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I am on Varian 600

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Preparation of the spectrometer

Tuning

Locking

Gradient Shimming

Making a new experiment in the workspace

Proton and carbon 1D

2D experiments and other exciting stuff

Saving my data

Finishing my work

Importing and processing NMR data to Topspin

Restarting VT/Gas control

Solvent reference data

 

 

 

Specialized procedures (require separate training!)

Using variable temperature

Restarting spectrometer (only by authorized users!)

Turning on the spectrometer after a power outage (only by authorized users!)

Restoring cable contact for carbon tuning (only by authorized users!)

 

 

 

 

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Preparation of the spectrometer

 

1. Verify functional state of the Air supply and VT module

As you walk into the room: check that variable temperature and air supply modules are functional. Your standard operation temperature will be 25 Deg C. For using other temperatures see Using variable temperature section.

1. Find Air supply and VT module in the room:

   
   

   
   

2. The VT module contains the FTS Systems control box  sitting on top of the AirJet.

   
   

   • First, check that the AirJet is OFF. If - not, then press the green switch to turn it off.
     
     
   • The FTS module on top has a display. If green "RUN" is lit, press white "RUN" button once to turn it off:

     

• Check air flow value in the Air supply unit (this is actually N2 not air):

  

   

  

NOTE: If you don't see normal gas flow value of about 12 L/min, you need to restart VT and air supply system. See: Restarting VT/Gas control

At this point, the VT module and Air supply (Pneumatics) are in a correct state.

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2. Start temperature control through VNMRJ

• Log into workstation
  
  
• start VNMRJ software
  
  
  
  
• Type on a command line:  vttype=0
  NOTE: You should do this every time after restarting VNMRJ!
  
  
• Set temperature to 25C
  
  • Open Start tab:Spin/Temp section
  • Check the checkboxes
    • Control spinner fromn this panel only and
    • Control temperature from this panel only
      
      
  • Enter 24 in the Temperature subsection
    
    
    
    
  • Hit Enter key on keyboard
    
    
  • click Regulate Temp button on screen.
    
    

    In 3-5 min you should see it stabilized on the VT display:
    
    
    
    NOTE: If temperature was very different before you came (10-20 degrees away from 24), you will need to wait 5-10 minutes to allow for thermal equilibriation of the probe and the sample.
    
    
    NOTE: Spinning on this machine is not stable and not recommended.
    

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3. Insert sample in the spinner

1. Carefully insert the sample in the spinner
   
   
2. Insert spinner in the depth gauge
   



Optimal sample volume for the 5-mm tube is 550 uL. For deuterated organic solvents and D2O, you may safely put more.

Adjust the tube in the spinner so that it touches the bottom piece of the depth gauge



The dashed area shows where the coils are. This is the "active volume" from where signal is detected. If your sample is smaller than 550 uL, you need to make sure top and bottom of the solution are at equal distance from the center line of the active volume.

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4. Insert sample in the magnet

• Unlock the instrument:
• Click on Start tab, Lock section
• Uncheck Lock checkbox
  
  
• Turn off spinning
• Click on Spin/Temp section
• Click Spin off




• Click Eject button
• Replace standard sample with your sample at the top of the bore
• Click Insert button

Your sample and spectrometer are ready for tuning, locking, and shimming.

 

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Tuning

Tuning may be done in any workspace. I recommend assigning the workspace #1 just for tuning

 

• issue trtune('remotely') on a command line. If re-using workspace 2 - no need for this command as trtune interface is already set in the workspace.
  
  
• Navigate to Acquire tab
  
  
• Select
  • 1st Center Frequency: H1,
  • 2nd Center Frequency: C13
  • # Traces : 2
    
    
• Click Start
  
  
• Change Span if necessary
  
  
• Change spectrum magnification: Autoscale, then click Vertical Display button
  
  
• Hint: To maximize the screen view to see it from the probe: click on [x] in the right-hand side of the Parameter panel. To bring it back you go to top menu bar View: Parameter Panel
  
  
• Go to the probe tune boxes. If you need to tune both proton and X nucleus, start with Broadband Channel

Broadband channel

• Set initial Span field for 100 MHz, Hit [Enter]
• If needed, click Autoscale
• Locate two ProTune boxes for Channel 2, find knobs for X Match,  X Tune 2, X Switch, and X Tune 1
• Tuning to 13C:
  Rotate X-Switch to move slider on the probe body to the 13C position. Turn X Tune 2  to see '07' in the window to the right of the slider face. Turn X Tune 1  to see '07' in the window to the left of the slider face.
• Tuning for 15N or 31P: look up the numbers next to the windows on the probe body
• Tuning for 17O: Center frequency - 81.33 MHz, Slider - to 80-90 position, X Tune 2 to 52, X Tune 1: start with 07.
• Rotate X Match to find a moving dip and make it sharper.
• Rotate X Tune 2 to position near the center line. 
• Switch Span  value to 10 MHz and fine-tune the positioning and depth of the dip

High-frequency channel: 1H or 19F

• Rotate HB Match to find a moving dip and make it sharper.
• Rotate HB Tune to position near the center line. 
• Switch Span and click Autoscale as necessary
  
  

Here is a view of a tuned probe with 3 MHz Span

NOTE: If the carbon profile is not looking symmetrical (above), this means the cable contact in the console is not good. Follow these steps to try to restore contact: Restoring cable contact for carbon tuning

 

Finishing Tuning

• Click Stop to stop tunning. 
  
• Proceed with locking.

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Locking

• Verify that your sample contains at least 10% of the deuterated solvent
  
  
• load the standard shimset:
  • issue rts
  • enter a name of a good shimset that you have saved before (if you don't have it - ignore this step)
  • issue su
    
    
• Join the first workspace
  • Viewport tab
  • Workspace section
  • Type 2 in the Current Workspace window and hit Enter
    
    
• Click on Start tab, Sample Info section
  
  
• Set Solvent to your solvent either clicking a button or selecting from the drop-down list.
  
  
• Click on Lock section
  
  
• Click Select Lock signal button,
  • Choose Measure 2H spectrum
    • on a spectrum, zoom in around the 2H line (left and right mouse buttons and click a toolbar on the right: Zoom In)
      NOTE: This step helps you verify if you have lock solvent in your tube. No spectrum - no lock solvent!
      
    • click on the 2H line
  • Click Move cursor to the nearest line
  • Click Adjust z0 NOW!
    
    
• Read value of Lock Level. 
  • If it is >20, you are good to continue with Tuning and Shimming.
  • If it is <=20, you need to try to adjust lock manually

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Manual lock adjustment

• Turn off lock regulation: Uncheck Lock checkbox. You should see Lock Status go to Off
  
  
• Click Lock Scan button
  
  
• Set
  • lock Power level to 40 (hit Enter)
  • lock Gain to 40 (hit Enter)
    
    
• Adjust Phase to put all signal into red trace (blue goes flat)
  
  
• Adjust Z0. Goal: the step-like FID without curvature - the higher the better
  • click on Z0 button to fine-tune: right click reduces the Z0 value, left click - increases, middle click changes step. Use step of 1
    
    
    
• Check if lock level is not saturated:
  • note the Lock level value (for example, 62)
  • change Power level down by 6 dB (for example, from 40 to 34), hit Enter
  • read new Lock level (for example, 32).
    • If it is
      • increased it certainly was saturated! Reduce Power level by another 6dB

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      • approximately 1/2 of the initial Lo ck level value (for example, 62 went to 32), the lock is not saturated: you can set the Lock Power back and continue;

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      • greater than 1/2 (for example, 62 went to 45), lock is saturated and will not be stable. You should set Power level to smaller than the original value by 3 dB and repeat this test.

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• Finally, turn on lock regulation:
  • Check Lock checkbox.
  • Note
    • Lock Status changed to Regulated
    • Record your lock level in your notebook
  • Unclick Lock Scan
    
    
• Proceed with tuning of your sample

 

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Gradient Shimming

You must shim every new sample and also re-shim if you changed temperature or did a very long acquisition (>3 hours).

NOTE 2: You must have a good lock level (>20) to for success of gradient shimming! If your lock level is very low, verify that you

1. have lock solvent in your sample
2. loaded good previous shims
3. went through manual locking procedure to adjust z0 and phase
4. verified that lock is not saturated - adjust power and phase (see Locking)

 

I recommend performing shimming in a dedicated workspace: #3

• Join experiment 3:  Enter 3 in Viewport:Workspace:Current Workspace field
  
  
• Issue gmapsys
  This command sets up a gradient shimming experiment. If you already did gradient shimming in this workspace before, this command is not necessary.
  
  
• In the Parameter Panel, navigate to Acquire:Gradient Shim
  
  
  
• Make sure you have
  • checked Shim z1-z4 first
  • Have 5 in # Shims Used
  • Verify you have the most recent shimmap shown in the Current mapname window
    
    
• Record in your notebook the current lock value
  
  
• NOTE: Spinning on this machine is not stable and not recommended. If you still want to use spinning:
  • Choose Sync with spinner in the drop-down list on the bottom of Parameter Panel
  • turn it on in Start:Spin/Temp
    
    
• Click on Gradient Autoshim on Z
  
  
• Open the system messages window (click on the left of two square buttons at the bottom of the screen):
  
  
  
  
  
  

How to understand the Gradient Shimming output:

1. Note Iteration #1 starts with relatively high rms err of 13.17 (Hz)
2. At Iteration #2, rms err was reduced by adjustment of z1-z4 shims
3. Addition of z5 to adjustment increases rms err (temporarily)
4. By Iteration #4, the rms err was reduced to 0.48, which is a good low value.
   
   
   

Important steps to complete the shimming:

• Save the shim set to be able to start from it in the future:
  • svs
  • Enter the filename (usually 'current')
    
    
• Adjust lock:
  • dial the value down to below 100 (range from 50 to 80 is good) by reducing Power in Start:Lock section
  • Verify if lock is not saturated (it may become saturated if the shims improved a lot and you use neat deuterated solvent).
    
    
• If you adjusted the lock down, you may want to run Gradient Shimming one more time to further improve shimming.

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Making a new experiment in the workspace

 

• Just enter a new number in Viewport:Workspace:Current Workspace field
  
  
  
• issue explib to view the current workspaces that are available
  
  
  • NOTE: it will not work out of the workspace where you do tuning
    
    
  • NOTE 2: sometimes - issuing explib twice is necessary to refresh the screen

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Proton and carbon 1D

 

Workflow for initial set up:

• Go to a workspace where you want to set up this experiment
  
  
• Go to Experiments: Proton or Carbon
  
  
• Change sample Information  Start Tab : Sample Info section,  Comments
  
  
• IMPORTANT: Change Solvent to your solvent. The default is D2O and will cause shifting of a ppm scale in the processed data of other solvents!
  
  
• in Parameter Panel, display Acquire tab
  
  
• Adjust necessary parameters: number of scans, spectral widths and center frequencies
  
  
• Make sure to change "Block size" to 4 (FID will be saved and reprocessed after every four scans)
  
  

 

How to run an experiment with the same parameters as before

• Go to a workspace you want
  
  
• Load the dataset that was acquired previously via  File:Open
  
  
• Change sample Information  Start Tab : Sample Info section,  Comments
  
  
• Adjust parameters

  
  

• Check time
  
  
• Make sure Autogain is checked
  
  
• Run it by clicking Go
  
  
• You may process incomplete experiment: see Process tab
  
  
• Save data after it is finished Saving my data
  
  
• Do processing and analysis in TopSpin Importing NMR data to Topspin

 

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2D experiments and other exciting stuff

To setup any complicated experiment :

• Run appropriate 1D from Experiments:Proton
  
  
• Convert parameters to the desired experiment using Experiments selection in a section Convert Current Parameters To Do
  
  
• IMPORTANT NOTE: All 2D experiments require accurate 90-degree pulse value. Some samples will work with the default values but some will not. For best sensitivity - determine 90 degree pulse time for proton and X-nucleus
  
  
• Adjust number of scans, spectral widths and center frequencies
  
  
• Adjust gain by Find Gain
  
  
• Run (hit Go)
  • To process incomplete experiment: unclick checkbox F1 linear pred in Process:Basic:Process Options
    
    
• Save data after it is finished Saving my data
  
  
• Do processing and analysis in TopSpin Importing NMR data to Topspin

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More on 2D and other experiments

• Complex NMR experiments: 2D, selective, etc. (separate HTML page)

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• DOSY experiments

 

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Saving my data

Every experiment performed in the workspace must be explicitly saved to a vnmrsys/data. This is where the NMR server pulls your data from.

• Select File:Save As
• Make a folder for current experiment set and enter it
• Add your file name to the path shown in File Name
• Click Save

NOTE: At a later time, you may open any of saved files into any workspace to look at the data or run a new experiment. This will replace data in the workspace but the source file in the vnmrsys/data will not be affected.

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Finishing my work

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Remember to save your data from every workspace where you did acqusition! See Saving my data

Insert a standard sample in the magnet

• Unlock the instrument:
• Click on Start tab, Lock section
• Uncheck Lock checkbox
  
  
• Turn off spinning
• Click on Spin/Temp section
• Click Spin off




• Click Eject button
• Replace your sample with a standard CDCl3 sample at the top of the bore
• Click Insert button
• Lock on the standard see Locking
  
  
• Exit VNMRJ
  
  
• Log out and answer all questions accurately.

You are done with the Varian 600.

 

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Importing and processing NMR data to Topspin

 

Importing data

• From main menu in Topspin, click File:Open
• choose "Open NMR data stored in special format"
• set File Type: VNMR
• click OK - browser window opens
  
  
• Navigate the window into the folder containing your NMR experiments (typically folders with .fid extension)
  
  
• Select one of the experiments (name.fid folder) and click VNMR data conversion button
  
  
• A vconv window opens
  • set EXPNO field to 1
  • DIR field should contain a full path to where your converted data should be. I suggest creating a separate folder on the same level with the original Varian data. Example:
    • My data were in /Users/kovrigin_laptop/Documents/Workspace/Data/Data.XVIII/EKN98.Dale.full_reaction.repeat/data
    • experiment was exp7.fid
    • I copy-paste the ENTIRE path from VNMR-name field into DIR omitting the actual experiment name
    • modify last folder name data to become data_converted
    • select entire path and copy it to clipboard - we will need it to set up a new folder in Topspin Browser (below)
      
      
      
    • Click OK
      
      
• Add the folder with converted data to the Topspin Browser:
  • Right-click in the Browser window of Topspin and select Add New Data Dir
  • paste the new path from clipboard to DIR field
  • Enter convenient name to in ALIAS field to be displayed in Topspin Browser (in my example Varian)
    
    
• View the newly converted dataset same way as standard Bruker data
  
  
• Now you can return to File:Open to convert more files
  • the conversion window remembers your paths. All you need to do is to select a new Varian .fid folder
  • to refresh a list of converted files in Browser you should fold and unfold the folder by clicking on an arrow next to its name
    
    
    
  • Whether you have .fid extension on Varian datasets or no extension - does not matter.
    
    
    
• NOTE: Sometimes Topspin hangs after conversion. To clear the condition navigate your file browser to the folder (on Mac) /Applications/TopSpin 3.5pl7 Utilities and launch the Terminate TopSpin.app.
  
  
  
  
• After that - start Topspin again
  

 

 

Processing a 2D Varian data in Topspin

For experiments performed with States-TPPI frequency discrimination mode (most common experiments):

• Set ACQUPARS:Experiment section: FnMode = States
• Set PROCPARS:Fourier Transform section, MC2 = States
• Click Process

If the 2D experiment was performed with Rance-Kay (Echo-Antiecho) mode, then you should choose this mode for both settings above.

 

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Using variable temperature

IMPORTANT NOTE 1: Only change temperature in steps of 10 degrees followed by 3 minutes wait time after every step.

IMPORTANT NOTE 2: Only change samples while you are within -80 to +80 Deg C. When above or below these limits: change temperature first to shift probe to the inside the limits then - change the sample.

Here is why: the probe contains expensive glass insert which is a double-walled evacuated insulator. Step-wise increase in temperature allows thermal stress to dissipate safely for the glass. Eject action passes a lot of room-temperature air through the probe - also stresses glass.

• Using the temperature HIGHER than a room temperature
  
  
  
  
  
• Using the temperature LOWER than a room temperature with Air-Jet FTSSystems chiller

 

 

 

 

 

   Using the temperature HIGHER than a room temperature

• Verify that the Air-Jet is off and FTSSystems box is not running
  
  
• Use Start tab, Spin/Temp page to start regulating temperature at 10 degrees above room temperature. Wait 3 min.
  
  
  
  
• Increase the temperature in 10-degree steps. Wait 3 min after each step.
  
  
• After you reached the final temperature, wait full 10-15 minutes (for equilibration of your sample and NMR system)
  
  
• It is necessary to lock, tune and shim again before you start acquisition. You can eject and insert the sample while below 80 Deg C. When you are above this limit - you must lower the temperature first.
  
  
• After you finished acquiring data, you must bring probe temperature back to room temperature in the same slow manner: 10-degree steps with 3 minute wait time in between.

 

 

Back to Using variable temperature

 

   Using the temperature LOWER than a room temperature with Air-Jet FTSSystems chiller

• Use Start tab, Spin/Temp page to start regulating temperature at 20 degrees C.
  
  
  
  
• Check whether the Air-Jet and FTSSystems box are running.  If not - turn on the Air-Jet (chiller) by using the green button.
  
  
  
  
• Set temperature on the VT gas supply 10 degrees lower than the desired temperature in the probe (use arrows on the FTSSystems control panel).
  
  
  
  The lowest temperature you can set is -80C. The actual lowest temperature in the probe will be, probably, -60 to -40 C.
  
  
• Push Run button to start temperature control for the VT gas. It will take some 10-15 minutes for the gas supply to become sufficiently cold.
  
• Use Start tab, Spin/Temp page in VNMRJ to reduce the temperature in 10-degree steps. Wait 3 min after each step.
  
  
• After you reached the final temperature, wait full 10-15 minutes (for equilibration of your sample and NMR system)
  
  
• It is necessary to lock, tune and shim again before you start acquisition. You can eject and insert the sample while above -80 Deg C.
  
  
• After you finished acquiring data, you must bring probe temperature back to room temperature in the same slow manner: 10-degree steps with 3 minute wait time in between.
  
  
• Once your are back to room temperature:
  • Set temperature in Start tab Spin/Temp page to 24 degrees.
  • Turn off Air-Jet
  • Push Run button on FTSSystems box to stop it (Run light should go out).

     

Back to Using variable temperature

 

 

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Restarting VT/Gas control

Go to Start tab, Spin/Temp page;

 

Reset air supply

1. Click Start : Spin/Temp
   
   
   • Setting for the VT Air Flow should be 10 L/min
     
     
2. click Reset Pneumatics
   
   
   • you should see the lights on the router stop flashing
     
     
   • Air flow  on the router gauge should be 10-12 L/min

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Reset temperature controller

1. Click Start : Spin/Temp
   
   
2. click Reset VT
   
   
   • watch the screen of the VT display show PASS and return to temperature value
     
     
   • Message bar shows "This operation takes a moment"
     
     
   • wait for it to switch to  "Set hardware operation complete"
     
     
3. Start temperature control
   
   
   1. Enter 24 (for 25C in the probe)
      
      
   2. click Regulate  Temp
      
      
      • you should hear a knocking sound of the pressure valves switching
        
        
      • NOTE: If you need a temperature below 20C you need to be trained to use FTS temperature control system! (see Using variable temperature)
        
        

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     Restarting spectrometer (only by authorized users!)

This is a procedure for complete reboot of the VNMRS system if you see some "weird" behavior. There are two versions of the sequence: Light and Full Reboot.

Light Reboot

Use as the first remedy. This procedure re-initiates communication between PC and the VNMRS system. Takes about 2-3 min.

1. Save shims first in VnmrJ
   1. type svs
   2. give an easy-to-remember file name:  current
      1. type 'y' if file exists

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2. Exit VnmrJ

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3. Stop communication with the console
   1. Open a terminal window (right-click on the screen desktop background, choose "Open Terminal")
   2. Type in su acqproc
   3. Wait till you see the command line prompt again
   4. type su acqproc again to start communication of the desktop computer with the console

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4. Start VnmrJ
   • you should see green status bar with "Idle" in it.
   • If you see a yellow bar with "Inactive" - stop and report a problem to NMR Center staff!

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5. Load shims
   1. type rts
   2. type the file name: current
   3. type su

You may proceed with locking/tuning/shimming, etc.

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Full Reboot

Use this procedure if the Light Reboot sequence did not help.

1. Save shims first in VnmrJ
   1. type svs
   2. give an easy-to-remember file name:  current
      1. type 'y' if file exists

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2. Exit VnmrJ

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3. Stop communication with the console
   1. Open a terminal window (right-click on the screen desktop background, choose "Open Terminal")
   2. Type in su acqproc
   3. Wait till you see the command line prompt again

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4. Log out of your account (this step may be skipped if no abnormalities to computer operation is observed)
   
   At this point you may also reboot the PC. It will create a completely clean state of the system.

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5. Log in

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6. Restart VNMRS system
   1. Push the reset button on the right-most board (labeled MASTER)
      
   2. Wait till the console restarts - the lights begin flashing again
      • you will hear a hiss at the pneumatic router and see flashing LEDS - normal!

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7. Start communication of the desktop computer with the console
   1. open the terminal window
   2. type su acqproc
   3. wait till the operation finished (you see new UNIX prompt)

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8. Start VnmrJ
   • you should see green status bar with "Idle" in it.
   • If you see a yellow bar with "Inactive" - stop and report a problem to NMR Center staff!

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9. Load shims
   1. type rts
   2. type the file name: current
   3. type su

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10. Reset air supply
    1. Click Start : Spin/Temp
       • Setting for the VT Air Flow should be 10 L/min
    2. click Reset Pneumatic Router
       • you should see the lights on the router stop flashing
       • Air flow  on the router gauge should be 10-12 L/min

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11. Reset temperature controller
    1. Click Start : Spin/Temp
    2. click Reset VT Controller
       • watch the screen of the VT display show PASS and return to temperature value
       • Message bar shows "This operation takes a moment"
       • wait for it to switch to  "Set hardware operation complete"
    3. Start temperature control
       1. Enter desired value
       2. click Regulate  Temp
          • you should hear a knocking sound of the pressure valves switching
          • NOTE: If you need a temperature below 20C you need to be trained to use FTS temperature control system!
            
            

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12. Turn on spinner (if needed)
    NOTE: Spinning on this machine is not stable and not recommended.
    1. Set spin speed to 20 Hz
    2. click Regulate Speed

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13. wait 5 min to allow for all values to equilibrate

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14. you may proceed with locking/tuning/shimming, etc.

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Turning on the spectrometer after a power outage

If there was a power outage and the UPS did not hold for long enough, the spectrometer console shuts down and does NOT automatically restart after the power has been restored. You will find spectrometer console silent and VNMRJ will be showing "Inactive" in its status bar. If you open the right door of the console cabinet you will see no lights:

 

You will need to turn on spectrometer console, reconnect with VNMRJ and reset the VT gas supply. To do this:

1. Exit VNMRJ

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2. Approach the back spectrometer console:
   
   
   

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3. Find "Main Power" switch and flip it down (if it was up) then flip it up. After that, push the green button to start the console.
   
   
   

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4. Check the startup of the console: open right door and look at the lights of the digital boards. Immediately after restart you may see only a few lights:
   
   
   
   which will change into a "dynamic display" of blinking lights running up and down -- similar on all boards:
   
   
   
   A this point, the console has been fully started.

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5. Close the console door

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6. Launch Topspin

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7. Follow this link to restart VT gas control:  Restarting VT/Gas control
   

 

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Restoring cable contact for carbon tuning

This procedure is due when the X-nucleus tuning curve in trtune('remotely') does not have a symmetrical shape like this (green):

When the console cable connection goes bad, the green curve would look very significantly lopsided or distorted. This leads to poor sensitivity on X channel.

Protocol to remedy the issue:

• Have the tuning experiment running and carbon and proton curves displayed
  
  
• Open the right console door:

• locate the X-channel cable

• gently move it sideways while looking at X-channel tuning curve - must shift to a symmetrical shape:
  
  

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