Trouble Shooting Page

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Troubleshooting

NB: All specific references to particular commands, menus, buttons to click, etc, are specific to the Varian NMR systems.

Why can't I lock the spectrometer?
Locking problems can be caused by incorrectly set lock parameters (Z0, lock power, lock phase, lock gain) and/or by very badly adjusted shims. If you are having difficulty locking, it is a good idea to start by loading a set of standard shims. Make sure that you are using a deuterated solvent and have selected the correct solvent under the setup menu. The indication of a successful lock is that, with the "LOCK: on" button near the top of the lock display selected, the dark area shows a short horizontal segment at the left, then a nearly vertical "step" to a horizontal or near-horizontal line at a higher level. The lock level has to be greater than 20% before the "NOT LOCKED" indication at the bottom left of the dark window changes to "LOCKED" If the system doesn't lock without intervention after you insert your sample, then click on the "LOCK: off" button and adjust Z0 until the lock signal is on-resonance. When the lock signal is off resonance, you should see something between several cycles of a sine wave to a fraction of a cycle. The frequency of the sine wave is an indication of how far off resonance you are; change Z0 in the direction that results in fewer cycles of the sine wave showing. Especially with weak lock solvents like CDCl3, it will help to temporarily increase the lock power to maximum, and increase the lock gain until you are sure that you see "noise" on the display. When you are very close to but not on exactly on resonance, you may not see any vertical "step", or it may change from up to down. When you are this close, clicking on "LOCK: on" should cause the lock to "pull in". Once you are locked, be sure to reduce the lock power to an appropriate value; for CDCl3 solvent in the Varian Mercurys, that would be about 28 db.
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How can I set a reasonable ("standard") starting set of shim values?
You can load a set of shim values with the Vnmr command 'rts' (retrieve shims). The set that we supply for each of the Mercury instruments is just called "standard". To load this set of values, type 'rts' into VNMR; you will be prompted for the name of a shim file. Type 'standard' and a message should appear stating that the shims have been loaded; now type 'su' to actually apply the new shim values that you have just loaded. The procedure is identical for the Unity 500, except that you need to specify a different filename (standard.hf, standard.bb, standard.id) according to which probe is currently installed. You can also store your own sets of shim values with the command 'svs'. This can be particularly useful if you frequently use "unusual" samples, e.g. smaller (shorter) sample volumes than usual.
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What if my sample (or the standard) won't eject?

You must NEVER, under any circumstances, attempt to extract a sample or spinner from the magnet by reaching into the magnet with any object whatsoever!

If you are unable to eject your sample normally because of a software problem (see below), you should be able to eject it using the manual EJECT button on the stand near the magnet. Note, however, that you should not use this button to insert another sample or the standard!
First determine if it is a problem with the software or with the hardware. If you don't hear a click and/or a change in the sound of air flowing when you type 'e' or click on "eject", then it is probably a software problem; see next question. If you do hear an audible change when you try to eject, then there is a problem with insufficient airflow or with the sample itself. The first thing to check is the VT gas connnection. to the probe. If the sample still doesn't eject with the VT gas line properly connected and the flow set correctly, then there is probably a problem with the sample itself. The most common problems are:

Someone has dropped a spinner without a sample tube into the magnet; because too much of the eject air can leak out through the central hole, the spinner won't eject.

Someone has dropped one sample and spinner in on top of another. The combined weight of the two is too much for the eject air to lift. When this happens it is very difficult to extract the samples without breaking one or both.

In either of these cases, leave a note on the console and notify facility staff; contacting us at the Forum is the best way. There is a possibility that no sample ejects because there is no sample in the magnet. Never immediately assume that this is the case! If you do, you are likely to create situation "B" above. There are several indicators you can use to determine if there is sample in the magnet. If the Acquisition Status or acqi window indicates a non-zero spin rate, then there is a sample present; likewise, if any lock signal is visible.
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What if: the acqi window is not responding correctly, or won't even open?
Or the instrument does not respond to commands that directly affect the hardware, like 'e' or 'go' or 'su'?
First, make sure you are joined to an experiment , then check the STATUS: line in the ACQUISITION STATUS window (top right of screen). It should say "Idle", "Acquiring" , or "Interactive", depending on what Vnmr is doing. If it says "Inactive", then it is necessary to restart the process that communicates between the Sun computer and the Varian console. To do this, type the command "su acqproc" in a shell window; then be guided by the messages you receive in response to this command. (This may involve resetting/rebooting the Varian hardware.)
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What does "Autogain Failure: Gain driven to zero" mean. What should I do about it?
This error message results when the Autogain procedure, which by default is run every time you type 'go' for an ordinary 1-D NMR spectrum, has decreased the gain to its lowest possible value (gain = 0), and the signal is still too large to avoid ADC Overflow. The error message also suggests a possible remedy: to reduce the parameter 'pw', the width of the RF pulse prior to signal acquisition. This will decrease the amplitude of the NMR signal by reducing the component of magnetization that is tipped perpendicular to the magnetic field after each pulse. Look for the parameter 'pw' in the parameter display, or type 'pw?' to see the current value of 'pw'. To reduce it by half, you can type 'pw=pw/2', or type in a different value. There are problems associated with reducing pw below 1 (microsecond), so if the Autogain failure problem persists even at a pw of ~ 1 microsecond, you can decrease the parameter 'tpwr', which controls the transmitter power and thus the strength of the RF field. Reducing tpwr by 6 dB ('tpwr=tpwr - 6') should have the same effect as halving the value of 'pw'.
And, next time, maybe you don't need such a high sample concentration?
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What does "ADC Overflow" mean?
This error message means that the NMR signal, after amplification in the preamp and receiver, has exceeded the maximum value that can be represented by the ADC (analog-to-digital converter, or digitizer). Normally, after a succesful "Autogain" procedure, ADC overflow should not occur, but it can occasionally happen. Reducing the 'gain' parameter less than that set by autogain (or less than the current value, if perchance autogain is not operative) will usually correct this. If the 'gain' parameter is inactive, typing 'gain?' will return, eg: "gain = Not Used ( 28 )",where 28 happens to be the gain value set by the last "Autogain" performed. If Autogain is not operative, the 'gain?' will just echo the current value of 'gain'. To reduce the gain, type, eg: 'gain=24', which will set the gain 4 dB lower, and also turn off the "Autogain" procedure for subsequent acquisitions.

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What do I do if I don't have an "Acqi" button on the top menu line?
First, make sure that you are joined to an experiment. Then type the command 'acqi' into Vnmr. The interactive acqi window should open up, and when you close it down with its "close" button, the "Acqi" button will appear on the top menu line.
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What is "Joining an Experiment", and how do I do it?
"Joining an experiment" is Varian's terminology for moving into a directory (folder) with the appropriate parameter files and subdirectories for collecting NMR data. Normally, when Vnmr starts up, you are automatically joined to whichever experiment you last used, but sometimes this doesn't work correctly. The topmost line of the topmost Vnmr window should have "Exp:n" near the center, where n is the number of the experiment you are in. If this is not there, you need to join an experiment; when you first started up VNMR, it probably complained about being unable to join an experiment. If you noticed this and remember what experiment number it complained about, try 'unlock(n)', where n is the experiment number. If you didn't notice this, try clicking on the "Workspace" button (far left in "Main" menu). There should be a button there labeled "Exp n" for each experiment 1 -9 that has been created; you can try to join an experiment by clicking on one of the buttons. If Vnmr complains that you can't join experiment n, try typing the command 'unlock(n)'
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What if 'unlock(n)' doesn't work, but just results in an error message about "unable to unlock experiment n"?
Sometimes VNMR is not able to "unlock" an experiment. For VNMR, "unlocking" experiment n means removing a file named "lock_n.primary" in your vnmrsys directory, which is the home directory for all your experiment subdirectories. This file is created whenever you join experiment n; its purpose is to avoid any possible collision between two people running Vnmr at the same time. The lockfile should automatically be deleted when you leave experiment n or exit VNMR, but sometimes one of the lock files doesn't get removed. If VNMR can't remove the lock file, you can do it from UNIX. Open a shell/terminal window to get a command line interface. You will be in your home directory; type 'cd vnmrsys'. If the response is "vnmrsys: No such file or directory", then your vnmrsys directory is not in your home directory, but in your group's directory, one level above; in that case, type 'cd ../vnmrsys'. (When the 'cd' command is successful, there is no response in the terminal window except the linefeed to a new line). Next type 'ls lock*' to see any lock files that exist in your vnmrsys directory. If you are not joined to any experiment, you can safely delete all of them with 'rm lock_*'. (Be careful when using the "*" wildcard, which matches anything - do NOT type 'rm *'! That would remove ALL of the files in the current directory! It is a good idea when using wildcard syntax to type 'ls [wildcard*expression]' first, to see what files it matches, before typing 'rm [wildcard*expression]') If you are prompted "lock_n.primary: override protection xyz (yes/no)?", it is safe to reply 'y'. After deleting the lockfiles, you should be able to join any previously locked experiment.
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What should I do if I have printing problems?
The most common remedy for correcting printing problems is to re-specify the plotter name on the VNMR command line. This can be done by typing the following:
plotter= ('plotter name')
Where the plotter name is hg400_plt for the 5th floor printer and hg402_lj3 for the 6th floor printer.
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I am interested in running a 2D spectrum. Is there a protocol that I can use to help me set things up?
While the facility does not maintain a protocol for running 2D experiments, users have access to the Varian "User Guide: Liquids NMR" manual. It does a nice job describing the step-wise process of acquiring and processing 2D NMR data, including optimizing the apodization for each dimension. It is advisable to start running 2D experiments with this guide. If this has been attempted and you are still experiencing problems, feel free to contact the NMR facility at nmr@chem.ucsd.edu
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How do I run a COSY?
The Varian set-up macros (typing "COSY" or "NOESY" on the command line, for example) do an adequate job of correctly setting most spectral parameters. It is recommended to use a standard sample the first time you run an experiment so that you may compare your final data set to those published in the Varian guides. To get started, of course, help beyond the Varian manuals is available: people wanting help setting up a multidimensional NMR experiment (or any unfamiliar experiments) should send an email to us.
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Why are there so many peaks in my 1H NMR spectrum?
If signals are being observed with a reasonable S/N ratio, it is unlikely that the additional peaks are due to a spectrometer malfunction. Make sure that the sample is properly shimmed. Excessively broadened lines or peak doubling is a common side effect of poor shimming.
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How can I control the temperature?
First of all, make sure that the VT gas supply to the probe is correctly connected and adjusted. You may also need to reset the VT controlleer. To access temperatures above ambient, type 'temp=x', (where x is the desired temperature in Celsius), on the Varian command line; then type 'su' to actually begin VT operation. It is crucial to observe the temperature limitations of each spectrometer. For a list of temperature ranges, please refer to the respective spectrometer web page on this website. For temperatures below ambient, it is necessary to chill the cooling coil and it may be necessary to use dry nitrogen gas, depending on the temperatures required. Filling the Styrofoam container or dewar that contains the cooling coil with ice should enable you to lower the temperature to ~ 12 degrees C. To access temperatures below this, please email us so we can assist in proper set-up.
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How should the gas supply for VT operation be connected and adjusted?
The tube between the probe and the VT gas supply frequently becomes disconnected; this is a black tube that runs between the base of the probe and the beige plastic top of the styrofoam bucket or dewar that holds the coolant for low temperature experiments. There is a black rubber "boot" that joins the tube (small end) to the beige plastic top (large end). The large end frequently pops off the beige plastic and needs to be reattached. One symptom of the VT gas being disconnected is a probe temperature above 30 degrees C even when the temperature controller is set to 25 degrees or not used. If it pops off again immediately, there is a problem with the air flow. Check the VT gas flow (the VT flowmeter is on the two-legged stand near the magnet - the black ball should be on "10" ("12-13" for the 500). Reduce it with the needle valve if it is too high). If the connection still pops off with the correct flow reading, then there is an obstruction to the gas flow within the probe - usually because the sample has been inserted too deeply into the spinner.
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How (and when) should I reset the VT controller?
The VT controller is an easily visible module located in the Varian console that is recognizible because it continuosly displays the temperature. On the Mercurys, it is located at the top center of the area behind the tranparent plexiglass door. On the Unity 500, it is located near the top on the side nearest the Sun computer. There are several conditions which will place it in an "error " state where it will not control the temperature. One such condition is being disconnected temporarily from the probe; another is excessive probe heater temperature caused by interruption of the VT gas flow. On the Mercurys, the error state is indicated by a red light at the lower left corner of the VT module; it can be reset as follows: type the command 'temp' (not 'temp=') into Vnmr. A small "Temperature Control"window will open up; click on "Reset VT" in the lower left corner of that window. The text ("Press 'Reset VT'......") to the right of the button will blink for a few seconds, and the red light on the VT module should go out. Now close the "Temperature Control" window, set the desired temperature ('temp=...') if you haven't already, and type 'su' to initiate temperature control. On the Unity 500, there is no external indicator of the error condition. To reset the VT controller, turn the unit off (press the power button to the left of the temperature display), wait a few seconds, then press the power button again to turn it back on. Establish temperature control as above.
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What if I break my sample in the magnet or drop my
sample into the bore?
If there is a sample broken inside the magnet, or if you even suspect that there is a sample broken in the magnet, DO NOT insert another sample, or the standard! Leave the spectrometer with no sample or standard inserted, and be sure to leave a note on the console.
If this should happen, it is imperative that you contact the NMR Facility staff. Please alert us as to the solvent, dissolved materials, and indicate if any of the materials pose a possible health risk. We realize that accidents do happen, however, failure to report a broken sample you are responsible for will result in suspension of your NMR accounts.

You must NEVER, under any circumstances, attempt to extract a sample or spinner from the magnet by reaching into the magnet with any object whatsoever!

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