NMR DIRECTIONS
Using Varian NMR Software (VNMR) on the SGI Workstations
Version 8/12/97
Getting Started:
A. Importing the data from the NMR system into your directory:
Before opening the NMR software you must download your spectrum
from the directory where it resides and copy it into your own directory.
1. Log on to an SGI workstation as usual.
2. In the winterm box, type get_nmr_data filename.fid at the % prompt,
where filename.fid is the name of the file that you wish to download
Note that there is a space between data and the name of your file!
Your filename will normally be your initials, followed by your lab
day, followed by the lab number, e.g. bjj-day4pm-lab3.fid.
3. The data will be placed in your vnmrsys/data directory. You are now
ready to run the VNMR software.
a. If it is not already open, open a Winterm (blue box) by
choosing Desktop/Unix Shell from the menu at the top of the screen.
b. If you need to see which files are available for downloading,
type fm /nmrdata at the % prompt. A window will appear showing
all the files that are available for downloading. Note that
there is a space between the fm and the backslash!
B. To Select a Printer
YOU MUST SELECT THE PRINTER AND PLOTTER AT THIS POINT.
1. Start the VNMR software by clicking, in order,
Applications/Chem/VNMR/VNMR(SGI).
2. In the top VNMR window, click the main menu button, then the more
button.
3. Click the Configure button.
4. Click the select plotter button until it selects the printer/plotter you
wish. This is a toggle switch which will scroll ahead to a
different option each time you click it. You want it to say
plotter set to AS233PS (the laser printer) in the top VNMR
window. If it doesn't, click on select plotter until it does. Do
the same with select printer(choose AS233PS).
5. Click the return button.
Notes:
a. If you did not log out of this software properly the last
time, the system will tell you that the experiment is locked by
remote host or it will tell you that it cannot read file that you
are trying to download. If this happens, close VNMR, go to the
winterm and type rm ~/vnmrsys/lock_1.primary. This will get you
properly logged off and allow you to proceed after you
restart VNMR.
b. When the VNMR software starts, three windows are generated.
In the top one, commands are typed on a command line or buttons
are selected to perform operations on the data. In the middle one,
the spectrum is displayed. In the lower (third) one, numerical
values are displayed. It is important to note that when the second
window appears, it obscures a second row of buttons in the top
window. Thus, the first thing you must do is drag the second box
down about a half an inch. A second row of buttons will appear.
c. If at any point you get lost in this software, it is a good
idea to return to the main menu. You should also know that most
menu pages in this software have more buttons than can be shown at
once; to view the others, you simply have to click on more or
return. Also, if at any time you find you can't interact with your
spectrum anymore (it seems "frozen"), you need to go to main
menu, click on display and then interactive.
3. To load a Data File in VNMR
Your data, once you have imported it, will be located in the directory
vnmrsys/data. These instructions let you change to that directory and load
the data.
1. In the top VNMR window, click the main menu button, then the
More button.
2. Click the file button.
3. In the middle window, a number of available files will be shown.
Click on the vnmrsys directory. Then, in the top window,
lick the set directory button.
4. In the middle window, click on the data directory. In the top window,
click the set directory button.
5. In the middle window, click on the filename.fid you wish to load, and in
the top window,click the load button.
6. Once the file is loaded, type wft in the top window (and hit enter) and
your spectrum will appear.
Basic Manipulations of Your Data
Note-For most of the operations below, all three buttons of the mouse
are active!!! When clicking on the spectrum with the left-hand,
middle, or right-hand button isappropriate, the word click will be
followed with LH, M, or RH to indicate whichmousebutton to use.
Clicking on menu buttons is always done with the left hand mouse button.
Phasing
If any of your peaks dip below the baseline, some phasing may be needed.
1. Type aph. (this applies autophasing).
Notes:
a. If autophasing doesn't work, you will need to do manual phasing.
1. To accomplish this, click on the phase button.
2. Click (LH) on a large peak near the right side of your
spectrum that is improperly phased. Some red lines will appear.
Click (LH) and slowly drag the mouse up or downuntil the peak
is well-phased (even at the baseline).
3. Now click (RH) on a second peak near the left side of the
spectrum, even if it appears to be well-phased already.
Repeat the procedure from the previous step.
4. If necessary, repeat steps 3 & 4 until the spectrum looks good.
5. Click on any menu button, such as box or cursor, to get out of
the phasing mode.
To Integrate
(You may need to click on return, more and integrals to get to the
point where you can begin this section. When you see integrals and
click on it, you will toggle through various options: no integrals,
full integrals, etc.)
1. Select part integral
2. Type region. This will break the integral line into smaller
segments, which may make analysis easier.
Notes:
a. If your integrals are tilted, you may need to adjust level
and tilt. Click on next, then lvl/tlt. Two red vertical lines
will appear. Dragging (RH) up and down will change the angle
of the integral line. Clicking on a button in the top window
will get you out of this mode.
b. If this method is not satisfactory, and you want to select
your own integral regions:
1. Click on part integral.
2. Select resets. Clicking the left mouse button will now put
breaks in the integral line; youmust click on both sides of a
desired peak to get its integral. Once you are finished,
alternating segments of the broken line will be discarded,
leaving integrals only in the desired portions of the spectrum.
If you make a mistake and want to reconnect the integral line,
click on the right mouse button. If you click on the right button
enough times, the entire integral line will be reconnected again.
3. When finished, click on any menu button, such as box, and
you will be returned to thenormal mode of operation.
To Print
(this assumes that you have already properly selected a printer -- see
above! Selecting a printer at this point will mess up your spectrum)
The spectrum will be plotted as it appears on the screen; make sure that's
what you want.
1. Click on Main Menu
2. Click on display
3. Click on Plot
4. Click on plot, scale, partial parameters and then page.
Notes:
a. You could actually choose any combination of characteristics for
your printout from the second row of buttons. The plot command
prints the spectrum, scale prints the axis on thespectrum,
parameters or partial parameters lists the instrumental options
used to run your spectrum, peaks lists the peak positions (if
selecting this option, check the threshhold asdescribed in the
helpful features section to make sure that there aren t too many or
too few.) You can also type pir and the plotter will print out
the integral values for you.
All these commands are stored temporarily; clicking the page
button sends them to the printer.
b. Alternatively, you could type pl (plots spectrum) pscale
(plots scale) pirn (prints integralvalues) ppa (prints the
parameters - you must do this) ppf (plots peak frequencies) and
then page(sends the commands to the printer) with a space in
between each command.
To exit the VNMR software.
Note-it is important to exit properly or else you may be locked out of your
data next time you call it up! Also, if something really bad happens as you
work up your data,exit as described below and then recall the file as
mentioned on pg 1. Only the original data is ever saved.
1. Click on Main Menu.
2. Click on More
3. Click on Exit VNMR.
4. Log out of the SGI as usual.
Helpful Features
Expanding Your Spectrum
Y-Scale Expansion
Use this feature if your peaks are too tall or too short for you to see them
clearly.a
1. If you need to make a peak taller or shorter, click (M) on the peak.
SLOWLY drag the peak up or down to the desired size.
2. Make sure the top of the tallest peak is on-scale (i.e. it doesn't go off
the screen). Otherwise it will be cut off when you print.
a. This only works when the integral is not currently being
displayed. When the integral is being displayed, the same
procedure makes the integral taller or shorter, but leaves the
peaks alone.
X-Scale Expansion
Use this feature if you wish to select a particular area of your spectrum
and expand it to the full screen width. This will allow you to better see
coupling patterns and integration, or to simply eliminate peaks due to the
solvent or TMS which are not useful to you.a
1. To expand on an area, click on cursor. Click (LH) on the red line and drag
it to the left side of the region that you want to see. Release the mouse
button.
2. Position the arrow on the right side of the region that you would like to
see expanded and click (RH). A second red line should appear.
3. Click on expand.
4. This process may be repeated to see individual peaks or a smaller region
of the spectrum.
5. Clicking on the full button will return you to the full spectrum if you
want/need to.
Note:
a. If you are unsure where the solvent or TMS peaks are, you may
want to do the following:
1. Type dscale to display the x axis. If it is not in ppm, type
axis= p .
2. The spectrum is automatically displayed from about -2 to
+13 ppm.
3. Typically your spectra will be run in CDCl3 that may contain
TMS. As a consequence, therewill be a peak at 7.24 due to a
small amount of CHCl3 in the CDCl3. This peak may be
eliminated. You may also safely eliminate the TMS peak at
0 ppm from your spectrum.
To select a threshold (for peak position printout)
1. Select th; a horizontal line will appear on the spectrum. Use the mouse
button(LH) to move the threshold line up or down. Clicking peaks in the
plot mode willprint the position of any peaks above this line.
To get Coupling Constants (in hertz) or Exact Peak Positions (in ppm)
1. Zoom in on the peak of interest (x-scale expansion).
2. Type dscale (hit a return)
3. type axis= 'p' (return)
4. To get exact peak positions in ppm, click on box. (Depending on what you
havedone earlier, you may need to click on more or next, followed by
interactive in orderto get this choice.)
5. Drag the red line onto the peak that is of interest. The exact chemical
shift in ppm will appear in the middle small yellow box that appears an
inset on the spectrum screen. Write it down.
6. To get coupling constants in hertz, zoom in on peaks of interest.
7. type axis= 'h' (return). The x scale will change to hertz. Follow the rest
of theprocedure in parts 4 and 5. The vaues of the chemical shift will
now appear in hertz in the yellow box. Drag the red line to the
appropriate second peak, note the new value in the yellow box, and the
difference between the two will be the coupling constant in hertz.
Integration tips
There are several ways to obtain integral values for your integrals:
1. Type dli to display the list of regions and integrals. This will appear
in the 3rdwindow. Write these numbers down and record them on the
spectrum.
2. When plotting, type pir before clicking on page and this list will be
printed out.
3. Alternatively, you could take your plot and measure the
height of each integral "step" with a ruler.
Last update on August 14, 1997