Getting Started with VnmrJ Liquids NMR · Getting Started with VnmrJ Liquids NMR Varian NMR Spectrometer Systems with VnmrJ Software Pub. No. 01-999150-00, Rev. C0503 Revision history:

Getting Started withVnmrJ Liquids

NMRVarian NMR Spectrometer Systems

with VnmrJ SoftwarePub. No. 01-999150-00, Rev. C0503

Getting Startedwith VnmrJ

Liquids NMRVarian NMR Spectrometer Systems

with VnmrJ SoftwarePub. No. 01-999150-00, Rev. C0503

Getting Started with VnmrJ Liquids NMRVarian NMR Spectrometer Systemswith VnmrJ SoftwarePub. No. 01-999150-00, Rev. C0503

Revision history:A0802 – Beta test releaseA1002 – Updated for VnmrJ 1.1BC0503 – Updated for VnmrJ 1.1C

Applicability of manual:Varian NMR spectrometer systems with VnmrJ 1.1C

Technical contributors: Bayard Fetler, Maj Hedehus, Dan Iverson, He Liu, Chris Price,Evan WilliamsTechnical writer: Everett Schreiber, Dan SteeleTechnical Editor: Dan Steele

Copyright 2003 by Varian, Inc.3120 Hansen Way, Palo Alto, California 943041-800-356-4437http://www.varianinc.comAll rights reserved. Printed in the United States.

The information in this document has been carefully checked and is believed to beentirely reliable. However, no responsibility is assumed for inaccuracies. Statements inthis document are not intended to create any warranty, expressed or implied.Specifications and performance characteristics of the software described in this manualcan be changed at any time without notice. Varian reserves the right to make changes inany products herein to improve reliability, function, or design. Varian does not assumeany liability arising out of the application or use of any product or circuit describedherein; neither does it convey any license under its patent rights nor the rights of others.Inclusion in this document does not imply that any particular feature is standard on theinstrument.

UNITYINOVA, MERCURYplus, MERCURY-VX, MERCURY, Gemini, GEMINI 2000, UNITYplus,UNITY, VXR, XL, VNMR, VnmrS, VnmrX, VnmrI, VnmrV, VnmrSGI, MAGICAL II,AutoLock, AutoShim, AutoPhase, limNET, ASM, and SMS are registered trademarks ortrademarks of Varian, Inc. Sun, Solaris, CDE, Suninstall, Ultra, SPARC, SPARCstation,SunCD, and NFS are registered trademarks or trademarks of Sun Microsystems, Inc. andSPARC International. Oxford is a registered trademark of Oxford Instruments LTD.Ethernet is a registered trademark of Xerox Corporation. VxWORKS and VxWORKSPOWERED are registered trademarks of WindRiver Inc. Other product names in thisdocument are registered trademarks or trademarks of their respective holders.

01-999150-00 C0503 VnmrJ: Gettiing Started with Liquids NMR 4

Table of Contents

Chapter 1. VnmrJ Road Map .......................................................................... 101.1 Menu Bar ..................................................................................................................... 11

Hiding and Showing the Menu Bar .................................................................... 22

1.2 Tool Bar ....................................................................................................................... 22Hiding and Showing the Tool Bar ...................................................................... 22

1.3 Locator ......................................................................................................................... 22

1.4 Holding Pen ................................................................................................................. 23

1.5 Graphics Controls Bar ................................................................................................. 23

1.6 Advanced Function Bar ............................................................................................... 23

1.7 Graphics Canvas .......................................................................................................... 24

1.8 Action Controls ............................................................................................................ 24

1.9 Parameter Panels .......................................................................................................... 25

1.10 Hardware Bar ............................................................................................................. 25Trash Can ............................................................................................................ 25Temp Button ....................................................................................................... 26Spin Button ......................................................................................................... 26Lock Button ........................................................................................................ 26Probe ................................................................................................................... 27Seeing Acquisition Status Details ...................................................................... 27Seeing Remaining Experiment Time .................................................................. 27Seeing a History of Acquisition Messages ......................................................... 28Seeing a History of All Messages ...................................................................... 28Message Display ................................................................................................. 28Hiding and Showing the Hardware Bar .............................................................. 28

Chapter 2. Locator ........................................................................................... 302.1 Locator Interface Elements .......................................................................................... 31

Locator Statements and Menu ............................................................................ 31Navigation in the Locator ................................................................................... 32Locator Groups ................................................................................................... 32Attributes ............................................................................................................ 32

2.2 Using the Locator ......................................................................................................... 33Searches .............................................................................................................. 33Dragging and Dropping Items from the Locator ................................................ 33Editing File Names from the Locator ................................................................. 34

2.3 Locator Statements ....................................................................................................... 34Sort Workspaces ................................................................................................. 34Sort NMR Data ................................................................................................... 34Sort NMR Parameter Files ................................................................................. 35Sort Shimsets ...................................................................................................... 35Sort Command Macros ....................................................................................... 35

Chapter 3. Running 1D and 2D Experiments ................................................ 363.1 Starting VnmrJ ............................................................................................................. 36

3.2 Checklist for Running an NMR Experiment ............................................................... 37

Table of Contents

5 VnmrJ: Gettiing Started with Liquids NMR 01-999150-00 C0503

3.3 Changing the Sample and Loading a Probe File .......................................................... 38Ejecting and Inserting a Sample ......................................................................... 38Loading a Probe File .......................................................................................... 38

3.4 Locking, Setting Spinning Speed, and Adjusting Homogeneity ................................. 39Setting Spinner Speed ......................................................................................... 39Finding Z0 and Establishing Lock ..................................................................... 39Adjusting the Field Homogeneity .................................................................... 40

3.5 Choosing, Loading and Setting Up a 1D Experiment ................................................. 41Menu Method ..................................................................................................... 41Locator Method .................................................................................................. 42Selecting a Solvent ............................................................................................. 42Naming a Sample (optional) ............................................................................... 43Setting Up Experimental Parameters .................................................................. 43Setting the Temperature for VT Control (optional) ............................................ 43Setting Up Auto Process and Plot ...................................................................... 43Setting Up Acquisition and Post Acquisition Actions ....................................... 44

3.6 Acquiring a Spectrum .................................................................................................. 44Menu Method ..................................................................................................... 45Parameter Panel Method ..................................................................................... 45

3.7 Processing and Displaying 1D NMR Data .................................................................. 45Parameter Panel Method ..................................................................................... 45Display Bar Icons ............................................................................................... 46

3.8 Saving the NMR Data (optional) ................................................................................. 46Menu Method ..................................................................................................... 47Parameter Panel Method ..................................................................................... 47

3.9 Plotting the Spectrum (optional) .................................................................................. 47

3.10 Stopping an Experiment ............................................................................................. 48

3.11 Choosing, Loading, and Setting Up a 2D Experiment ............................................... 48Choosing and Loading a 2D Experiment ........................................................... 48Naming the Sample, Selecting the Solvent, Setting VT, and Post Acquisition Events

49Setting Up Experimental Parameters .................................................................. 49Acquiring a Spectrum ......................................................................................... 49Processing 2D NMR Data .................................................................................. 49Saving the 2D Data ............................................................................................. 49Plotting the 2D Spectrum ................................................................................... 49

Chapter 4. Parameters, Data Saving, Template Editor, and Shim Buttons 504.1 Getting New Parameters and Environment Variables .................................................. 50

4.2 Disabling Automatic Data Saving ............................................................................... 50System Settings .................................................................................................. 50Current Experiment ............................................................................................ 51Saving Selected FIDs ......................................................................................... 51

4.3 Using the Template Editor ........................................................................................... 51Hints When Viewing a Panel ........................................................................... 52Commonly Used Panel Items ............................................................................. 52Attributes of Commonly Used Items .................................................................. 52Hints When Editing a Panel ............................................................................... 53

4.4 Using the Shim Buttons ............................................................................................... 53

Table of Contents


Chapter 5. DSP and ECC Utilities .................................................................. 565.1 Hardware Requirements .............................................................................................. 56

5.2 Using the ECC Software .............................................................................................. 56Setting Up the System for ECC .......................................................................... 56Determining the ECC Parameters ...................................................................... 57Updating the Probe File and Enabling ECC ....................................................... 60

5.3 Integrating ECC into Each User Account .................................................................... 60Enabling ECC for Each User Account ............................................................... 61

5.4 Using the Enhanced DSP ............................................................................................. 61

5.5 Shaped Gradients ......................................................................................................... 62

5.6 Decoupling Tests .......................................................................................................... 62

5.7 Utilities ......................................................................................................................... 63

Index .................................................................................................................. 64

List of Figures


List of Figures

Figure 1. VnmrJ Interface (for Experiments) .............................................................................. 10

Figure 2. Array Parameter Window ............................................................................................. 12

Figure 3. Pbox Tool ...................................................................................................................... 14

Figure 4. Plot Designer ................................................................................................................ 14

Figure 5. System Settings Window .............................................................................................. 15

Figure 6. SpinCAD Create New Parameters Window ................................................................. 16

Figure 7. Save Data Setup Window ............................................................................................. 17

Figure 8. Select Devices Window ................................................................................................ 17

Figure 9. Display Options Window ............................................................................................. 18

Figure 10. Import Dialog Window ............................................................................................... 18

Figure 11. Save Custom Locator Statement Window .................................................................. 19

Figure 12. Delete Custom Locator Statement Window ............................................................... 19

Figure 13. Tool Editor .................................................................................................................. 20

Figure 14. SpinCAD Program ..................................................................................................... 21

Figure 15. Edit Panel ................................................................................................................... 21

Figure 16. Graphics Canvas ......................................................................................................... 24

Figure 17. Process Panel Buttons ................................................................................................ 24

Figure 18. Parameter Panel Tabs ................................................................................................. 25

Figure 19. Trash Can Mode ......................................................................................................... 26

Figure 20. Probe Window ............................................................................................................ 27

Figure 21. Acquisition Status Window ........................................................................................ 27

Figure 22. Locator Statement ....................................................................................................... 31

Figure 23. Locator Groups Menu ................................................................................................ 32

Figure 24. Generic Locator Statement ......................................................................................... 35

Figure 25. VnmrJ in CDE Tool Bar ............................................................................................. 36

Figure 26. Setup Panel ................................................................................................................. 38

Figure 27. Spin/Temp Panel ......................................................................................................... 39

Figure 28. Finding Lock .............................................................................................................. 39

Figure 29. Lock Panel .................................................................................................................. 40

Figure 30. Lock Options .............................................................................................................. 40

Figure 31. Shim Panel .................................................................................................................. 41

Figure 32. Experiments Accessed from the Menu Bar ................................................................ 42

Figure 33. Loading an Experiment from the Locator .................................................................. 42

Figure 34. Acquire Panel - Default Tab ....................................................................................... 43

Figure 35. Process when done Button ......................................................................................... 43

Figure 36. Flags Panel ................................................................................................................. 44

Figure 37. Future Actions Panel .................................................................................................. 44

Figure 38. Default H1 Panel ........................................................................................................ 45

Figure 39. Process Panel .............................................................................................................. 45

Figure 40. Display Icons Bar ....................................................................................................... 46

Figure 41. Save Data Setup Window ........................................................................................... 47

Figure 42. Plotting the Spectrum ................................................................................................. 47

Figure 43. 2D Experiments Accessed from the Menu Bar .......................................................... 48

List of Figures


Figure 44. System Settings Window ............................................................................................ 51

Figure 45. Template Editor .......................................................................................................... 51

Figure 46. Acquire Tab - Acquisition panel ................................................................................. 58

Figure 47. Acquire Tab - ECC panel ........................................................................................... 58

Figure 48. Recovery with No Eddy Current Compensation ........................................................ 59

Figure 49. Calculated Fitting of the Data .................................................................................... 59

List of Tables


List of Tables

Table 1. List of Commonly Used Items in a Panel ....................................................................... 52

Table 2. Attributes of Commonly Used Items .............................................................................. 52

Table 3. ECC Parameter and Ranges ............................................................................................ 57


Chapter 1. VnmrJ Road Map

The VnmrJ interface for liquids experiments is shown in Figure 1. The interface contains10 interaction areas. This chapter describes each of those areas.

• 1.1, “Menu Bar,” on page 11

• 1.2, “Tool Bar,” on page 22

• 1.3, “Locator,” on page 22

• 1.4, “Holding Pen,” on page 23

• 1.5, “Graphics Controls Bar,” on page 23

• 1.6, “Advanced Function Bar,” on page 23

• 1.7, “Graphics Canvas,” on page 24

• 1.8, “Action Controls,” on page 24

• 1.9, “Parameter Panels,” on page 25

• 1.10, “Hardware Bar,” on page 25

Figure 1. VnmrJ Interface (for Experiments)

1. Menu bar

2. Tool bar

3. Locator

6. Advanced function window

7. Graphics canvas

8. Action controls

9. Parameter panels

10. Hardware bar

4. Holding pen

5. Graphiccontrols



1.1 Menu Bar

The menu bar sits along the top of the interface. Its function is twofold.

• The first function of the menu bar is to give you, as a new user, access to operationsneeded to acquire, process, and plot a spectrum. As you continue to use the interfaceand become more expert at using VnmrJ, you might have less use for the menu bar.

• The second function of the menu bar is to provide access to little-used features, settingpreferences, and other things that are rarely done and can be found in the Utilities, Edit,and Help menus.

The following sections describe the options in the main menu.

Experiments

This menu contains a list of available pulse sequences.

Solvent

This menu contains a list of available solvents.

Acquisition

This menu enables you to perform the following acquisition-related operations.

Parameter arrays...

This menu choice opens the Array Parameter tool shown in Figure 2. It can be used to setarrayed parameters.

The top panel in the window is a table of currently arrayed parameters. The ParameterName, Description, array Size, array Order and On/Off status are displayed. You can addparameters with the New Array button and remove parameters with UnArray. You canturn on or off an arrayed parameter by double-clicking On/Off. You can edit the array order(except for implicit arrays ni, ni2, etc.) to enable nested or parallel arrays. Onlyparameters of the same array size can be parallel or have the same array order.

Click to hide or show menu bar

1.1 Menu Bar


You can highlight the array parametertable one row at a time with singleclicks. The values of the highlightedarray parameter (Active Param) aredisplayed in a table in the middle panel,along with editable entries for ArraySize, First Value, Increment, and LastValue. You can also edit the parametervalues. There are also buttons forincrement style (Inc. Style), linear orexponential, and randomizing(Randomize) the order of array values.

The Current Value of the parameter isdisplayed above the array parametervalues. You can select this value fromthe arrayed values or you can manuallychange it. When the parameter isunarrayed or turned off, it is set to thecurrent value.

Abandon restores the original state ofthe window (the state it was in when itopened) and closes the window. Closekeeps the changes and closes the window.

Show Pulse Sequence

Use this function to show a pulse sequence (comparable to the VNMR command dps).

Experiment Time

Use this function to show the total acquisition time for a pulse sequence (comparable to theVNMR command time).

Set up Hardware

Use this function to initialize the hardware with values present in the current parameter set(su).

Set Shims Into Hardware

Use this function to load the current shim values into the hardware (comparable to theVNMR command load='y' su).

Acquire Data

Use this function to acquire data without performing any data processing (comparable tothe VNMR command go).

Acquire and WFT

Use this function to acquire data and process it with a 1D weighted Fourier transform(comparable to the VNMR command ga).

Acquire and Process

Use this function to acquire data and perform user-defined processing (comparable to theVNMR command au).

Figure 2. Array Parameter Window



Abort Acquisition

Use this function to abort an acquisition (comparable to the VNMR command aa).

Pause Acquisition

Use this function to pause an acquisition at the next block size (comparable to the VNMRcommand sa).

Resume Acquisition

Use this function to resume a paused acquisition (comparable to the VNMR command ra).

Do Gradient Shimming

Use this function to perform gradient shimming. Gradient shimming must be set up on yoursystem before it can be performed. See Utilities -> Set Up Gradient Shimming.

Process

This menu has the following choices to perform processing functions.

• Process and Display 1D performs a 1D Fourier transform and shows a spectrum.

• Full Process performs automatic processing for 1D and 2D data and displays theresults.

• 1D FDM opens a tool that performs the Filter Diagonalization Method of processing1D data (optional).

• Drift Correct Spectrum performs a 1D drift correction on a spectrum.

• Automatically Set Integrals automatically defines the integral regions for a 1Dspectrum.

• Baseline Correct performs a 1D baseline correction on a spectrum.

• Set Spectral Width between Cursors moves the spectral window to the windowdefined by the cursors.

• Set Transmitter at Cursor moves the carrier frequency to the current cursor position.

• Pbox opens the tool shown in Figure 3. Use Pbox to generate shape files for RF andgradients. For more information about Pbox, see the section “Pandora’s Box” inchapter 7 of the User Guide: Liquids manual.

• Full Process 2D performs automatic processing of 2D data and displays the results.

• Process 2D (Individual Steps) opens a menu for 2D processing steps.

• Add and Subtract 1D Data opens a menu for adding and subtracting 1D spectra.

Clear Buffer and Add Current Spectrum clears the buffer and adds the currentspectrum.

Add Second Spectrum Into Buffer adds a second spectrum into the buffer for addingand subtracting.

Display

This menu enables you to control how data is displayed in the graphics canvas.

• Display Multiple Spectra Horizontally presents a horizontal view of multiplespectra.

• Display Multiple Spectra with Labels presents a view of multiple spectra withidentifying LABELS.

1.1 Menu Bar


• Display Multiple Spectra Vertically presents a vertical view of multiple spectra.

• Increase Vertical Separation by 20% increases the vertical separation betweenmultiple spectra by 20%.

• Decrease Vertical Separation by 20% decreases the vertical separation betweenmultiple spectra by 20%.

• Plot result automatically plots the spectrum.

• Create a Plot Design opens the Plot Designer tool shown in Figure 4. Plot Designerenables you to see and design a plot before you print it. For more information aboutPlot Designer, see the section “Plot Designer” in chapter 9 of the VNMR GettingStarted manual.

Figure 3. Pbox Tool

Figure 4. Plot Designer



• Create an Inset of the Current Display opens a menu for making an inset display,with the following submenus:

Save Current Display Parameters saves the current display parameters.

Plot Current Display before Making Inset plots the current display before makingan inset.

Make Inset creates an inset spectrum.

Plot Inset and Return Original Display plots an inset spectrum and restores theoriginal display.

Utilities

This menu has the following choices to perform system utilities functions. They are usefulfor setting the system configuration and interface settings.

• System Settings... opens the System Settings window, shown in Figure 5, whichenables you to set system parameters. It also has a System config button or checkboxthat displays the system configuration.

• Create SpinCAD Seq Parameters makes pulse sequence parameters.

Creating Pulse Sequence Parameters in VnmrJ

To create pulse sequence parameters, change the pulse sequence name in the currentparameter set, then click on the Utilities menu. From Utilities, choose CreateSpinCAD Seq Parameters, which also compiles the pulse sequence if necessary.

Figure 5. System Settings Window

1.1 Menu Bar


The Parameter Creation Process

After you begin theparameter creation processfrom either SpinCAD orVnmrJ, SpinCAD parsesthe pulse sequence andlooks for new parametersthat are not in the currentparameter set. It forms a listof new parameters that donot exist and presents thelist with other informationin a pop-up window, shownin Figure 6.

Correcting Parameters

SpinCAD attempts toascertain the type of theparameter from the usagebut might not always beaccurate. Various detailsabout the new parametersare shown: name,parameter type (such aspulse, delay, string etc),maximum limit, minimumlimit, increment size, andinitial value. If the type of the parameter is incorrect, you can easily correct it by usingthe Type pull-down menu. In such a case, you must also change the other field forlimits and initial values. If you do not want to create a parameter, set Type toIGNORE.

Constructing VnmrJ Parameter Panels

Before you click OK to start the parameter creation process, set the panel template tobe used as a starting point for making the Acquire panel for the new pulse sequence.VnmrJ parameter panels are constructed by adding a panel tab (SpinCAD PS) to theAcquire panel group. You can model the panels after any other template pulsesequence that has a layout directory.

To construct a panel, enter the name of the starting template pulse sequence in the entryfield for Start Acquire Panel from template: If you do not specify another templatepulse sequence, SpinCAD uses the default template.

If you want to cancel the entire process so that no parameters or panels are created,click Cancel. Otherwise, click OK at the bottom of the pop-up panel.

• Create a Workspace makes a new workspace of the next available workspacenumber.

• Set Up Gradient Shimming loads the pulse sequence and panels for making a shimmap for gradient shimming.

• Standard Calibration Experiments has the following submenus:

Calibrate Probe opens a window for running a series of experiments to calibrate theprobe.

Start Autotest opens a window for starting the system autotest.

Autotest settings opens a window for showing or setting parameters used in systemAutotest.

Figure 6. SpinCAD Create New Parameters Window



• Save data setup opens the window shown in Figure 7 for configuring automatic datasaving settings (svfdir and svfname parameters).

• Save data saves the current FID with a filename constructed from the svfdir andsvfname parameters.

• Printers... opens a window, shown in Figure 8, for setting printers and plotters frompreviously defined printers and plotters. For information about connecting printers, seethe manual Host Computer Setup for VnmrJ.

Figure 7. Save Data Setup Window

Figure 8. Select Devices Window

1.1 Menu Bar


• Display options... opens a window, shown in Figure 9, for setting symbolic colors andfonts in the interface.

• Update locator has submenus for updating various parts of the Locator.

• Import files to locator opens the window shown in Figure 10 for importing files tothe Locator.

• Save custom locator statement opens the window shown in Figure 11 for saving thecurrent Locator view.

Figure 9. Display Options Window

Figure 10. Import Dialog Window



• Delete custom locator statement opens thewindow shown in Figure 12 for deleting customLocator statements.

• Exit closes the VnmrJ interface.

Figure 11. Save Custom Locator Statement Window

Figure 12. Delete CustomLocator Statement Window

1.1 Menu Bar


Edit

This option enables you to edit objects.

• Tool Bar... opens the Tools Editor, shown in Figure 13, for editing the Tool Bar.

To create a new tool bar button, drag the New Tool button onto the tool bar.

To edit a button that already exists, click on the button in the tool bar

To select an icon for a button, click on an icon in the scrolling list.

The Command entry contains the command or macro executed when the button isclicked.

The Set Command entry contains the command or macro executed when the buttonis held down for 5 seconds.

The Tool Label entry contains the text label for the button if an icon is not used.

The Tool Tip entry contains the text for the tool tip.

Click on the Edit button to perform the following actions:

Return to initial state restores the initial state of the tool bar.

Make a snapshot creates a snapshot of the current state of the tool bar.

Return to snapshot restores the snapshot state of the tool bar.

Return to system defaults restores the tool bar to the system defaults.

To exit the Tool Editor and save your changes, click on the Close button.

To exit the Tool Editor without saving your changes, click on Abandon.

• Pulse Sequence... opens the SpinCAD program, shown in Figure 14, for editingSpinCAD pulse sequences. Click on Sequence, then Exit, abandoning unsaved

Figure 13. Tool Editor



changes to exit the program without saving a new pulse sequence. For moreinformation about this program, see the SpinCAD manual.

• Parameter Panels... opens the Edit panel, shown in Figure 15, for editing the VnmrJparameter panels. In the window you can see the commands performed by the variouswidgets in the template, and the parameters they depend upon. Double-click on awidget to view its properties. Click on the Close button at the bottom of the windowto exit the editor. For more information about the template editor, see section 4.3,“Using the Template Editor,” on page 51.

Help

This menu contains the VnmrJ online help manuals.

Figure 14. SpinCAD Program

Figure 15. Edit Panel

1.2 Tool Bar


Hiding and Showing the Menu Bar

To hide the menu bar, click the left mouse button on the arrowhead in the menu bar. Themenu bar closes and the arrowhead changes to a rectangular box. To show the menu bar,click the left mouse button on the box.

1.2 Tool Bar

The tool bar is directly below the menu bar. These buttons provide quick access to commonfunctions. The following tools are the default available in this tool bar:

• save the current locator data sort display. To save the display, click on oneof the buttons and press the mouse button for five seconds. To return to the saveddisplay, click again on the button.

• save the current screen layout (graphics, a parameter panel, locator sizes).To save the layout, click on one of the buttons and press the mouse button for fiveseconds. To return to the saved layout, click again on the button.

• cancels commands.

• stops acquisition.

Hiding and Showing the Tool Bar

To hide the tool bar, click the left mouse button on the arrowhead in the menu bar. The toolbar closes and the arrowhead changes to a rectangular box. To show the tool bar, click theleft mouse button on the box.

1.3 LocatorThe Locator provides access to data sets,experiments, shim sets, and commands. For moreinformation about the Locator, see Chapter 2,“Locator,” page 30.

Clicking the magnifying glass with the left mousebutton opens a menu of searches. Selecting onechanges the search sentence (next to the magnifyingglass). The results of the search are displayed in thelist. Those items in the white part of the list satisfy thesearch sentence. Those in the gray part do not. Foreach item that is found by the search, three attributesare displayed. These correspond to the three columnsin the list. Clicking on the attribute name at the top of the list with the left mouse buttonopens a menu of attribute choices.

Clicking on an item in the Locator list selects that item. That item can then be dragged tothe graphic area or the parameter panel area to cause the appropriate action. For example,



dragging a data set to the graphic canvas retrieves that data set into the current workspace(experiment) and displays the spectrum. Dragging a workspace to the graphic canvascauses that workspace (experiment) to be joined with the graphic area. Double-clicking onan item performs the same action as dragging the item to the graphics canvas.

1.4 Holding PenUse the holding pen to store commonly accessed items from the Locator. To add an itemfrom the Locator to the holding pen, select (click on) the item and drag it into the holdingpen. The item remains in the holding pen even if the Locator view changes.

Selecting an item or dragging it from the holding pen performs the same actions as selectingan item or dragging it from the Locator.

You can remove an item from the holding pen by selecting it and dragging it to the trashcan.

1.5 Graphics Controls BarThe graphics control bar is to the left of the graphics canvas. Use the buttonsin the bar to control the interactive display in the graphics canvas. When aspectrum or FID is displayed, these buttons enable you to performinteractive actions on the spectrum or FID. These actions include integraldisplays, phasing, threshold adjustments, and other actions. These buttonschange depending on the type of data that is displayed in the graphicscanvas.

1.6 Advanced Function Bar

Clicking on the button in the advanced function bar opens a command entryfield and a text output field. Open the fields by clicking once on the button or by clickingon the button with the mouse, then holding and dragging the button down. Any commandor macro can be entered into this command window. Error and information messages arecurrently displayed in the scrolling text window above the command line. Commandhistory can be shown if you click on the arrow with the left mouse button. Select acommand from the command history by highlighting it and pressing Return to execute it.

Click on and drag

1.7 Graphics Canvas


1.7 Graphics CanvasThis portion of VnmrJ, shown in Figure 16, is used to display and interact with graphic andtext information. This is very similar to the graphics area in previous versions of VNMR.

• Resize the graphics canvas by clicking on the canvas boundary line with the left mouse(the cursor changes form) and dragging the line (e.g., between graphics and parametertemplates or between graphics and Locator).

• Toggle the graphics canvas to show or hide the parameter templates area by clickingthe small arrow between the graphics canvas and templates with the mouse button.

• Flip the parameter templates behind the graphics canvas without resizing the graphicscanvas by clicking the small arrow with the middle mouse button.

• Toggle the parameter area to maximum height required to remove the parametertemplate scroll bar by clicking on the small arrow with the right mouse button.

• Toggle the graphics canvas to show or hide the Locator area by clicking the smallarrow between the graphics canvas and Locator with the left mouse button.

• Flip the Locator area behind the graphics canvas without resizing the graphics canvasby clicking on the small arrow with the middle mouse button.

• Toggle the Locator area to maximum by clicking on the small arrow with the rightmouse button.

1.8 Action ControlsTo the right of the parameter panel selection tabs, shown in Figure 18, are series of buttonsthat change, depending on the currently displayed panel. For example, the buttons shownin Figure 17 appear when you select the Process panel.

Figure 16. Graphics Canvas

Figure 17. Process Panel Buttons



1.9 Parameter PanelsSelect parameter panels by clicking on the tabs, shown in Figure 18, across the top of thepanels.

Use the Setup panel to perform basic functions for setting up a new sample and preparingto run experiments. This panel mimics many of the features of the VNMR acqi program.

Use the Acquire panel to set acquisition parameters.

Use the Process panel to adjust processing parameters and process data.

Within each panel, there is a vertical list of tabs to help navigate among the parameters.These tabs are similar to the tcl-dg tabs in VNMR 6.1B.

To edit a parameter panel, select Edit in the main menu, then select Parameter Template.This template editor is also useful for viewing commands and parameters that are used inthe panels. For more information about the template editor, see section 4.3, “Using theTemplate Editor,” on page 51.

1.10 Hardware Bar

The left portion of the hardware bar contains the trash can and hardware monitor. The rightportion reflects the current state of the acquisition system and system messages.

Trash CanDragging an item to the trash can from the Locator or other area generally removes theitem and adds it to the trash can.

Double-clicking on the trash can enables you to view items in the trash can area. In thismode, you can restore objects from the trash can by selecting them and then clicking

Figure 18. Parameter Panel Tabs

Acquisition status display

Acquisition message history

Message history

Message display

1.10 Hardware Bar


the Restore items button. In Figure 19, the trash can is empty. To exit this mode,double-click on the trash can.

WARNING: Emptying the trash can deletes data from the disk.

Temp Button

Click on this button to see a history of the sample temperature.

Spin Button

Click on this button to see a history of the sample spin rate.

Lock Button

Click on this button to see a history of the sample lock level.

Figure 19. Trash Can Mode



Probe

Click on this button to open the Probewindow shown in Figure 20. Use it toperform the following actions:

• To select a probe from the list ofavailable probes, click on the SelectProbe menu.

• To open the probe tuning (Q tune)window, click on Tune sweep. Do notuse this for normal probe tuning.

• To edit a probe entry, click on EditProbe.

• To open a window to edit probeattributes for a particular nucleus,click on the nucleus menu.

• To select initial parameter attributesfor adding a probe, click on theParameters menu.

• To add a new probe, enter a new probe name and then click on Add Probe.

• To remove a probe name from the list of available probes, enter the probe name andthen click on Delete probe.

• To open a window for running a series of experiments to calibrate the probe, click onAutocalibrate Probe.

Seeing Acquisition Status Details

To open a window showing acquisition status details, as shown in Figure 21, click onthe icon. To close the window, click on the icon again.

Seeing Remaining Experiment Time

The acquisition status bar is always visible in the hardware bar.During an acquisition, the bar shows the remaining experiment time as a thermometerdisplay. Click the right mouse button inside the bar to change the displayed text.

Figure 20. Probe Window

Figure 21. Acquisition Status Window

1.10 Hardware Bar


Seeing a History of Acquisition Messages

To show acquisition message history, click on the icon. To close the window, click onthe icon again. Click the right mouse button within the scrolling message window to changethe text view options.

Seeing a History of All Messages

To show a history of all messages, click on the icon. To close the window, click on theicon again. Click the right mouse button within the scrolling message window to changethe text view options.

Message Display

The message display shows the lastmessage that occurred. Messages can be informational, a warning, or an error message.

Hiding and Showing the Hardware Bar

To hide or show the hardware bar, click on the arrow icon to the left of the trashcan with the left mouse button.




Chapter 2. Locator

Sections in this chapter:

• 2.1, “Locator Interface Elements,” on page 31

• 2.2, “Using the Locator,” on page 33

• 2.3, “Locator Statements,” on page 34

The Locator, shown below, is a database browser that provides access to data sets,experiments, shim sets, commands, and other things.

The Locator is designed to enable fast access to information on all or part of your diskenvironment. The scope of the Locator’s actions is determined by your administrator whowill globally and locally set the scope of the Locator.

The Locator works similar to a directory or file manager, but uses minimal filtering of theinformation. Rather than only showing the files that satisfy the requirements, it shows twoor three lists of information. With two lists, one list shows the items (or objects) that satisfy

Locator

Chapter 2. Locator


all terms of the search while the other list shows the objects that do not. Where some termshave a boolean relationship, the Locator shows three lists:

• Objects that meet all criteria

• Some of the boolean terms met

• Remaining objects

The determination of which of these lists it are shown is determined by the construction ofthe underlying Locator statement.

Within each list, the Locator displays three attributes for each object. The displayedattributes need not necessarily be those in the Locator statement. Any one of the attributescan be designated as the sort attribute, in which case the objects in each list are sorted bythe value each has for this attribute.

2.1 Locator Interface Elements

Locator Statements and Menu

At the top of the Locator is a magnifying glass and the current Locator statement, as shownin Figure 22.

Clicking on the magnifying glass opens a menu of currently available Locator statements.This menu includes both statements provided by Varian, Inc. and those customized andsaved by the user.

Statements are Locator sentences in which a number of words or phrases are colored andunderlined in a manner reminiscent of links in a web page. Each link hides a menu of

Current Locatorstatement

Statementnavigationarrows

Operationalicons

Locatorstatementmenu

Attribute header bar

Figure 22. Locator Statement

2.1 Locator Interface Elements


choices, of which the currently displayed phrase is one. The choices available vary with thetypes of data currently known to the Locator.

Navigation in the Locator

Below the Locator statement is a pair of arrows (statement navigation arrows), whichenable you to move forward and back through past Locator operations, applying each to thecurrent Locator environment. Thus a set of Locator statements can be rapidly applied in achanging environment.

Locator Groups

To the right of the arrows is the tag icon for adding and removing Locatorgroups. Use this tool to define (tag) new user groups and apply those to existingor new objects, for example, to tag FIDs with a given project name. Clicking on

this icon opens a pop-up menu, shown in Figure 23.

Using Locator Groups

To use Locator groups, do the following steps:

1. Select a statement from the Locator statement list (described in section 2.3, “LocatorStatements,” on page 34) that sorts on groups, such as Sort NMR Data by group.

2. Select the group that you want to see from the pull-down menu in the statement.

Attributes

Below the icons is the attribute header bar. This bar enables you to select the attributesdisplayed and to arrange the objects in each list in a number of ways.

The padlock enables you to lock an object against archival (this feature is not yetimplemented).

The next three fields are the currently displayed attributes. You can change any columnsimply by clicking on the attribute label and selecting a different attribute from the drop-

Figure 23. Locator Groups Menu

Chapter 2. Locator


down list. Below each label is its “Hot zone”. The hot zone can be either a block or atriangle. Only one attribute has a triangle and it is the attribute that serves as the sort termfor each list.

• Click on a block to change the sort attributes.

• Click on the triangle to reverse the sort order.

The boundaries between the attribute labels are adjustable. Simply place the mouse cursoron the boundary you wish to adjust. When you get the adjust cursor, click and drag theboundary to its new position, and release.

Objects in the Locator are available for a number of actions. Currently, a single click selectsan object. The selected object can then be dragged to another part of VnmrJ in which casethe action taken will depend on the type of object and where the object is dropped.Alternatively a double click on an object will cause the most likely action to occur. Theseactions will be discussed shortly.

The value of an attribute might be longer than the width of the column in the Locator. Whenthe mouse cursor rests on an attribute value, a tool tip appears for a period of time. The tooltip contains the full value of the attribute.

2.2 Using the LocatorUse the mouse to select or drag-and-drop items in the Locator interface.

Searches

Clicking the magnifying glass with the left mouse button brings up a menu of searches.Selecting one changes the search sentence displayed at the top of the Locator. The resultsof the search is displayed in the list. Those items in the white part of the list satisfy thesearch sentence. Those in the gray part do not. For each item that is found by the search,three attributes are displayed. These correspond to the three columns in the list. Clickingon the attribute name at the top of the list with the left mouse button brings up a menu ofattribute choices.

Dragging and Dropping Items from the Locator

Clicking on an item in the Locator list selects that item. That item can then be dragged tothe graphic area or the parameter panel area to cause the appropriate action. For example,dragging a data set to the graphic area retrieves that data set into the current workspace(experiment) and (optionally) displays the spectrum. Dragging a workspace to the graphicarea selects that workspace (experiment). Dragging on an object causes the most likelyaction to occur.

An item can be dragged from the Locator and dropped into the holding pen. The item isthen available for further selection no matter what Locator statements are active. One suchexample might be when you use the Locator to inspect the available shim sets. You can thenselect the current best set and put this into the holding pen. This set of shims is thenimmediately available.

Dragging and dropping an item has an action appropriate to the context. In many cases thesame effect can be obtained by double-clicking on an object. Some examples are:

• Dragging a protocol experiment into the graphics canvas loads the experiment.

2.3 Locator Statements


• Dragging a FID from NMR data retrieves the FID. The process macro can also beinvoked so that the FID is transformed.

• Double-clicking a workspace joins that workspace. Dragging and dropping aworkspace into the graphics area also joins the workspace (jexp).

• Double-clicking a parameter set loads that set in the current workspace, as will adragging and dropping a parameter set.

• Double-clicking a shim set loads the shims. Dragging and dropping a shim set to thecurrent shim buttons also loads the shims into acquisition.

• Dragging either data or shims and dropping them in the trash can (in the lower leftportion of the hardware bar) moves the item to the trash can. You can retrieve an objectfrom the trash can by double-clicking on the trash can, selecting it, and then clickingthe Restore items button.

Editing File Names from the Locator

When a new file is added to the locator from within VnmrJ, the new item appears in itsappropriate spot in the Locator, and it appears in green at the top of the locator window. Ifone of the columns in the Locator is “filename,” you click on the green file name andchanged it.

After changing the file name, press Return or click on another line to remove the old namefrom the Locator and add the new one. The Locator redisplays to show the new name.

2.3 Locator StatementsWe supply a number of Locator statements with VnmrJ. You can add to or edit thesestatements in the following ways:

• Save the current Locator statement by clicking on Utilities in the main menu, thenSave Custom Locator Statement. In the Custom Locator Statement pop-up window,enter a name for the statement.

• To delete a Locator statement, click on Utilities, then Delete Custom LocatorStatement. A Custom Locator Statement Removal window appears. Select thestatement from the list in the window, then click on Delete to remove it or Cancel toexit the window without removing the statement.

• Sort Protocols Entries show the know protocol experiments. Double click on theprotocol to execute the associated macro,

Sort Workspaces

You can sort all workspaces in numeric order or selectively sort workspaces by groups.Click on the tag icon to create locator groups. Double-click on a workspace to jointhe workspace (this action is comparable to the VNMR command jexp).

Sort NMR Data

Entries show the known NMR data sets, but differ in the actual format of the statement aswell as the initial set of attributes shown. The most comprehensive statement is the last one,by user defined attributes and date (this is also the one that is least likely to be used, butit is discussed here to explore the scope of the data statements).

Chapter 2. Locator


The generic statement is shown in Figure 24.

There are two separate underlined choices inthis statement: Std1D and on any date.

Clicking on either of the underlined phrasesproduces a drop-down menu of the choices inthis position. The menus are environmentsensitive so they will not display choices that do not exist.

The logic of this statement is of the form:

Show attributes A and B of type C with additional limitations.

First, the additional limitations phrases enable you to select the owner of the data. Currentlythis selection is determined by the administrator at the time a directory is made available tothe Locator. In in the future, it will become a more rich criterion.

Second, the additional limitations enable you to reorder by date. There are various datesassociated with data, for example, the time started or the time saved. You can specify thesedate fields several ways, for example, since a certain date, by changing on any date tosince.

You can alter the date by using the left or right arrows to decrease or increase the date byone day each click.

All other statements supplied by us are simpler than the generic one. If there are certainstatements that you use frequently, these can be promoted to the top of the menu simply bysaving them again as your local variants.

Sort NMR Parameter Files

The statements in this category show the list of NMR parameter sets. One major categoryof parameter set is My Param Files. You can also select the statements Test Files and byuser defined attributes to do other selective searches. After you select a category, theLocator statement changes, e.g., Test Files.

Sort Shimsets

The statements in this category enable you to access the shim sets that you have saved. Notethat the shim sets can be saved with a descriptive shim name provided by you using theSave Shims button in the Shim panel.

Sort Command Macros

The generic statement in this category enables you to find a VnmrJ command or macrobased on its attributes. The Locator enables you to reorder commands and macros by anumber of attributes. Once you find the command that you wish to use, a double click willexecute it.

Figure 24. Generic Locator Statement


Chapter 3. Running 1D and 2D Experiments


3.1, “Starting VnmrJ,” this page

3.2, “Checklist for Running an NMR Experiment,” on page 37

3.3, “Changing the Sample and Loading a Probe File,” on page 38

3.4, “Locking, Setting Spinning Speed, and Adjusting Homogeneity,” on page 39

3.5, “Choosing, Loading and Setting Up a 1D Experiment,” on page 41

3.6, “Acquiring a Spectrum,” on page 44

3.7, “Processing and Displaying 1D NMR Data,” on page 45

3.8, “Saving the NMR Data (optional),” on page 46

3.9, “Plotting the Spectrum (optional),” on page 47

3.10, “Stopping an Experiment,” on page 48

3.11, “Choosing, Loading, and Setting Up a 2D Experiment,” on page 48

This chapter is a basic introduction on how to use VnmrJ to run 1D and 2D NMR liquidsexperiments. These instructions assume the probe is installed in the magnet, tuned, and aprobe file with probe calibrations exists. Instructions for these procedures are found in theVNMR manual Getting Started. For more detailed information on running NMRexperiments, see the chapter “Preparing for an Experiment” in the VNMR manual GettingStarted.

3.1 Starting VnmrJTo begin running an experiment, start VnmrJ. There are two ways to start VnmrJ:

• In CDE, click on the VnmrJ icon in the CDE tool bar, shown in Figure 25.

• In CDE, open a host window and enter the following command:

user1> vnmrj

Figure 25. VnmrJ in CDE Tool Bar



3.2 Checklist for Running an NMR ExperimentBefore you perform the following tasks, the probe should have already been in installed inthe magnet, tuned, and a probe file with probe calibrations should exist.

1. Eject the existing sample and insert the new sample.

— See section 3.3, “Changing the Sample and Loading a Probe File,” on page 38.

2. Load the probe file for the currently installed probe.

— See section 3.3, “Changing the Sample and Loading a Probe File,” on page 38

3. Set the spinner speed and VT.

Set spinning speed — See, “Setting Spinner Speed,” on page 39.

Set VT (optional) — See, “Setting the Temperature for VT Control (optional),” onpage 43.

4. Find Z0 adjust the lock.

— See, “Finding Z0 and Establishing Lock,” on page 39.

5. Adjust the field homogeneity.

— See, “Adjusting the Field Homogeneity,” on page 40.

6. Select an experiment.

• 1D Experiments

See section 3.5, “Choosing, Loading and Setting Up a 1D Experiment,” on page41.

• 2D Experiments

See section 3.11, “Choosing, Loading, and Setting Up a 2D Experiment,” onpage 48.

Set the lock solvent — See, “Selecting a Solvent,” on page 42.

Name the sample (optional) — See, “Naming a Sample (optional),” on page 43.

7. Set up experimental parameters and post acquisition actions.

— See, “Setting Up Experimental Parameters,” on page 43.

8. Acquire NMR data.

— See section 3.6, “Acquiring a Spectrum,” on page 44.

9. Process, display, plot, and save the NMR data.

Process and display — See section 3.7, “Processing and Displaying 1D NMR Data,”on page 45.

Save the NMR data file (optional) — See section 3.8, “Saving the NMR Data(optional),” on page 46.

Plot the spectrum (optional) — See section 3.9, “Plotting the Spectrum (optional),”on page 47.

10. Stop or abort the experiment.

— See section 3.10, “Stopping an Experiment,” on page 48.

3.3 Changing the Sample and Loading a Probe File


3.3 Changing the Sample and Loading a Probe FileYou should always click on the eject button first (even if there is no sample is in themagnet). This will start the airflow to float the sample when you place a sample to beinserted atop the upper barrel. If a sample is present when the ejection air is turned on thesample rises to the top of the upper barrel. You can now remove the sample and replace itwith another sample and insert the new sample into the magnet.

Ejecting and Inserting a Sample

1. Click on the Eject button in the Setup-Standard panel, shown in Figure 26 to ejectthe sample from the magnet.

2. Remove the sample from the upper barrel.

3. Place a new sample atop the upper barrel.

4. Insert the sample into the magnet by clicking on the Insert button in the in theSetup-Standard panel, shown in Figure 26.

Loading a Probe File

1. Click on the Probe button at the bottom left corner of the VnmrJ interface.

The probe selection window appears.

2. Click on the desired probe in the Select Probe menu and click on Close to dismissthe window.

For more information about setting up a probe , see section “Probe” on page 27.

Figure 26. Setup Panel



3.4 Locking, Setting Spinning Speed, and AdjustingHomogeneity

Setting Spinner Speed

You can set spinner speed in your experiment in the Standard tab in the Setup panel andregulate spinner speed by clicking on Spin/Temp tab in the Setup panel. The panel inFigure 27 appears. Spinner control options are explained in the VNMR manual GettingStarted.

Finding Z0 and Establishing Lock

You can find Z0 and establish the lock either manually or using Autolock. Both methodsare accessed through the Standard tab of the Setup panel, see Figure 29.

Manual or Simple Method

Establishing lock using simple or manual locking uses the LOCK panel. The line thatcrosses the spectral window represents how close the deuterium resonance field is to thelock frequency. When the two are matched, the line should be flat (with perhaps somenoise, depending on the lock gain and lock power). The poorer the match, the greater thenumber of sine waves in the line. Figure 28 represents the changes from a poor match to agood match.

1. Click on the Lock tab in the Setup panel. The panel in Figure 29 appears.

2. Click on either Spin On or Spin Off.

3. Click Lock Scan to open the lock display.

4. Find Z0 by clicking on and dragging the Z0 slider bar until lock signal is onresonance, see Figure 28.

5. Adjust the lock power, gain, and phase by clicking on and dragging the slider bars,or click the button, shown in Figure 29.

Figure 27. Spin/Temp Panel

Figure 28. Finding Lock

ON RESONANCE

3.4 Locking, Setting Spinning Speed, and Adjusting Homogeneity


6. Click the Lock On button.

7. Click Lock Scan again to close the lock display.

AutoLock

1. Click on the Standard tab of the Setup panel. The panel in Figure 30 appears.

2. Click on either Spin On or Spin Off.

3. Choose Find Z0 or AutoLock.

Clicking on the button next to Autolock opens a drop-down menu of options, asshown in Figure 30.

4. Select an option, click on the AutoLock button, and the spectrometer will find Z0and make all specified adjustments.

Adjusting the Field Homogeneity

Field homogeneity can be manually or automatically adjusted. Access controls foradjusting the homogeneity through the parameter panel or the drop-down menu (automatedshimming only).

Figure 29. Lock Panel

Click on Lock Scan to display the lock

Click on and drag to adjustZ0Lock PowerLock GainLock Phase

signal in the graphics canvas

Figure 30. Lock Options

Click to open or close lock display Click to access autolock options



Manual Shim Method

You can adjust shims by clicking on Shim in the Setup panel and clicking the left mousebutton on the shim buttons shown in Figure 31.

You can also shim using the dial, or by clicking on the Lock Scan or FID Scan buttons.

Change the shim step size from fine to coarse by clicking the left mouse button on the shimbuttons. The cycle changes from fine to medium to coarse and back to fine with each click.

To save a set of shims, enter a name into the entry box next to the Save Shims button; thenclick the button to save the shims. To retrieve a set of shims, select Sort Shimsets in theLocator, and double-click or drag entry onto the Shims buttons.

AutoShim Method

You can adjust the field homogeneity of your experiment in the Standard tab in the Setuppanel. Choose Gradient Autoshim, Lock Autoshim, or manually adjust a shim byclicking on the Lock Scan or FID Scan buttons in the Setup-Standard panel, or theTransform button in the Process panel.

You can also click on Acquisition on the menu bar and click on the shimming method. Ifthe system is equipped with a gradient probe, the menu shows gradient shimming as themethod. If a nongradient probe is present, lock shimming is displayed as the method.

3.5 Choosing, Loading and Setting Up a 1D ExperimentVnmrJ provides you with several ways to choose and load an experiment. This sectiondescribes two, from the menu bar or using parameter panels.

Menu Method

Click on Experiments in the menu bar, then click on a 1D experiment in the list. The listof experiments contains some submenus. For example, Carbon-Proton Multiplicity

Figure 31. Shim Panel

Lock level Shim buttons

3.5 Choosing, Loading and Setting Up a 1D Experiment


Determination includes a variety of related pulse sequences. VnmrJ reads and loads thestandard parameters and then reads the probe file and loads the probe calibrations.

Locator Method

Click on an experiment in the Locator and drag it into the graphics canvas (or double-clickon the experiment), as shown in Figure 33. VnmrJ reads and loads the standard parameters,then reads the probe file and loads the probe calibrations, and sets up the experiment.

Selecting a Solvent

Menu Method

In the menu bar, click on Solvents, then make a selection from the drop-down list.

Parameter Panel Method

In the Setup-Standard panel, click on the Solvent button and make a selection from thedrop-down list.

Figure 32. Experiments Accessed from the Menu Bar

1D experiments

Figure 33. Loading an Experiment from the Locator



Naming a Sample (optional)

If you want to name your sample, enter a name for the in the field Sample in the Setup-Standard panel, shown in Figure 26. You can further define your sample by filling in thefields Notebook and Page.

Setting Up Experimental Parameters

To set up experimental parameters, use the Acquire panel, shown in Figure 34.

For more detailed instructions on setting parameters, see the chapter “Preparing for anExperiment” in the VNMR manual Getting Started.

Setting the Temperature for VT Control (optional)

You can set the temperature for VT control in the Setup-Standard panel and regulate thetemperature by clicking on Spin/Temp tab in the Setup panel. The panel in Figure 27appears. Temperature control options are explained in the VNMR manual Getting Started.

Setting Up Auto Process and Plot

To automatically process a spectrum upon completion of data acquisition, check the box inthe Process tab, shown in Figure 35. When you check the box, the Process when done boxin the Acquire panel is automatically checked. Click on Plot results box to add automaticplotting. Click the checked box in the Process tab to turn off automated processing andplotting.

When an experiment is loaded, the Process and Plot check boxes may or may not beselected. This behavior is set by user preferences in the Utilities -> System Settingswindow. Select Process data after Acquisition to automatically check the Process tab.

Figure 34. Acquire Panel - Default Tab

Enter values in the fields Click box to select or deselectClick on to select

Figure 35. Process when done Button

Click to add automatic plotting

3.6 Acquiring a Spectrum


Select Set processing when loading experiment and Set plotting with loading expt. toautomatically select the other two check boxes.

Setting Up Acquisition and Post Acquisition Actions

Before starting the acquisition you can determine the data acquisition precision (32-bit ordouble precision is normal), what actions to take during acquisition if the spinner or VT failto remain in regulation, how often to save the FID during the acquisition (block size), andother acquisition related actions. These actions are set in the Flags tab of the AcquisitionPanel, see Figure 36.

When the acquisition is completed, you can specify actions that are to occur automatically.These actions are specified in the Future Actions tab of the Acquisition panel, see Figure37.

3.6 Acquiring a SpectrumDuring acquisition VnmrJ reads the probe file and sets up the experiment. The defaultexperiment is determined by the type of probe that is being used. If a gradient probe isinstalled, the default experiments are gradient-based experiments. If you want to run anongradient experiment, you must select one from the Pulse Sequence menu in theDefaults tab of the Acquire panel.

Figure 36. Flags Panel

Figure 37. Future Actions Panel



Menu Method

To start an acquisition, in the menu bar, click on Acquisition. A drop-down list ofacquisition-related operations appears. For a description of the operations, see section 1.1,“Menu Bar,” on page 11. After you make your selection, a message appears in the messagedisplay window.


You can set acquisition parameters in the Acquire panel, shown in Figure 38. To see thepanel, click on the Acquire tab.

1. You can accept the Default settings or set acquisition parameters by clicking on theAcquisition, Pulse Sequence, or Channels tab.

2. When you are finished setting the parameters of your experiment, click on the greenAcquire button.

3. Click on the Stop button to stop the experiment.

3.7 Processing and Displaying 1D NMR Data

Menu Method

In the menu bar, click on Process. A drop-down list of data processing functions appears.For a description of these functions, see the section 1.1, “Menu Bar,” on page 11.


You can control data processing functions in the Process panel. To see the panel, click onthe Process tab, shown in Figure 39.

Figure 38. Default H1 Panel

Click Acquire to begin data acquisition Click Stop to halt data acquisition

Figure 39. Process Panel

3.8 Saving the NMR Data (optional)


1. In the Process panel, click on Process in the list and set the parameters in theProcess and Linear Prediction panels. Only the processing parameters that youselect are applied to the data.

2. After you have set the parameters, click on the Transform or the Autoprocessbutton.

• Use the Display tab to adjust the display.

• Use the Cursors/Integration and Line Lists tabs to perform integration andline listing.

Display Bar Icons

Next to the graphics canvas is a row of icons for controlling the display. These icons willappear as shown in Figure 40 after you click on either the Transform or the Transform allbutton. Click on the icon to activate the function, click the same icon again to turn off thefunction. The icon bar will change when certain functions are activated to reveal additionaloptions. Move the mouse over the button to view a tool tip description of the button.

3.8 Saving the NMR Data (optional)If you acquired the data but did not select the Automatic FID save feature in the FutureActions tab of the Acquire panel and you now want to save the data, you can save the datausing either the menu method or the parameter panel.

Figure 40. Display Icons Bar

Show 1 cursor or click to show two cursors

Zoom in to region bounded by cursors or click again to zoom out

Display integrals

Display scale

Grab and moveSet threshold

Phase

RefreshGo back to previous set of icons



Menu Method

To save data, click on Utilities in the menu bar, then Save data. You can control how andwhere data is saved by clicking on Save data setup. The window shown in Figure 41appears.


To save data, click on the Acquire tab, Future Actions tab, and Save FID Now buttonshown in Figure 37. If you checked the Automatic FID Save in the Future Actions panelbefore starting data acquisition, the data has already been saved when acquisitioncompletes.

3.9 Plotting the Spectrum (optional)If you acquired the data without selecting Process when done and Plot results in theDefault tab of the Acquire panel shown in Figure 34, and you now want to plot the datause Plot tab of the Process panel shown in Figure 42. Select the plotting options and pressthe Plot Page button.

Figure 41. Save Data Setup Window

Figure 42. Plotting the Spectrum

Type of buttons used to select plot optionsSend the plotting instructionsto the plotter for plotting

Clear all plotting options

3.10 Stopping an Experiment


3.10 Stopping an ExperimentThere are four ways to stop an experiment:

• Clicking on the Stop button .

• Clicking on Acquisition in the main menu, then Abort Acquisition.

• Clicking on the Stop button in the Acquire panel (shown in Figure 34).

• Enter aa on the command line

3.11 Choosing, Loading, and Setting Up a 2D ExperimentThis section describes how to use VnmrJ to run a 2D experiment. Typically a 1 Dexperiment will have been run and lock, shims, and VT have been set.

Choosing and Loading a 2D Experiment

You typically set up a 1D experiment before you set up a 2D experiment. Parameters in a1D experiment will be the foundation for a 2D experiment. The procedure for loading a 2 Dexperiment is similar to the one for loading a 1D experiment.

Menu Method

1. Click on Experiments in the main menu.

2. Click on a 2D experiment in the list (e.g., Homonuclear Correlation Experiments).

The list of experiments contains submenus for all 2D choices. For example,Homonuclear Correlation Experiments includes a variety of related pulse sequences.VnmrJ reads and loads the standard parameters and then reads the probe file andloads the probe calibrations.

Locator Method

Click on a 2D experiment in the Locator and drag it into the graphics canvas, as shown inFigure 33.

Figure 43. 2D Experiments Accessed from the Menu Bar



Naming the Sample, Selecting the Solvent, Setting VT, and PostAcquisition Events

Some of these options were set if you first acquired a related 1D experiment. These optionsare set in much the same way as they were for the 1D experiment, see section 3.5,“Choosing, Loading and Setting Up a 1D Experiment,” on page 41. The appearance of thepanels might be different depending upon the experiment.

Setting Up Experimental Parameters

1. Follow the procedure in the section, “Setting Up Experimental Parameters,” on page43 (use the Acquire panel).

2. Set the spinner speed to 0, nD data is rarely acquired with the sample spinning.

3. For more detailed instructions on setting parameters, see the chapter “Preparing foran Experiment” in the VNMR manual Getting Started.

Acquiring a Spectrum

Follow the procedure in section 3.6, “Acquiring a Spectrum,” on page 44 for acquiring aspectrum. The appearance of the panels might be different depending upon the experiment.

Processing 2D NMR Data

Follow the procedure in section 3.7, “Processing and Displaying 1D NMR Data,” on page45 to process the 2D NMR data. The processing options will be different from those shownfor a 1D experiment.

Saving the 2D Data

Follow the procedure in section 3.8, “Saving the NMR Data (optional),” on page 46 to savethe 2D NMR data.

Plotting the 2D Spectrum

Follow the procedure in section 3.9, “Plotting the Spectrum (optional),” on page 47 to plotthe 2D NMR spectrum. The plotting options will be different then those shown for a1D experiment.


Chapter 4. Parameters, Data Saving, TemplateEditor, and Shim Buttons


• 4.1, “Getting New Parameters and Environment Variables,” this page

• 4.2, “Disabling Automatic Data Saving,” this page

• 4.3, “Using the Template Editor,” on page 51

• 4.4, “Using the Shim Buttons,” on page 53

4.1 Getting New Parameters and Environment VariablesVnmrJ uses several global parameters and UNIX environmental variables. It also usesseveral new local parameters. Local parameters are created by the macro fixpar, whichis automatically run every time a data set or parameter set is retrieved. fixpar is also runon all current workspaces (experiments) when you run makeuser. Both fixpar andmakeuser are run when setting up a new account using the VnmrJ administration tool,which you start with the command vnmrj adm.

To set up a new VnmrJ account, see the chapter “VnmrJ Administration” in the manualHost Computer Setup for VnmrJ.

4.2 Disabling Automatic Data SavingAfter acquisition is finished, the FID can be automatically saved to the disk and added tothe list ofvnmr_data in the Locator. Data can be saved when you start normal acquisitionwith the tools that call the go, ga, or au commands.

The file names under which data is saved are determined by the svfdir and svfnameparameters, which are similar to the autodir and autoname parameters that are used inautomation. These parameters are initialized when makeuser updates the globalparameter tree.

System Settings

Disabling Automatic FID Saving

To prevent FIDs from being automatically saved after normal acquisition, do the followingsteps:

1. Click on Utilities in the main menu, then click System Settings.

Chapter 4. Parameters, Data Saving, Template Editor, and Shim Buttons


2. In the popup window, shown in Figure 44,uncheck (click on) the box Autosave dataafter acquisition.

Enabling Automatic FID Saving

To reenable automatic saving of FIDs, click onUtilities, then System settings, then check (clickon) the box Autosave data after acquisition.

Current Experiment

1. Click on the Acquire tab.

2. Select the Future Actions page.

3. Place a check mark in the Automatic FidSave box to activate automatic fid savingor click on the checked box to remove thecheck and deactivate automatic fidsaving.

Saving Selected FIDs

With autosaving disabled, you can save selected FIDs two ways:

• Click on Utilities, then Save data.

• In the Acquire panel, go to the Future Actions page and clicking on Save FID now.

4.3 Using the Template EditorThis section provides hints for using the template editor. In the main menu, click on Edit,then Parameter Panels to open the template editor shown in Figure 45.

Figure 44. System Settings

Figure 45. Template Editor

4.3 Using the Template Editor


Hints When Viewing a Panel

To select an item in a parameter panel, double-click on it with the left mouse button. Theitem is surrounded by a yellow border.

To select a page, click on the page title in the left column.

To select a group, double click on an empty area within the group.

To close the editor, click on the Close button.

Commonly Used Panel Items

Table 1 lists commonly used items in a parameter panel The item name is shown as Typeof element in the template editor.

Attributes of Commonly Used Items

When you select an item, its attributes are shown in the template editor. Attributes are usedin some items but are not used in others. Common attributes are listed in Table 2.

Table 1. List of Commonly Used Items in a Panel

Item Function

button Button to execute a command, macro, or string

check Check box (status is on/off), and an optional label

entry Box for entering a parameter value or expression

label Static text label

menu Menu with a series of choices. A final choice is given that does not match anychoices in the list.

radio Radio button (status is on/off), and an optional label

textmessage Dynamic text label which responds to parameters

toggle Toggle button (status is on/off), and an optional label

group Group of items within a box

Table 2. Attributes of Commonly Used Items

Attributes Description

Label of item Text label of the item.

Vnmr variables VNMR parameters that can change the Value of item, Enable condition, orShow condition of the object.

Value of item The value of the item. This string is a MAGICAL expression that sets the valueof $VALUE. The value of some items (check, radio, and toggle) can be eithertrue (1) or false (0).

Decimal Places The number of decimal places to truncate to in a real expression in Value ofitem.

Vnmr command The command sent when the item is executed or selected. This string is aMAGICAL expression that can use $VALUE, which is read from the valueentered in or set by the item.

Vnmrcommand2

The command sent when the item is deselected. This is used only by someitems (check, radio, and toggle).



Hints When Editing a Panel

The following hints are provided to help you edit a parameter panel.

• To move an item in a panel, select it and drag with the left mouse button. Shortcut:also use the arrow keys on your keyboard to move a selected item.

The item is snapped to the grid.

• To resize an item in a panel, select the edge of the item and drag with the left mousebutton. Shortcut: after you select an item, hold down the Control (or Ctrl) key whileusing the arrow keys to resize the item in the panel.

The item is snapped to the grid.

• To add an item to a panel, select an item from the Locator and drop it in the panel.

• To copy an item or group of items in a panel, select the object, hold down the Ctrl keyand drag with the left mouse.

• To remove an item or group of items from a panel, select the object and drop it in thetrash can or use the Clear Item button in the template editor.

• To save changes to a page, select the whole page and click on the Save Page button inthe Edit popup window.

• To reread the last changes saved and close the template editor, click on the Abandonbutton.

4.4 Using the Shim ButtonsThe following hints are provided to help you use the shim buttons in the Setup panel.

• Clicking the left mouse button on the button decrements the value by the amount of the“increment” displayed on the right side of the button.

• Clicking on the right mouse button increments the value.

Enable condition The expression which determines whether an item is active or not. This string isa MAGICAL expression that sets $ENABLE or $VALUE, which can evaluateto either active (1), inactive (0), or disabled (–1). A disabled item does notallow the item to change the parameter value, while an inactive item simplychanges the background color to dark gray but still allows parameter entry.

Label of choices Text labels used in a menu item.

Value of choices Values in a menu item used to set the VNMR command.

Status parameter Parameter from the acquisition or hardware status. A status parameter canchange the item or value of the item to display. Status parameters cannot beused in MAGICAL expressions. (Used in button, check, textmessage, toggle.)

Show condition In a group, the expression which determines whether a group is shown or not.This string is a MAGICAL expression which sets the value of $SHOW, whichevaluates to show (1) or hide (0).

Vnmr commandon show

In a group, the command sent when the group is shown. This string is a MAGI-CAL expression.

Vnmr commandon hide

In a group, the command sent when the group is hidden. This string is aMAGICAL expression.

Table 2. Attributes of Commonly Used Items

Attributes Description

4.4 Using the Shim Buttons


• Clicking the middle mouse button toggles the amount of the increment among threevalues.

• Holding down the Shift key and clicking the left mouse button enables you to type ina new current value. Press Return to make the value take effect.

• Holding down the Shift key and clicking the middle mouse button enables you to typein a new value of the increment.




Chapter 5. DSP and ECC Utilities


• 5.1, “Hardware Requirements,” on page 56

• 5.2, “Using the ECC Software,” on page 56

• 5.3, “Integrating ECC into Each User Account,” on page 60

• 5.4, “Using the Enhanced DSP,” on page 61

• 5.5, “Shaped Gradients,” on page 62

• 5.6, “Decoupling Tests,” on page 62

• 5.7, “Utilities,” on page 63

This section provides instruction on the use of the Eddy Current Compensation (ECC)software, modifications of DSP, and shaped gradients. The ECC software is applicable toZ axis gradient liquids probes and is not applicable to imaging probes. This section alsoprovides instructions for utilities used in installation of the Varian Cryogenic Probe.

5.1 Hardware Requirements• Highland L700 PFG amplifier with ECC.

5.2 Using the ECC SoftwareThe ECC software automates the determination of the eddy current time constants andamplitudes. These values are automatically written to the probe file from where they areaccessed during PFG experiments. The ECC software is controlled through panels shownin Figure 47 and Figure 46. ECC parameters for each pair of time constant and amplitudecan be determined, fine tuned, written to the probe file, and set into the global parameters.Tools are provided for analysis and plotting of test results.

Determine the time constants and amplitudes of the four eddy current compensationparameters as follows:

• “Setting Up the System for ECC” on page 56

• “Determining the ECC Parameters” on page 57

• “Updating the Probe File and Enabling ECC” on page 60

Setting Up the System for ECC

1. If you are not currently logged in, log in to your the user account.

2. Start VnmrJ.



3. Enter cexp(1000) jexp1000.

All the experiments for ECC will be run from this experiment. You could use anyexperiment, except exp5, but it is recommended you set aside an experiment just forthis purpose.

4. If there is a sample in the probe, eject the sample and insert the2 Hz 1% H2O 99% D2O sample (01-901855-01).

5. Set the VT flow to 15 lpm.

6. Enter rtp('/vnmr/tests/shmd2o') to retrieve the test parameter set to thecurrent experiment.

7. Enter at=2 sw=2000 d1=2 nt=1 lb='n' spin='n' dsp=’i’ srof2temp=25 su.

8. Allow the probe and sample to equilibrate (minimum 15 minutes) before continuing.

9. Tune the probe using a doped 2-Hz D2O sample

10. Acquire a normal spectrum and shim the water signal to less than or equal to 3-Hzlinewidth at 50%.

It is important to setup the lock and homogeneity properly. Poor homogeneity andan improperly set lock will significantly hinder determination of the ECCparameters.

Determining the ECC Parameters

There are four eddy current compensation parameter pairs of time constant and amplitude:tc1z / amp1z, tc2z / amp2z, tc3z / amp3z, and tc4z / amp4z. The ECC parametersand the allowed ranges are given in Table 3.

Each pair eddy current compensation parameters are determined as follows:

• Acquire recovery data

• Extract the time constants and amplitudes from the recovery data

• Repeat the procedure for each of the four ECC parameter pairs

Acquiring Recovery Data

This process will begin with the longest time constant and amplitude, typically tc4z andamp4z, and is repeated for each of the remaining three pairs; tc3z/amp3z, tc2z/amp2z, and tc1z/amp1z, until the shortest time constant and its amplitude isdetermined. It is possible that one or more of the pairs will have an amplitude of zero.

Table 3. ECC Parameter and Ranges

Time constant Time constant range, msec. Amplitude Amplitude range

tc1z 0.0210915 to 0.235000 amp1z 0 to 100

tc2z 0.2091500 to 2.350000 amp2z 0 to 100

tc3z 0.214 to 2.36 amp3z 0 to 100

tc4z 2.019150 to 23.5000 amp4z 0 to 100

5.2 Using the ECC Software


Setting Up the Experiment

1. Enter ecc_off g2pul_ecc su.

The ecc_off macro will set the global parameters to zero and convert the currentparameter set to the parameter set for the ECC experiment.

2. Click on the Acquire tab and select the Acquisition panel to display the acquisitionparameters, see Figure 46.

3. Click on the Acquire tab and select the ECC panel to display the panel shown inFigure 47. Refer to this figure during the procedure as necessary to locate the variousbuttons and controls.

4. Click on each of the Zero buttons for each amplitude. This initialized all theparameters.

Measuring the Time Constants and Amplitudes

1. Press the Run 10 ms button. This is one of the three preset recovery experimentbuttons.

A d2 array will be set up and the data will be acquired, processed, and displayed. Atypical data set is shown in Figure 48.All the time constant amplitudes were set tozero in the previous step so the data will be acquired with no eddy currentcompensation.

2. Press on the Points to skip button and select 5. The first five points are not importantto the determination of long time constant and can distort the result if the data points

Figure 46. Acquire Tab - Acquisition

Figure 47. Acquire Tab - ECC panel



have a constant amplitude, as in the case of the first three spectra in the example inFigure 48.

Optionally, press the Autofit button. An automated routine will attempt to determinehow many points to skip and pass the results into the next available fields. If, afterusing Autofit you decide to manually fit the data, the data set must be reprocessedbefore fitting.

3. Click on the Process button. The time constant and amplitude will be calculatedfrom the data set. The data points, fitted curve, and time constant and amplitude willbe displayed as shown in Figure 49.

4. Refer to Table 3. Each time constant has a specific range. Note the value of the timeconstant and compare it with the range of values in Table 3.

5. Press the button Set in XXX that corresponds to a range that encompasses thecalculated time constant. In this example the time constant is 13.51 msec which is inthe allowed range for tcz4 therefore press the Set in tcz4 button.

The time constant and amplitude values will be automatically entered in theappropriate fields.

6. Continue with “Fine Tuning the Amplitude and Time Constant” on page 60.

Figure 48. Recovery with No Eddy Current Compensation

Figure 49. Calculated Fitting of the Data

5.3 Integrating ECC into Each User Account


Fine Tuning the Amplitude and Time Constant

Optimize the amplitude for the time constant that was determined in the previous step asfollows:

1. Press the Tweak X button corresponding to the time constant that was just measured.In this example, press the Tweak 4 button.

Pressing the Tweak button will do the following:

• Set d2 = time constant value, in this example; d2=0.013511.

• Create an array of amplitudes based on the calculated value from the fit data.

• Acquire, process, and display a data set.

2. Identify the spectrum with the highest intensity.

3. Enter this amplitude in the field corresponding to the time constant beingdetermined.

4. Determine the remaining time constants and amplitudes as follows:

a. Press the Run 2 ms button.

b. Examine the arrayed spectra. If the amplitudes of the initial spectra areincreasing, go to step d. If any of the initial spectra have a constant amplitudeor are distorted continue with the next step.

c. Click on the Points to skip button and select the number of pointscorresponding to the data points that have a constant amplitude. Continuewith the next step.

d. Follow the same instructions beginning with “Measuring the Time Constantsand Amplitudes” on page 58, step 3.

e. Repeat this process using the Run 1 ms until all the time constants andamplitudes are determined.

Updating the Probe File and Enabling ECC

1. Press the Update probefile button to create the ECC fields in the probefile and writeall of the ECC time constants and amplitudes into the probefile.

2. Enter ecc_on. Data is written from the probefile to the global parameters andPSG control of ECC is enabled.

ECC is now calibrated and enabled for the user.

5.3 Integrating ECC into Each User AccountIntegration with VnmrJ involves creating the probe file in /vnmr/probes, and theexecution of the macro makeeccglobals in the user account of each user that will useECC. Proceed as follows:

1. Create the probe file.

• Enter the following:

cd /vnmr/probes

cp -r ../$vnmruser/probes/<probe_name>.

2. Configure the account of each user that will be working with ECC.



a. Logout of the current account.

b. Login to the user account.

c. Start VnmrJ.

d. Enter makeeccglobals on the VnmrJ command line.

e. Enter ecc_on on the VnmrJ command line.

f. Exit VnmrJ

g. Logout

h. Repeat step a through step g for all affected accounts.

3. This completes the integration of the ECC software, continue with “Enabling ECCfor Each User Account” on page 61.

Enabling ECC for Each User Account

Each user account will have to turn on PSG control of the ECC.

1. Login to the account of the user that will be working with the ECC software.

a. If the macro has been run, continue with the step b. If themakeeccglobals macro was not run in this account, entermakeeccglobals in the VnmrJ command line then continue with the stepb.

b. Enter ecc_on in the VnmrJ command line of the user. The commandecc_on will load the correct ECC parameters from the probe file into thenewly created global parameters and enable PSG control for ECC.

2. Logout of the user account.

3. Repeat steps 2 and 3 for each account affected.

5.4 Using the Enhanced DSPThe Varian Cryogenic Probe requires a longer dead times following the RF pulses than aconventional probe to achieve a flat baseline. Flat baselines in spectra are achieved usingthe VnmrJ global parameter, qcomp, to provide the additional settings for the dsp.

The parameter qcomp should exist, but if it does not, create it as follows:

• Type createqcomp on the command line.

Then set qcomp = 'y' and either

• dsp='i' — best performance when using a Varian Cryogenic Probe

or

• dsp='r' and fsq = 'y' — mixed mode is also useful

Setting qcomp = ‘y’ will check the dsp and fsq conditions, use a longer dead time,and adjust the dsp parameters to yield a flat base line.

If it is necessary to have a user specified delay (overriding the software calculated delay)before receiver turn on, create a parameter called prealfa by typing the following on thecommand line:

• create (prealfa, pulse, current) to create a delay with units ofµseconds. Use this parameter definition with Spin Cad created pulse sequences.

or

5.5 Shaped Gradients


• create (prealfa, delay, current) to create a delay with units of seconds.

Set qcomp = 'y'.

Set the prealfa parameter with the user-specified delay. Software might adjust the userset prealfa by a small amount to better optimize the dsp parameters.

If it desired to use the default delay calculated by the software, the user should destroy theprealfa parameter.

qcomp is not effective in explicit acquisition experiments. Set qcomp='n' to disable thisfeature.

5.5 Shaped GradientsGradients are set to shaped gradients using the parameter gradientshaping. If theparameter gradientshaping does not exist, create it by entering:

create('gradientshaping','flag','global')

• Enter gradientshaping='y' to activate this feature and produce a WURSTshaping of gradient amplitudes.

• Enter gradientshaping='n' to deactivate this feature and produce rectangulargradients of gradient amplitudes.

This feature works only with the Z gradient pulses, specified using the zgradpulse(…)psg statement.

5.6 Decoupling TestsSome low boiling point elements, principally H2, remain adhered to the surface of variouscomponents of the probe. During routine operations these gasses are pushed off the surfacesbut remain in the probe and excited by the rf. In their excited state they generate broadbandnoise that is detected by the probe. This procedure measures the broadband noise andremoves the traces of these low boiling point elements. The cryo_noisetest macroand the cnd macros measures the broadband noise and removes the traces of these lowboiling point elements with the applications of rf pulses on all channels to drive off whilethe probe is attached to a turbo pump.

Use the following procedure to evaluate decoupler noise:

1. If there is a sample in the probe, eject the sample and remove it from the magnet.This test is run with the probe empty.

2. Attach the turbo pump to the probe and begin the pump down procedure as specifiedin either of the following manual:

• Varian Cryogenic Probe Installation,Publication Number 01-999196-00

• Cryogenics System Installation and Operation,Publication Number 01-999189-00

3. Enter cryo_noisetest.

4. At the prompt from the macro enter 40.

Any value is acceptable, 40 to 120 is recommended for overnight probeconditioning. Two sheets of paper are output and the results archived in vnmrsys/



data/testlib each time a cycle is completed. An entire test requires ~ 5 minutesplus the burn-in/conditioning time period.

Typing cryo_noisetest('NOBURN') <time> runs only the noisemeasurement test over a period specified by <time>without applying the rf pulses.The macro will wait for operator input after each noise evaluation before startinganother evaluation.

5.7 UtilitiesTwo macros are provided to facilitate the evaluation of sensitivity and sample temperaturegradients:

• dsnarray

• tempcalc

The macro dsnarray is customized to report the statistical S/N of a series of repeatedgNhsqc data sets acquired with a labeled protein sample. The tempcalc macro isnormally run after shimming on a ~1% HOD CH3CN sample to output the approximateactual sample temperature and the actual sample temperature gradient.


Index

Index

Numerics1D Experiment, running a, 411D Fourier transform, processing a, 131D, 2D Experiments, running, 362D Experiment, running a, 482D experiment, running a, 48

Aaborting acquisition, 13accessing data sets, experiments, shim sets, and

commands, 22acquiring an experiment, 45acquiring data, 12acquisition

pausing, 13pausing an, 13resuming, 13resuming a paused, 13stopping, 13system, current state of, 25

acquisition functions, performing, 11Acquisition menu, 11adding

printers, 17adjusting

threshold, 23Amplitude and Time Constant

fine tuning, 60amplitude, ECC, 57arrayed parameters, setting, 11Autolock, 39

Ccanvas

controlling display in graphics, 23graphics, 24

carrier frequency, setting, 13closing VnmrJ, 19colors, setting, 18command entry field, 23commands

accessing, 22configuring

your system, 15connecting printers, 17controlling display in graphics canvas, 23correcting parameters, 16creating

a new tool bar button, 20a workspace, 16

cryo_noisetest, 62

Ddata

acquiring, 12processing, 45processing NMR, 45

saving, 17, 47data set

accessing a, 22data setup, saving, 17decoupler noise test

cryogenic probes, 62description of interface, 10Display menu, 13displaying

a spectrum, 13menu bar, 22tool bar, 22

dsnarray, 63DSP

enhanced, 61DSP, modification, 56

EECC, 56

compensation parameter pairs, 57integration with VnmrJ, 60parameters and ranges, 57set up, 56software, 56updating probe files, 60

Eddy Current Compensation, 56Edit menu, 20editing parameter panels, 21editing the Tool Bar, 20ejecting a sample, 38enabling ECC software, 61exiting VnmrJ, 19experiments

accessing, 22acquiring, 45loading, 41, 48running, 36shimming, 41

Experiments menu, 11

FFID, saving current, 17field homogeneity, adjusting, 41finding z0, 39fonts, setting, 18Fourier transform

processing a 1D, 13frequency

setting carrier, 13

Ggradient shimming, 13graphics canvas, 24

controlling display in, 23

Hhalting an acquisition, 13hardware bar, 25hardware, setting up, 12

Index


Help menu, 21hiding

menu bar, 22tool bar, 22

holding pen, 23homogeneity, adjusting field, 41

Iinitializing hardware, 12integral displays, 23

Lloading

a probe file, 38an experiment, 41shim values, 12

Locator, 22LOCK display, 39

Mmaking

a workspace, 16manual locking, 39menu bar, 11

hiding/showing, 22

Nnaming a sample, 43NMR data

processing, 45

Oonline help manuals, 21opening SpinCAD, 20

Pparameter

panels, editing, 21parameters, correcting, 16parameters, creating pulse sequence, 15pausing acquisition, 13performing

a 1D Fourier transform, 13acquisition functions, 11

performing user-defined data processing, 12phasing, 23plotters, setting, 17printers, setting, 17probe file

updating for ECC, 60probe file, loading a, 38Process menu, 13processing

a 1D Fourier Transform, 13data, 45

pulse sequence parameters, creating, 15

Qqcomp, 61

Rregulating spinner speed, temperature, 39restarting a paused acquisition, 13resuming acquisition, 13running

a 1D experiment, 41, 48a 2D experiment, 48an experiment, 16SpinCAD, 20

running 1D, 2D experiments, 36

Ssample

inserting a, 38naming a, 43

savingdata, 17, 47

saving data setup, 17seeing

a spectrum, 13menu bar, 22tool bar, 22

selectingitems in the holding pen, 23solvents, 42

settingarrayed parameters, 11carrier frequency, 13colors and fonts, 18printers, plotters, 17shim values, 12spinner speed, 39temperature for VT control, 43

setting uphardware, 12

shaped gradients, 56, 62shim sets, accessing, 22shim values, loading current, 12shimming an experiment, 41shimming, doing gradient, 13showing

a spectrum, 13menu bar, 22

shutting down VnmrJ, 19simple locking, 39Solvent menu, 11spectrum, showing a, 13SpinCAD, opening, 20spinner speed, controlling, 39starting

VnmrJ, 36stopping an acquisition, 13storing

data, 47Locator items, 23

systemconfiguration, 15messages, 25


Index

Ttempcalc, 63temperature, setting for VT control, 43time constant, 57Time Constants and Amplitudes

measuring, 58setting initial values, 59

tool bar, 22Tool Bar, editing, 20trash can, 25trashing items, 23

UUtilities menu, 15

Wweighted Fourier transforming data, 12windows

Array Parameter, 12workspace, creating a, 16

Index


Documents

Getting Started with VnmrJ Liquids NMR · Getting Started with VnmrJ Liquids NMR Varian NMR Spectrometer Systems with VnmrJ Software Pub. No. 01-999150-00, Rev. C0503 Revision history: