Table of Contents

1. Unable to write, unable to jump experiments or display experimental library.

2. What do I do if the lock window disappears ?

3. What do I do if I break a sample in a magnet or in the NMR facility?

4. Why can't I log on as biopack?

5. Why can't I plot from vnmr?

6. Why is the plotter undefined?

7. When I have a spectrum I can only phase it in one small display at a time.

8. How to paste spectra by vnmr into Word or Word Perfect?

9. Adding data files (FIDS) after a you stop(sa or aa) and experiment and was unable to resume (ra).

10. Printed spectrum is too small and in a corner of the paper.

11. Viewing two spectra simultaneously

12. Rebooting console

13. Rebooting the SUN computer

14. Printing Stacked Spectra

Printed spectrum is too small and on a corner of the paper.

 The following command will help you adjust for the size of the spectrum printed. Please refer to the following manual for this and much more information.

Getting Started

Chapter 9 , Display, Plotting and Printing

Display Limits

wc= width of chart. Adjust the value of this parameter . This parameter varies with the type of printer installed. To check the max value allow for the printer type wcmax? and set wc= wcmax.

Also you can use the following commands to expand the width of you displayed spectrum.

full for full width 

f for full spectrum range.

Viewing two spectra simultaneously

Did you ever want to look at two spectra at the same time and determine any differences (e.g. to see if changing the probe temp affects peak location or to look at the progress of a reaction by comparing to the starting material)?
It's easy with the addi program.

NOTE: Prior to using addi, you should be sure you don't have any valuable unsaved spectra, parameters in exp5, because exp5 is the workspace used for this program. If you have never used exp5, you should be fine.

To view two spectra at a time and see the difference between them:

I. In VNMR, type: jexp1 and hit Return
II. Acquire or load a saved file as usual and type: wft f and hit Return.
III. type: clradd and hit Return. This clears exp5, which is the default add/sub buffer.
IV. type: spadd and hit Return. This adds the current spectrum to the add/sub buffer (i.e. exp5).
V. type: jexp2 and hit Return. Acquire or load a saved file as usual and type: wft f and hit Return.
VI. type: addi and hit Return. This will add the spectrum in exp2 to the add/sub program.
You should now see three stacked spectra:
The bottom spectrum is from the current window (in this case it's from exp2);
the middle spectrum is the one from exp1 that you added to the add\sub buffer using spadd;
the top spectrum is the sum of the two spectra (this is the default setting).
Interacting with Spectra:
On the bottom middle of the screen, you have two display terms; active: and mode:.
active: designates which spectrum is currently selected. Any actions you take, such as scaling size with the middle mouse, will change the active spectrum. To select a different spectrum, click on [Select]. Note that active: will change each time.
mode: designates the action taken to generate the result spectrum (top spectrum) from the other spectra. The initial mode is add, which is the sum of the two spectra. To switch to sub (subtraction of the spectra) or min (minimum points between each spectra), just click on [sub] (note that mode is now sub), click on [min] to get min, etc.
Printing the result (e.g. Difference between two spectra):
I. Once you have chosen the result you want, click [save].
II. type: jexp5 ds and hit Return. Now you have the result of either adding two spectra or subtracting two spectra.
III. Print, expand, etc. in the usual manner.
(e.g. type: pl pscale page)

Printing Stacked spectra
Did you ever want to stack multiple spectra and save them as an array (e.g. the stacked view and plotting for DEPT) for printing and displaying? Well, you’re in luck because it can be done. You can stack as many spectra as you want either horizontally or vertically, view individual spectra, and then save them as an array for later use.
TO PRINT STACKED SPECTRA: You will need to create an arrayed dataset, which will allow you to view and print all stacked spectra.
Note: type what’s in the ‘’ and hit Return.
Important Commands for Arrayed Spectra:
ds(#) - where # is the spectrum number in the array. The first spectrum is 1, the second is 2, etc. (e.g. ds(1) to display first spectrum.
dssa - displays all spectra vertically
dssh - displays all spectra horizontally
dssl - displays the spectrum number(#) to be used with ds(#)
pl(‘all’) - print all stacked spectra

I. Load the spectra in exp1 and add them to an array: type ‘jexp1’ - join experiment 1
II. Type ‘clradd’ - clear the add/sub buffer in exp5. This will erase anything in exp5.
III. Click Main Menu => File and select the first desired spectrum and click Load.
IV. Type ‘add’ - adds FID to add/sub buffer.
V. For adding all additional spectra, click File, select the desired spectrum, click Load, and type ‘add('new')’.
VI. Join exp5 and create array parameters: type ‘jexp5’ - join experiment 5.
VII. type ‘gain='y' ‘- turns off autogain, which is not allowed in arrayed experiments.
VIII. type ‘d2=1,2,3’... - sets arrayed variable. Use same number of variables as spectra. For example, if you want 10 spectra, type ‘d2=1,2,3,4,5,6,7,8,9,10’.
IX. Type ‘calcdim’ - calculates the array dimension.
X. Type ‘groupcopy('current','processed','acquisition')’ - updates parameters.
XI. Type ‘ai’ - resets to absolute intensity mode.
XII. Type ‘wft dssa’ - Fourier Transform all FIDs and display stacked spectra vertically. If you want horizontal stacks, type ‘dssh’.
XIII. Type ‘svf('your filename')’ to save the arrayed spectra.
You may need to adjust the phasing. If phasing is incorrect, type ‘ds(1)’ (this displays the first spectrum), or click Interactive. Type ‘aph’.
To adjust the scale of each spectrum: type ‘ds(spectrum number)’ (where spectrum number is an integer. For the first spectrum, spectrum number is 1: ds(1); for the second spectrum, spectrum number is 2: ds(2); etc.). Adjust the scale as usual. To check, type dssa.
XIV. To print, use standard printing commands except replace pl with pl('all'). For example, pl(‘all’) pscale pltext page.

What do I do if the lock window disappears?

If the lock window disappears try the following:

    a.  Type acqi.

If this doesn't work then try the following:

    a.  exit VNMR

    b.  logout of the console

    c.  log back into the console and reopen VNMR

If the window still does not appear then call someone on the NMR staff.  The instrument needs to be rebooted.

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What do I do if I break a sample in a magnet or in the NMR facility?

There are two cases of broken samples.  First, identify which category you fit into and then follow the directions given below:

    a.  Broken NMR tube on the bench (i.e. not in the magnet)

                Then, you need to clean up the mess!  Please wipe up all chemicals, remove broken glass from the NMR Facility, and take care of any other mess.  If you  broke a standard sample then please tell an NMR Staff Member so that the sample may be replaced.  If it is after hours then leave a note in the logbook.

    b.  Broken NMR tube in the magnet (i.e. the broken tube and its contents are now inside the NMR)

                Then, you need to notify an NMR Staff Member as soon as possible.  The NMR Staff Member will need to know what was in the sample and what instrument you are on.  If it is after hours then page someone on the contact list.  YOU MUST CONTACT SOMEONE!!!  If you fail to contact anyone and damage occurs to the probe, you are ultimately responsible.

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Why can't I log on as biopack?

You obviously don't have the password
 Sorry...

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Why is the plotter undefined?

The reason is that when your account was created default  parameters were used. This means that your account has the wrong  plotter configurations. On the inova300 the nearest plotter is called hplj4000 (landscape) and hplj4000_p(postcript).

On the vnmr command line please type 

        plotter='hplj4000' or plotter='hplj4000_p', or printer='lp'.

 Alternatively, you can use the menu buttons.

[main]->[more]-> [configure]->[select plotter]

Note new account are now created with the correct plotter and printers names.

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When I have a spectrum I can only phase it in one small display at a time.

You can only phase one small increment of your spectrum at a time because the 'phasing variable is set incorrectly.  This is an old parameter present since the time when computers had limited memory capacity (e.g. Gemini's, XL...). 

On the vnmr command line consult the variable phasing?

phasing=20  'this means 20% of your spectrum

phasing=100 'this means 100% of your spectrum'

Set phasing=100

Problem solved!!!

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How to paste spectra by vnmr into Word or Word Perfect?

Download the following document. 

Pasting_vnmr.pdf  

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Adding data files (FIDS) after a you stop(sa or aa) and experiment and was unable to resume (ra).

When stopping an acquisition you can resume the acquisition with the command ra. Sometime the acquisition will restart from the last ct point but some other times it will not.

You could save this experiment and begin another one and at the end add both data sets. Here is how to do it.

Assuming you upload both experiments in exp1 and exp2 respectively

         clradd jexp1 add jexp2 add

         jexp5

         setvalue('nt',<nt + extra_nt>,'processed')

         setvalue('ct',<ct + extra_ct>,'processed')

         wft

It works!

Provided by  John Tomaszewski in an AMMRL letter to a user.

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Printed spectrum is too small and in a corner of the paper.

Part I

The following command will help you adjust for the size of the spectrum printed. Please refer to the following VNMR manual for this and much more information about displaying spectrum.

Getting Started

Chapter 9 , Display, Plotting and Printing

Display Limits

wc= width of chart. Adjust the value of this parameter . This parameter varies with the type of printer installed. To check the max value allow for a given printer type wcmax? and set wc= wcmax.

Also you can use the following commands to expand the width of you displayed spectrum.

full =for full width 

f =for full spectrum range.

Part II

If this doesn;t work do the following.

I have found that some of the accounts have wcmax set to 200 not 250. The maximum wcmax for laser printer is 250. Somehow wcmax have been reset by a previous user to 200 and it remains at 200 until someone for the same group resets it to 250.

Set wcmax =250

then type wc=wcmax

This should take care of the problem.

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Unable to write, unable to jump experiments or display experimental library.

One possible reason is, you are not a member of the user group. A staff member should check the /etc/group file and add your name to a group.

another possible reason is that the ownership of the ownership of the experiment is not set up properly. the correct mode for the file under ~/vnmrsys/exp# should be rwerwer-e or 775. this is setup upon log in by a parameter know as umask which should be 002 i the files .login. Alos can be set up at the global level from the file ./etc/defaults/login

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Rebooting the SUN

If you have to reboot the SUN, do the following.

First type su acqproc on the sun. This stops communication between the spectrometer console and the Sun computer.

Then login as superuser:

su

see me for password

then type:

init 5

this will shut the computer down.

To restart just push the button on the form of the sun computer

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Rebooting spectrometer

If you have to reboot the spectrometer, do the following.

First type su acqproc on the sun. This stops communication between the spectrometer console and the Sun computer.

You can now either reset the console cpu or completely shutdown the system.

To reset the cpu:

-Open the first cabinet door on the console

-Press the reset button on the cpu board

-wait for ~ 1 minute until the lights ppear on the remote display

-type su acqproc again in the console

For a complete console reboot:, after su acqproc

-Go to the second console cabinet

-At the bottom is a card cages switch. Turn this off (pull it towards you and down)

-Then go to the back of the 2^nd cabinet and flip the black switch down

To start up the system:

-flip the black switch at the back of the 2^nd cabinet up

-wait for 30 seconds until the fans start, then press the green button just above the black switch

-after 2 minutes, go to the front of the second cabinet and turn the card cages switch on (pull towards you and up).

-once again you have to wait one or two minutes until the lights on the remote display come up. The type su acqproc

-Note after rebooting you will have to reset the temperature. In most cases you will have to search for the lock again, and the loack phase has a 75% chance of not being correct any longer

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