University of California, Riverside

NMR Facility

Varian Inova 500 Help Sheets

1D Basics || Console Reboot || Probe Cabling || Probe Change || Common Commands

Basic Operation Guide: Varian Inova 500 NMR Spectrometer

Conventions used in this guide are as follows:

LMB indicates the Left mouse button.
MMB indicates the Middle mouse button.
RMB indicates the Right mouse button.

Unless otherwise noted, "Click" means clicking with the left mouse button and all commands typed on the command line are followed by a <return> keystroke.

I  Logging in to VnmrJ

  1. Sign the logbook with your name, adviser’s name, date, time in, nucleus and solvent.
  2. If the screen is black, move the mouse.
  3. Type in your user name <return>, type in your password <return>.
  4. Click the VnmrJ icon in the top bar to open the VnmrJ interface. (Do not double click!!)

II  Loading a probe file and a shim file

                                           Inova 500 Probes
                                Probe Probe Name
  5 mm 500 SW VT 5mm_sw
  5mm HCN Triax VT ID/PFG HCNtriax
  5 mm 500 Dual VT-PFG 5mm_dual
  8 mm 500 VT ID/PFG 8mm_id_pfg
  1. Click the Probe button on the Hardware bar, the Probe window will open.
  2. Click the Select Probe drop-down menu, select the desired probe and close the window.
  3. To load a shim file, select the Shim page in the Start tab. Go to Tools on the menu bar and select Locator..., click the Locator Statements button vnmrj magnifying glass (magnifying glass icon). Go to Sort Shimsets and select by probe & shims. Select and load the desired shim file by dragging and dropping it onto the graphics canvas.
  4. Select the Lock page in the Start tab and click the Load shims into Hardware button.
  5. For the 5mm_sw probe, type gradtype='nnh' pfgon='nnn' su. Make sure the gradient amplifier is in Standby mode. For the HCNtriax probe, type gradtype=’ttt’  pfgon=’yyy’  su.  Make sure the gradient amplifier is in Run mode. For the 5mm_dual and the 8mm_id_pfg probe, type gradtype=’ttt‘  pfgon=’nny’  su.  Make sure the gradient amplifier is in Run mode.

III  Ejecting and inserting sample

  1. Click the Start tab and select Standard page, click the Eject button to turn on the eject air.
  2. Position your sample properly in the spinner using the depth gauge. Wilmad 528PP or equivalent NMR tubes are required for this instrument. The normal sample height should be 4.5 cm or more (approx. 0.7 ml). For normal height samples the bottom of the NMR tube will go to the bottom of the depth gauge. For shorter samples the sample must be centered on the middle line of the depth gauge. This will make shimming on short samples easier.
  3. With the eject air still on, place the sample and spinner into the top of the magnet. Click the Insert button to lower the sample. Caution! never place a sample in the magnet bore without eject air flowing.

IV  Lock and shim

In the Lock and Shim pages, the buttons (Z0, Lk Power, Lk Gain, Lk Phase, and Z, X, and Y shims) provide on-the-fly configuration.  The slider values can be moved with the mouse or entered directly.                      

Lock buttons and controls:

     vnmrj lock controls

Shim buttons and controls:

vnmrj shim controls

Mouse control of buttons and sliders:

vnmrj mouse function                      

To change the increment value: Shift-middle-click on the button, enter a new value and press <return>.

To change the DAC value: Shift-left-click on the button, enter a new value and press <return>. 

1.  Optimizing lock

 a) Select the Standard page in the Start tab, click the Solvent drop-down menu and select the solvent you are using. Select the Lock page in the start tab.  If lock is On (status shown is either NotReg or Regulated), click on Lock Off, then click Lock Scan to open the lock display.  The line that crosses the spectral window represents how close the solvent deuterium resonance is to the lock frequency.  When the two are matched, the line should be flat.  The poorer the match, the higher the frequency of the sine wave.

b) Adjust the lock Gain to the maximum setting (=48) and the lock Power to a proper value in accordance with the solvent by mouse clicking the button or dragging the slider bars.  Adjust Z0 by mouse clicking the button or dragging the slider bar until the lock signal changes from a sine wave to an essentially flat line (looks like a step function or a square wave).  Click the Lock On button.  Adjust the lock Phase to achieve the maximum Lock Level.  Once the Z0 field is optimized adjust the lock Gain such that the Lock Level is ~60%.

vnmrj lock resonance

2.  Shimming on the lock signal

Start by selecting the Shim page in the Start TabAdjust Z1 by mouse clicking the button or dragging the slider bar until the lock level is maximized.  Next, adjust Z2 to maximize the lock level.  As these two shims are coupled, iterate back and forth between Z1 and Z2 until you can no longer increase the lock level.  If the lock level goes off the top of the lock display window, decrease the lock gain until the lock level is ~70%, start shimming again. 

 If needed, shim Z3 (then re-optimize Z1 & Z2).  If you feel you need to adjust the X-Y shims, please see a staff member for assistance. 

V  Setting up and running an NMR experiment

1.  Selecting an experiment

VnmrJ provides you with several ways to choose and load an experiment.  This section describes two, from the Locator (a) or from a saved data file in your folder (b).

a)   Go to Tools on the menu bar and select Locator, click the Locator Statements button vnmrj magnifying glass, go to Sort Protocols and select for liquids experiments.  Click on an experiment in the Locator and drag it into the graphics canvas (or double-click on the experiment).
b)   Go to File on the menu bar and select Open.  Click on a data file and select Open (or double-click on the experiment).


2.  Set up the acquisition parameters and start acquisition

Click the Acquire tab and select the Default page by clicking on the drop-down menu, set up the spectral width, relaxation delay (3 sec.), and number of scans (n=8*). Select the Acquisition page. For 1H select Auto for Receiver Gain. For X nucleus detection set Receiver Gain = 60. Click the green Acquire & Transform button (or the blue Acquire button) to start acquisition.  To abort acquisition, click the red Stop button.

3.  Save the data file

Go to File on the menu bar and select Save as …  Navigate to your Directory (/data/user name), type the file name in and click Save.          

If you want to view the spectrum before the acquisition has finished, type wft aph.     

VI  Processing data and plotting a 1D spectrum

1.  Fourier transform                            

Click the Process tab and select the Default page. Select exponential under Weighting and click on the Auto Process button to display the spectrum.  Click the Display scale button scale to display the scale.

2.  Graphics control buttons

two cursor One cursor in use, click to toggle to two cursors. one cursor Two cursors in use, click to toggle to one cursor
full display Click to display full spectrum. pan and stretch Pan & stretch mode.
integral Display integral. scale Display scale.
peak threshold Show/Hide peak threshold. phase Phase spectrum.
redraw Redraw display. return Return to previous tool menu.


The graphics control buttons are located on the right side of the graphics display.  Use the buttons in combination with the mouse buttons for complete interactive control of the displayed spectrum.

3.  Zooming – In/Out using the mouse

To expand a region, click the Cursor button one cursor small, place the cursor at the left side of the region of interest, then place the right cursor by clicking the RMB.

Select the Zoom in button zoom in small.  You should now see the expanded region on the screen.  Click the Show Full spectrum button full display small to go back to a full spectrum or the Zoom out button zoom out small to return to the previous zoom. Alternatively you can click the Zoom mode button zoom mode small and put the cursor at one edge of the desired zoom region, click-hold and drag the cursor to highlight the desired zoom region, then release the mouse button. You should now see the expanded region on the screen. Click the Redraw button redraw small to exit the mode.

To automatically adjust the vertical scale, type vsadj.  By clicking the MMB you can manually adjust the vertical scale.  To increase the height of the spectrum, click the MMB above the peaks of interest.  To decrease the scaling, click below the peaks.   

4.  Phasing

By clicking the Auto Process button, the Fourier transform and auto-phasing of the spectrum has been done.  If auto-phasing does not work properly, manual phasing must be performed.

a) To start phasing, click the Phase Mode button phase small.  Click above a peak near the right edge of the spectrum.  Adjust the phase of the peaks between the cursors by clicking and dragging up or down with the LMB (coarse) or the RMB (fine) until the peaks are properly phased (pure absorption line shape). 

b) Once the peaks on the right side of the spectrum are properly phased, click above a peak near the left edge of the spectrum, and drag up or down to phase these peaks properly.  If the values of lp and rp are outside of + 360, you may want to type lp=0 and rp=0 and start over.

c) When the spectrum is phased, click the Redraw button redraw small.

5.  Calibrate the chemical shift

Click the Process tab and select the Default page.  Zoom-in on the reference peak, click the reference peak to move the cursor to that peak and click the Find nearest line button under Display.  Under Reference cursor to, select ppm and enter the reference value followed by <return>, the spectrum will be calibrated and re-displayed.  To reset zooming to the full spectrum, click the Show Full Spectrum button full display small.   

6.  Integration

a)   Click the Process tab and select the Integration page. Set the Integral Display Mode to Full and type cz to remove any previously defined set points. Click Scale display to fit to automatically scale the display. Placing the cursor above/below the integral and clicking the MMB can also be used to adjust the vertical scale of the integral

b)  To adjust the level and tilt of the integral click the Integral Lvl/Tlt button integral level tilt. This works much like phasing. First click on an integral region towards the right side of the spectrum and adjust the integral line by clicking and dragging up or down with the LMB (coarse) or the RMB (fine) until the integral is flat in the baseline regions to the left and right of the peak. Then click on an integral region towards the left side of the spectrum and drag up or down with the LMB or RMB until that region looks correct. Click the Redraw button redraw small to exit the mode. To print the spectrum with the full integral,    select Plot page, click the Auto Plot button. 

c)   To manually do partial integration, type cz and expand a region of interest.  Click the Define Integral Region button integral define. Click the LMB on the left then the right for every peak you want integrated.  Click the Redraw button redraw small to display the partial integrals.          

d)   To calibrate a given integral, select the Integration page and place the cursor over the desired region.  Select Single Peak under Set Integral Area and type in the value in Integral Area, click the Set Integral Value button to show the integral list.  Click the Show Integral Value button to display the integral values under the spectrum.

e)   To print the spectrum with the integral values under the axis, select the Plot page, click the Plot Spectrum and the Plot Spectrum Scale buttonsUnder Integrals, click the Plot Integrals button and click the Integral Values drop down menu, select Scaled, Horiz, then click the Black button.   

7.  Peak picking

a)   Click the Process tab and select the Display page.

b)   Click the Show/Hide Threshold button peak threshold small.  This will display a yellow horizontal line that can be dragged up and down using the LMB to set the appropriate level for peak picking.

c)   Once you have set the threshold, click the Find Peaks button to pick all peaks above the threshold line and display those frequencies.

d)      To print the spectrum with peak picking, go to the Plot page and click the Plot Spectrum and the Plot Spectrum Scale buttons.  Under Peak Frequencies, select On peaks, var, ppm or On peaks, var, list and click the Manual Plot button.

VII  Logging out

  1. Click the Start tab and select the Standard page, click the Eject button to eject your sample, remove your sample from the spinner. Click the Insert button to turn off the eject air.
  2. Go to File on the menu bar and select Exit VnmrJ to close the window.
  3. Click Actions in the top bar and select Log Out, then click the OK button.
  4. Sign the logbook with time out.


Inova 500 Console Reboot

Reboot the console if:

  • The spectrometer ignores your command to start an acquisition or to eject the sample.
  • The spectrometer queues your acquisition even though no acquisition is currently running.
  • The lock signal is a strange-looking series of vertical lines.


  1. Exit vnmrj. With the right mouse button pressed, select "Open Terminal".
  2. Within the terminal window type su acqproc<return>. The system will respond with "Stopping Acquisition Communication". Wait until the system displays a new prompt before proceeding.
  3. Open the left door of the console. Locate the "Magnet/Sample Regulation" module (8 slots to the right of the left edge), depress the RESET button. Then press the RESET button on the CPU module (the left most board). You will see the LED on the "Magnet/Sample Regulation" module turn red. Wait until it turns green and you see the LEDs on the remote status module (The unit sitting to the left of the computer monitor) cycle.
  4. Return to the terminal window and type su acqproc<return>. The system responds with "Acquisition Console at 500 MHz Ready". Press <return> to get the prompt, type exit to exit the Unix terminal shell. Type load='y' su<return> on the vnmrj command line. The system should display a message "setup complete". If is doesn't try exiting vnmrj and repeating the above procedure. If it still doesn't work contact one of the NMR Facility Staff.


Inova 500 Probe Cabling Diagrams

Changing the Probe

  1. After logging in and starting vnmrj select the probe you are installing from current probe list.
  2. Make sure there is no sample in the probe by typing e. Remove the sample if there is one then type i.
  3. Type jexp1 and load a file from your directory with appropriate parameters for the probe you are using. If you don’t have a file for the probe and only want to acquire a proton spectrum you can draq in the proton experiment from the locator window which will set the parameters appropriately. If you are going to run any other nuclei or experiment and don’t have a parameter file ask for assistance. Note: If you have loaded or setup a file that uses 1H broadband decoupling (i.e. 13C, 11B) set dm=’nnn’ before proceeding to step 4.
  4. You can load shims from your parameter file by typing load=’y’ su or if you used AuH in 3 above type rts(‘probe_name’) su. Where probe_name is the same as you used in 1 above.
  5. Type temp <return>. A new window will pop up. Select turn VT off. The green led on the remote status module should go off and the temperature should begin to drop.
  6. If you are removing a gradient probe you need to set the gradient power supply to standby. Facing the console open the left door and about midway is the gradient power supply. Position the toggle switch so that the display reads standby.
  7. Disconnect the VT connector, body air, VT air and all remaining coaxial cables from the probe. Make sure you disconnect the VT connector first!
  8. Unscrew the two screws on the mounting flange and lower the probe to remove it from the magnet. Put the red cap on the top of the probe and place it in it’s box with the VT air inlet pointing up. Close the box.
  9. Find the box with the probe you will be using and remove it. Take off the red cap. Make sure the upper stack is pushed all the way down then slowly insert the probe into the magnet. Some of the probes are keyed so that they will only engage the upper stack if properly oriented. Therefore you may need to rotate the probe back and forth a bit to get it to go all the way in. You still only need to apply gentle upward pressure to insert the probe properly (note: The VT inlet will always point toward the VT gas supply when inserted correctly). Once seated properly secure the probe in the magnet with the two mounting flange screws. Check that the upper stack has not been pushed up during installation. If it has, remove the probe and push the upper stack back down and reinsert the probe.
  10. Reconnect the cables and air lines to the probe. Make sure you reconnect the VT air supply and body air first and finish with the VT connector. Check the cabling diagrams for proper routing of the cables to the magnet leg.
  11. Return to the computer console and click on the reset VT button in the window that opened in 5 above. If the cursor is inside the spectrum display window it will show as a clock. Wait until it turns into an arrow. The displayed temperature should now be around 19-20 C. If it is significantly different than this you should remove the VT connector and reconnect it then do the VT reset again. If the temperature is okay you can now click on the turn VT on at 25 degrees button. The green led should start flashing and the temperature should start rising. Make sure it stops and is regulated before continuing with the next step.
  12. Type e <return> and place your sample in the upper stack. Type i <return> to insert it into the probe. You are now ready to tune the probe.

Probe Tuning

  1. Make sure you have inserted your sample and loaded a file appropriate for the probe and nuclei you will be tuning. Make sure dm=’nnn’ and type su. Note which nuclei the transmitter and decouplers are set for. When tuning, the transmitter nucleus will always be channel 1, the first decoupler will be channel 2 and the second decoupler will be channel 3.
  2. The following assumes you loaded a proton file with the first decoupler set for carbon. To tune the 1H channel start from the probe and follow the cable connected to the 1H or decoupler channel to the other end. Disconnect it and connect it to the connector labeled tune input. Next disconnect the cable from the 1H/19F preamp output connector and reconnect it to the connector labeled tune output. Select channel 1 using the push button selector and set the attenuation to 9. The led tuning scale should now be illuminated. Adjust the tune and match on the probe to minimize the reading. You should be able to get a reading of 001 but anything less than 010 is fine. Set the channel selector back to 0 then return all cables to their original connections. To tune the 13C channel, again starting from the probe connection labeled 13C or X follow the cable to the other end. Disconnect it and reconnect it to the tune input connector. Next disconnect the cable from the broadband preamp output connector and reconnect it to the tune output. Select channel 2 using the channel selector and an attenuation of 9. The led scale should light up and you can tune the 13C or X channel with the appropriate tune and match rod. Tuning for 13C or X nuclei is facilitated by the use of the numeric reading on the 5mm_sw and 8mm_id_pfg probes. Once a minimum value is obtained on the tuning scale return the channel selector to 0 and restore the original connections. Note: Other nuclei may require insertion of a capacitor or inductance rod. For some of the nuclei this is indicated on the probe base.
  3. You are now ready to lock and shim. 

Common Commands And Parameters


e            eject sample.

i             insert sample.


nt          number of transients to collect nt=64

ss         number of dummy scans to run before acquisition ss=4

ct          number of completed transients cannot be set by user

tn          transmitter nucleus tn=’H1’

dn         decuopler nucleus dn=’H1’

tof         transmitter offset, corresponds to the center of the spectrum tof=-167.4

dof       decoupler offset corresponds to a single peak frequency for home decoupling or the center of the indirecetly detecte dimension dof=22300.3

ga         start acquisition and do a wft when nt scans are complete.

go         start acquisition and do nothing when nt scans are complete. This is best for 2D and 3D experiments.

aa         abort acquisition immediately

sa         stop acquisition after end of phase cycle

bs         transfer from acquisition computer to workstation after bs scans bs=4

ni          number of 2D increments to perform. ni=256

phase  variable that controls how 2D data is collected phase=1,2

np         number of data points


ft           fourier transform the data and display the spectrum.

wft        do a weighted fourier transform of the data and display the spectrum.

wft2d    process magnitude mode 2D data set

wft2da  process phase sensitive 2D data set

lb            exponential line broadening applied when using wft. For 13C lb=3 for 1H lb=0.1


nl            moves cursor to nearest peak

rl             sets reference line. Select peak with cursor type nl then rl(7.26p)

cr            set cursor position cr=5.0p

cr1          set cursor in 1st indirect dimension cr1=5.0p for 1H,1H cr1=77.0d for 1H,13C

delta       sets second cursor position relative to first delta=3.0p

delta1     set second cursor position in 1st indirect dimension relative to cr1 delta1=10p for 1H,1H delta1=10d for 1H,13C

vp             vertical offset for displayed spectrum

dg            display parameter group in text mode.

ds            display spectrum on the screen.

dpf           display peak frequencies

dscale    draw a scale under the spectrum on the screen.

axis=’p’  set the axis values to ppm.

axis=’h’  set the axis values to hz.

f full         display full spectrum full x scale.

vsadj       vertical scale adjust. Scales displayed regions y axis to fill the window.


svf            save FID to disk. svf(‘file’)

svp           save parameters to disk svp(‘param file’)

rts            retrieve shim set rts(‘shim file’) 


pl              plot spectral display

pscale     plot scale

pap           plot all parameters

ppf            plot peak frequencies

pir             plot displayed integral data (vp must be > 12)

pltext       plot text associated with file

page        send plot buffer to plotter (i.e. pl pap pscale page)


text          text {cr} displays string, text(‘string’) sets text to string

jexp#       join experiment, you can have multiple acquisition blocks each containing different parameters/spectra #= 1-9.

cexp(#)   create new experiment, #= 1-9.

explib      lists contents of all existing experiments.

su             set up hardware.


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