1 Enter the command spinner in the input window The Spinner Control window appears Set the desired spinning speed by clicking the diamond next to Turn Spinner On and enter the speed value in Hz To disable experimental control of spinning click the button next to Allow spin control in an experiment with go A button that is indented and red is selected When experimental control of spinning is disabled you can choose how spinner errors are handled by the system a warning is issued or acquisition is stopped Select a spinner mechanism type low speed liquids type spinning high speed solids type spinning or automatic spinner type selection If you select high speed you can choose to set the spinner air flow instead of the speed If you select the automatic spin selection you must also enter threshold values that tell the system when to switch to solids type spinning 01 999083 00 A1298 Getting Star
547. ure 58 Attenuator Configurations Part 1 Of 2 oo ceeeecesseeceecseeeeeseceeeeeeseaecareeeaesaeeeeenenee 191 Figure 59 Attenuator Configurations Part 2 Of 2 oo ciceeeeseesescseceeeseeseceeeeeeseeaeeaseeeacsareesenenes 192 Figure 60 Temperature Control Window ou cseeseseseeeceeeeseeeeeseecneescesecnecaeescesecaseeseaesaeeesseeeas 196 Figure 61 Acquisition Window acqi Program c i ceeeeseeseeeceecsseseeeecsecaeeseesecaeeaeeecsaeeaseeees 200 Figure 62 SHIM Window During Acquisition acqi Program oo eee eeeseseesecseeeeeeceseeeeeeeees 201 Figure 63 Acquisition Status Window acqstat Program oo ceeeesecseesseeceeeeseecescsereeeerenes 204 Figure 64 Acqstatus Setup Window Acqst atuS Program occ ceeeesecsessseeceseeeseeeescnereeeseenes 206 Figure 65 Digital Filters Compared to Analog Filters oo teeeeesessesecseeeceseeseceseeesacereeseeenee 214 Figure 66 Interactive FID Display Af Program oi eeeseseeeceecsseeeeeceecseeeeesecaeeeeeeceaeeaseneees 233 Figure 67 Interactive Spectrum Display ds program o e ee eeeeseseeeeceeceeeecesecaeeeteecaeeeteeeees 238 Figure 68 Color Selection Window color Program o eeesceesseseeeeceecsceccesecaeeeteecaeeeseeeees 258 Figure 69 2D Phase Color Selection Window Color Program escssssecceseeeeeeceeeneeeeterenes 259 Figure 70 2D Absolute Value Selection Window o ccececesseseescsecseeseeseceeeseeecsaecareeesecsereesenenes 259 Figure 71 Image Color Selection Window
548. urn key For example to set the parameter sw to 1000 type sw 1000 and press Return Or to turn off temperature regulation type temp n and press Return To input more than one parameter at the same time separate each parameter entry with a space and press Return after the last entry for example type nt 16 dm yyy temp 40 and press Return To avoid repetition in this manual pressing the Return key after each entry should be assumed and will not be mentioned except in special cases Parameters can be arrayed by entering a series of values separated by commas Both numeric parameters and string parameters can be arrayed in this fashion For example entering nt 1 1 1 1o0rdm nnn nny makes nt or dm an arrayed parameter For easy entry of linearly spaced array values you should use the array macro To change a specific element of an arrayed parameter provide the array index in square brackets to access the element e g nt 3 2 sets the third value of the nt array to 2 Multiple elements of an array can also be altered or added by entering a series of values Again using the nt example nt 5 4 4 4 4 adds elements 5 6 7 and 8 to the nt array and sets the value of each of these elements to 4 01 999083 00 A1298 Getting Started VNMR 6 1B 95 Chapter 5 Using the Command Mode Parameter Display To display the current value of any parameter type the name of the parameter followed by a question mark pressin
549. used To start wt i from the menu system select Adj Weighting in the 1D Data Processing Menu in the 2D Data Processing Menu or in the 2D Interferogram Processing Menu During the wt i display a single menu with the following buttons is active this menu is not user programmable next fid 1b sb sbs gf gfs awc return Each button in this menu functions as follows next fid Increments the FID interferogram index Ib Selects line broadening or exponential weighting A negative value gives resolution enhancement sb Selects the sinebell constant A negative value gives squared sinebell sbs Selects the sinebell shift constant only if sinebell is active gf Selects the Gaussian time constant gfs Selects the Gaussian time constant shift only if Gaussian time constant is active awc Selects the additive weighting constant return Returns to the last menu before wt i was entered Currently active weighting parameters can be changed by moving the mouse cursor to the appropriate field in the weighting function box and pressing the left mouse button New values for weighting parameters can also be typed in Note that all other parameters unless set to not used are also used to calculate the weighting function To adjust FID intensity parameter vf use the center mouse button within the FID box To adjust spectrum intensity vs use the center mouse button within the spectrum box The right mouse button turns off
550. used See Mapping the Shims on page 169 for details Starting Gradient Shimming To start shimming from the system administrator menu enter gnapsys and then click on Autoshim on Z This button starts gradient shimming using current parameters and displays the curve fit for each iteration The curve fit plot shows the raw data as 1 and the curve fit as 2 see Figure 50 Getting Started VNMR 6 1B 01 999083 00 A1298 6 12 Gradient Autoshimming 30000 20000 140000 0 10000 20000 30000 Fit Frequency vs Field Figure 50 Curve Fit Plot Shim adjustments for each iteration are also displayed see Figure 51 and have converged when the rms error number is less than 1 0 Gradient shimming continues until convergence or until a maximum of 10 iterations are reached mapname 5mm_Triax_0O1l shimset 4 gzsize 6 rms err 1 892 Shim Offset Old New DIFE Error z1 800 9405 9269 136 48 Z2 800 3118 3104 14 13 Z3 3200 4356 4321 3 5 37 z4 3200 4049 4885 836 104 Z5 3200 13443 14537 1094 322 z6 3200 15619 12568 3051 467 Z 3200 0 0 0 0 z8 3200 0 0 0 0 Figure 51 Display of Shim Adjustments for Each Iteration If a shim goes out of range the shim is set to maximum and shimming continues with the remaining shims If convergence is then reached shimming is tried once more with all Z shims and continues unless a shim goes out of range again If the parameter gmap_z1z4 is setto y then if
551. utton Description T1 Proc Weight Fourier transform phase each FID in a 7 data set T1 Analysis Perform an exponential least squares analysis on each peak in the spectrum to determine its T value T2 Proc Weight Fourier transform phase each FID in a T data set T2 Analysis Perform an exponential least squares analysis on each peak in the spectrum to determine its T gt value Plot Produce a horizontal stacked plot of the spectra used in the exponential analysis Print Print the information from the exponential least squares analysis Return Display the Main menu page 66 Automatic DEPT Analysis Menu The Automatic DEPT Analysis menu is activated by selecting the DEPT button in the Analyze menu or by entering the command menu dept Button Description Process Weight Fourier transform phase each FID in the data set Display Display the current spectra edited or unedited 01 999083 00 A1298 Getting Started VNMR 6 1B 81 Chapter 4 Using the VNMR Menu System 82 Button Description Plot Plot the current spectra edited or unedited Edit Edit processed spectra to obtain separation of CH CH2 and CH3 peaks Printout Print editing information contained in the dept out text file in the current experiment directory Full Analysis Process spectra plot unedited spectra edit spectra plot edited spectra and print editing information each action within this selection can be accomplished individually by button
552. ve them in a file as follows 1 Enter a name in the Color Selection File Name field in the bottom right hand corner of the Color Selection window The bottom list box is updated with the new file name Getting Started VNMR 6 1B 01 999083 00 A1298 General l l Contour 3 Contour 4 Contour 5 Contour 6 ers Femara Contour 13 Contour 12 Fone Fema Foner a ono Foner Fears Fera Contour 2 Figure 70 2D Absolute Value Selection Window Fora 1 Ar EERE ERE 01 999083 00 A1298 9 7 Plotting VNMR Color Selection 2D_AV snow GhostWhite WhiteSmoke gainsboro Floralwhite OldLace ue PeachPuff DEFAULT snow GhostWhite WhiteSmoke AntiqueWhite Papayawhip BlanchedAl mond bisque PeachPuff DEFAULT Getting Started VNMR 6 1B 259 Chapter 9 Display Plotting and Printing VNMR Color Selection General 20 Pit 2D_AV background pian Ghost Whi te foreground WhiteSmoke gainsboro Floralwhite OldLace linen Anti queWhite Papayalhip bisque PeachPuff DEFAULT Y color selection File name Load xit Figure 71 Image Color Selection Window 2 Click on the Save button The color file is saved in the designated place in the VNMR system file Loading A Color File To retrieve a color file 1 Click on the color file name in the scrollable list box at the bottom of the window The color file name appears on the entry area of the Color
553. veossw macro 213 movesw macro 185 movetof macro 184 mt command 289 310 Getting Started VNMR 6 1B multi FID experiments 31 multiple data processing operations 30 multiple data sets 32 multitasking 30 my command 276 mxconst parameter 202 N N15 button 68 name of a macro 32 nearest line 246 needle micrometer 25 network timeout 285 network use of a tape 291 new users 59 newfs command UNIX 292 newshm macro 143 next fid button 72 223 nitrogen contact with body 18 nitrogen gas flowmeters caution 20 nl command 246 247 nli command 253 nm command 232 245 NMR spectrometer system units 23 NMR system administrator 36 NMR system console 24 No Imag button 71 234 No Integral button 73 239 No WT button 72 74 nodes file 282 NOE 2D correlation 69 NOESY button 69 noise command 209 noise level of a FID 209 noise limit 246 noise reduction 209 noislm macro 246 non linear baseline correction 252 non saturating lock power 139 non spin shims 163 Normal button 72 74 normal size transform 72 74 Normalize button 80 normalize vertical scale 80 normalized display mode 232 245 notational conventions 21 np parameter 187 223 nt parameter 187 188 nuclei selection 110 111 nucleus lookup files 34 Nucleus Selection menu 68 110 nucleus standard parameter sets 36 nucleus table 183 Nucleus Solvent button 67 nuctables directory 34 nuctabref f
554. verflowing 16 bits the dp n mode can cut the storage data size by a factor of 2 No down scaling is performed on UN YTNOVA so that the full available signal is always used This use requires care in the cancellation cycle and an estimate when averaging will overflow 16 bits so that dp y is still preferable for robust operation Automatic Processing To examine data from the experiment in progress the parameter bs and the concept of the block size is provided The data system uses two independent computers the host computer and the acquisition computer When the parameter bs is set to some number say 64 the acquisition computer is instructed after every 64 transients to provide the accumulated data up to that point to the host computer to be stored in an appropriate disk file overwriting earlier data Thus every bs transients an updated version of the 01 999083 00 A1298 Getting Started VYNMR 6 18 203 Chapter 7 Acquiring Data 204 experiment in progress is available for viewing by the user who is communicating with the host computer Typing wft see Chapter 8 Data Processing for weight and Fourier transform processes the current FID as of the last bs transients and display the resulting spectrum on the screen This process can be made automatic because the host computer can detect whenever new data is present on the disk using the parameter wbs which means when block size If you set wos wft and the
555. w Applies only to all systems but type of Autolock software or hardware see above depends on the system e Enter alock y Autolock is activated at the start of acquisition if it has not already been activated Optimizing Autolock Optimizing Autolock uses a sophisticated software algorithm to search the field over the full range of ZO as opposed to hardware simple Autolock captures lock and automatically adjusts lock power and gain but not lock phase Using the Inout Window e Enter alock a or alock s If alock a at the beginning of each experiment each initiation of an acquisition the system searches for the lock signal if necessary and then optimizes lock power and gain but not phase whenever an acquisition is initiated with go ga au or with any macro or menu button using the go ga or au If alock s the same process as alock a occurs but only if the sample has just been changed under computer control and go ga or au is entered when manually ejecting or inserting a sample the software cannot keep track of the action and alock s has no effect If z0 is inactive and you start an autolock operation with either the Lock command or by setting the alock parameter to an appropriate value then autolock searches for the lock signal by changing the lock frequency Figure 36 is an example of a lock frequency acquisition window Be aware that spectrometer frequencies are computed from the lock frequency s
556. wever was designed with the user in mind so it is easy to operate This section briefly describes how you interacts with the data system through three devices the mouse the keyboard and the display monitor Chapter 2 VNMR Basics contains a detailed description of the user interface and VNMR display VNMR Software The host computer for the spectrometer is a Sun Microsystems workstation that runs the Varian NMR software program called VNMR The VNMR software package supports data acquisition processing display and data analysis for the entire range of applications liquids pulsed field gradients solids and imaging VNMR is available in three versions The VnmrX version is used if the Sun is running OpenWindows or the Common Desktop Environment CDE windowing environment both are based on the X Window System This version allows remote operation from other workstations X terminals or personal computers such as a PC or a Macintosh Spectrometer status can be monitored data processed during acquisition shims adjusted and new experiments queued from a remote location e The Vnmrl version is available for workstations from IBM and the VnmrSGI version is intended for Silicon Graphics workstations VnmrI and VnmrSGI have essentially the same user capabilities look and feel of the VnmrX version 01 999083 00 A1298 Getting Started VNMR 6 1B 25 Chapter 1 Overview of Varian NUR 26 A YN TYINOVA 500 Syst
557. window then click on the Connect button in the window when it appears 2 Inthe SAMPLE menu click on the eject button Manual Ejection Applies to systems without spin control hardware It is used only in emergencies on other systems e Press the black button on the top of the left leg of the magnet Getting Started VNMR 6 1B 01 999083 00 A1298 6 2 Ejecting and Inserting the Sample To Insert a Sample Without a Sample Changer When inserting a sample the sample tube gradually lowers down the upper barrel under computer control After a five second delay the bearing air is turned off momentarily allowing the turbine to seat properly The two stage sample insertion operation is provided for safety reasons particularly when working with the 5 mm upper barrel which uses smaller turbines Because the tube itself is used as the bearing surface in this barrel the tube must drop down the barrel slowly enough to avoid breaking when contact is made with the conical guide The second stage drop then permits the tube to slide into the bearing cylinder Operation using the larger upper barrel which can hold 5 10 and 16 mm tubes is less susceptible to these problems because the turbine makes initial contact and alignment before the sample tube encounters any close tolerance Using the Inout Window Applies to all systems if the optional spin control hardware is installed 1 Perform a sample ejection even if no sample is in the magne
558. x wc2max and maxpen are global and have an effect on all experiments exp1 through exp 9 simultaneously wcmax wc2max and maxpen are set up during the plotter configuration to certain values but can be changed by the user Certain maximum plotter values as listed below cannot be exceeded The following Hewlett Packard pen plotters are supported Plotter Type Paper Size Code DraftMaster ABCDE DraftMaster_A etc DraftPro C D DraftPro_C DraftPro_D HP 7475A B HP7475A HP 7550A A B HP7550A8 HP7550A The following Hewlett Packard and Postscript raster printers which can effectively act as plotters are supported Printer Type Paper Size Dots inch Code LaserJet Plus 11x8 150 300 LaserJet_150 LaserJet_300 QuietJet Plus 14x11 96 192 QuietJet_96 QuietJet_192 ThinkJet 8x11 96 192 ThinkJet_96 ThinkJet_192 01 999083 00 A1298 Getting Started VWMR6 1B 255 Chapter 9 Display Plotting and Printing Printer Type Paper Size Dots inch Code Postscript 8x11 PS_A Postscript 11x8 PS_AR Default configuration and maximum values for plotters and printers are the following Plotter Configuration Values Maximum Plotter Values Code wcmax wc2max maxpen wcmax wc2max maxpen HP7475A 400 210 6 400 210 6 HP7550A8 250 155 8 250 155 8 HP7550A 400 210 8 400 210 8 DeskJet_300 200 140 1 200 140 1 DeskJet_30R 240 180 1 240 180 1 DraftPro_C 520 350 8 520 350 8 DraftPro_D 800 480 8 800 480 8 DraftMaster_A 220 1
559. xt step is to apply a digital filter to the time domain signal or FID to remove signals and noise at frequencies outside the final desired spectral width Digital filters are defined by the filtering algorithm and the 01 999083 00 A1298 Getting Started VWMR6 1B 209 Chapter 7 Acquiring Data 210 number of coefficients for the filter The more coefficients the sharper the filter cutoff however the more complex the filter function and the greater the number of coefficients the longer the calculation time required In the example of oversampling above the digital filter would be used to cut off all frequencies outside the 5 kHz spectral width e The final step is to downsample the data Downsampling sometimes referred to as decimation means reducing the number of data points in the FID to the number actually required for spectral analysis at the chosen spectral width the same number that you would have chosen if you had not used DSP Again referring to the example above the final FID would have 8 Kword data points and a final downsampled spectral width of 5 kHz Types of Digital Filtering The main types of DSP provide digital filtering during the acquisition of data e Inline DSP uses software on the workstation to perform digital filtering and downsampling immediately after each oversampled FID is transferred from the console Only the digitally filtered and downsampled data is written to disk The advantages of the
560. y ct une turns on the 3c transmitter directing 0 5 watts of rf to the probe and tuneof f turns off the transmitter CAUTION Only qualified service personnel should tune the lock channel An incorrectly tuned lock channel can damage equipment and cause erratic results e Onall GEMINI 2000 systems dt une turns on the lock CH transmitter for tuning the lock channel e On all GEMINI 2000 systems the macro sethw tune n is used internally by btune nis 4or 5 ctune n is 2 dtune n is 3 htune nis 1 and tuneoff n is O or 6 set hw is not normally entered by the user directly Getting Started VNMR 6 1B 01 999083 00 A1298 6 6 Tuning the Probe The procedures below are typical in tuning a GEMINI 2000 probe For further information refer to the manual NMR Probes Installation Observe Coil Tuning on MERCURY VX MERCURY BB GEMINI 2000 This example shows how to tune to 13C To tune to another nucleus enter the name of that nucleus instead of C13 in step 1 1 2 W Se A Oy a S Join an appropriate experiment and enter tn C13 su Move the cable from the 3C connector J5302 to the TUNE connector J5402 Move the cable from the 3C connector J5603 on the rear of the magnet leg to the TUNE connector J5604 just above it Enter btune Turn the meter switch to the TUNE position Adjust the TUNE control knob for a mid range reading Turn the observe coil tuning rod until the meter reaches a minimum
561. y greater than 50 turn down the lock power If the lock power is too high the deuterium nuclei become saturated the signal oscillates goes down and then back up and it is difficult to establish lock The correct amount of lock power is difficult to determine but it is helpful to remember that acetone is more easily saturated than most solvents 01 999083 00 A1298 Getting Started VNMR 6 1B 153 Chapter 6 Preparing for an Experiment 154 6 Adjust ZO until the signal changes from a sine wave to an essentially flat line If the solvent is concentrated the line may start to move up on the screen as the lock condition is approached 7 Inthe LOCK menu click the on button The signal should move up and look like the on resonance diagram in Figure 40 If the lock signal displays a dip at the point where it starts or the signal slopes downward incorrect lock phase is the probable cause To adjust phase use the SHIM display because it is much easier to use the thermometer like indicator on this display for phase adjustment Select z0 pwr gn ph from the SHIM menu in the SHIM display FID Spectrum Shimming Windows The FID Spectrum display appears first when B troi ACQUISITION lal the FID button is clicked CLOSE LOCK SHIM LARGE Style 2 from any Acquisition 7116 bits FID Spectrum PANEL Shin IPA window VNMR provides sa _ Single Signal fvg OFF Trace 9 Blo 4 two styles of
562. y invariant with sw as long as maximum oversampling is used The calfa macro has also been modified for used with DSP cal fa now sets alfa to the default value of about 6 us and then adjusts rof2 to set the appropriate timing for 1p 0 If a value of alfa other than the default value is found to be preferable using the above methods use crof2 to adjust acquisition timing for the 1p 0 condition without changing the preferred value of alfa Getting Started VNMR 6 1B 01 999083 00 A1298 7 5 Applying Digital Filtering Postacquisition DSP The software allows postacquisition digital filtering and downsampling to selectively detect aregion of a spectrum The digital filtered and downsampled FID can then be saved to disk The digital filtering and downsampling processes are integrated into the ft and ft2d commands and occur when these commands are executed as specified by the parameters below The digital filtering and downsampling are done just prior to the Fourier transform so all apodization linear prediction solvent suppression etc are done prior to digital filtering Postacquisition digital filtering uses the same algorithm as inline DSP with a transition bandwidth correction enhancement to minimize baseline distortion Application of postacquisition DSP takes the following steps 1 Acquire a data set with sw N final desired sw and np N final desired np dscoef 2 with N the oversampling factor In most situations you
563. y itself e Commands requiring one or more arguments The command svf save an FID file on disk for example requires the input of the name of the FID file The needed argument is enclosed in parentheses using the syntax svf file Because a file name is a text string the file name is required to be enclosed in single quote marks when entered svf export home vnmrl mydatafile Numbers and variables such as parameters do not require the single quotes If two or more arguments are required each argument is separated by a comma e Commands with optional arguments A good example here is ds lt index gt the angled brackets identify optional arguments To display a 1D spectrum the command 01 999083 00 A1298 Getting Started VNMR 6 1B 93 Chapter 5 Using the Command Mode is ds However if a series of spectra have been acquired the number of the spectrum to be displayed can be specified as in the command ds 3 e Interactive commands An interactive command obtains information by asking the operator questions For example when the command dot 1 is entered the system displays a series of prompts that guide the operator in setting up a T experiment Command Entry Commands are entered by typing the name of the command typing the command arguments if appropriate in parentheses and then pressing the Return key There should never be a space between the command name and the left parenthesis e g ds 3 is incorre
564. y screen and the following controls e Five knobs whose gradient assignments are selected by toggle switches e Two identical toggle switches each labeled YES NO e Eight buttons MODE BANK FILE LOAD VIEW STORE DRIFT and C F A small indicator above each button turns green if the button is active The MODE BANK and FILE buttons select the system mode Getting Started VNMR 6 1B 01 999083 00 A1298 6 11 Shimming Using the Ultraenmr Shim System RUN FILE 0 STORE_FILE 56 A counts YES A YES NO I 00000 laleldlelelelele MODE BANK FILE LOAD VIEW STORE DRIFT C F Figure 48 Ultrasnmr Shim System Interface Controls and Display e MODE mode allows the user to reconfigure the system and the display screen by using the toggle switches to select configuration options e BANK mode makes shim gradient control accessible through the knobs In this mode the toggle switches select banks of knob to gradient assignments which are displayed on the display screen directly above the knobs e FILE mode lets the user load from view or store to whichever STORE_FILE file number is selected by the toggle switches These file actions are initiated by the LOAD VIEW or STORE buttons respectively Immediately after any LOAD or STORE operation the RUN_FILE and STORE_FILE file numbers are identical If any changes are subsequently made to the existing gradient DAC values RUN_FILE is reset to 0 The last button on t
565. yntax and then acts on the input Refer to Chapter 5 Using the Command Mode for a detailed description of entering commands and parameters into the input window including editing your input from the keyboard Menu System Buttons Below the input window are two rows of menu system buttons Each row is considered a separate menu Figure 11 shows a typical arrangement of the buttons on a data station on a system configured as a spectrometer an Acqi button appears on the top is the Permanent menu below that is the Main menu which is displayed by clicking on the Main menu button in the Permanent menu Abort Acq Cancel Cmd GLIDE Main Menu Help Flip Resize Workspace Setup Acquire Process Display Analyze File More Figure 11 Menu System Buttons To make a selection in the menu system click on the desired menu button with the left button of the mouse The menu system is organized so that the menu and button you most likely will need is on view but if the button you want is not visible clicking a series of buttons should bring it into view For example one way to exit VNMR is to click on the Exit VNMR button but if the menus displayed on your screen appear the same as shown in Figure 1 the Exit VNMR button is not on view You quickly realize that clicking on the More button in the Main menu makes anew menu appear that includes Exit VNMR as the fourth button labeled as Exit VNMR This means that to exit
566. you can now insert the lineshape sample CHC1 in deuteroacetone for H and dioxane in deuterobenzene for 13C and examine the line shape to make certain that you are close to the original specs especially for the line shape at 0 55 and 0 11 of the total peak height Also examine the height of the spinning sidebands Refer to the Acceptance Testing Procedures manual for the system for measurement methods 01 999083 00 A1298 Getting Started VNMR 6 1B 163 Chapter 6 Preparing for an Experiment 6 11 Shimming Using the Ultraenmr Shim System 164 The Ultraenmr Shims unit is a matrix shim system designed to achieve a high level of sample homogeneity over large sample volumes e g 10 mm diameter to generate more orthogonal shim gradients that are easier to use and to provide this in a more reproducible and stable manner Ultrasnmr Shims are integrated with the Y YJNOVA system and all shim functions are available Select the Ultraenmr Shims from the CONFIG window or use the Ultraenmr Console Data button in the window The Ultrasnmr Shims unit can be connected to either port 2 of the console host CPU or PJ1 of the Magnet Sample Regulation MSR board The MSR connection is preferred If the interface box is present the shims set by the console should be visible in its window but the box should not be used CAUTION if an Ultrasnmr shim system can be controlled from the Acquisition window do not set the shim value beyond 32000 DAC counts
567. ystem or by entering the 1 f command Using the Menu System 1 Click on Main Menu gt File The File menu appears with the following buttons Set Directory File Info Tape Load Data Delete More Return l In the graphics windows is a list of files and directories the directory entries have a slash at the end for example st dpar for the current directory 2 To examine the stdpar or tests standard system parameter sets you need to be in vnmr stdpar or vnmr tests To examine local parameter sets you need to be in the appropriate user directory In either case you are probably not in the directory you want To change directories click on Set Directory The Directory menu appears with the following buttons Change Default Set Default Parent Home Nmr More Return Repeatedly click on Parent until the entry for the top level directory you want appears e g vnmr If you have saved parameter sets in your home directory click on the Home button to immediately display the files there Move down to the subdirectory you want e g st dpar by clicking on the entry for the next subdirectory in the path with the left mouse button so that the entry reverses instead of dark type with a white background the background is dark and the type is white and then clicking on Change Repeat this step until you can view the entries for the directory you want For example for the standard parameter set directory vnmr st
568. zero The second value can be increased for better signal to noise in the phase maps up to about the point where the amplitude of the second profile is half that of the first about 2 3 T gt without radiation damping radiation damping can be severe in water IH However longer d3 values increase the phase excursion and can make it difficult to shim large shim corrections especially Z1 Typical H values are 5 to 30 ms and typical H values are 30 to 200 ms Getting Started VNMR 6 1B 01 999083 00 A1298 6 12 Gradient Autoshimming When reinstalling a probe make sure it is in the same vertical position in the magnet barrel as when the shimmap was made If you are unsure make a new shimmap which typically takes only a few minutes Alternate between z axis gradient shimming and shimming the low order x and y axis shims by other methods e g on lock level The z axis shims account for the majority of sample volume changes changes in height and the x and y shims are relatively insensitive to change in height Evaluate shimming for a particular application since the ideal lineshape may vary with the application The high order shims can sometimes be set off scale during shimming This may occur if the sample is short or if the sample is improperly seated in the probe or if the high order shims are weak In such cases the off scale shim is set to maximum and shimming continues with lower order shims Superior results can be obtained

Getting Started - Center for Structural Biology

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