How-Tos, & Useful Information:
- Transferring files via UNIX
Generating a PostScript plot file
How can I control the temperature?
How should the VT gas be connected & adjusted?
How (and when) should I reset the VT controlller?
What (and why) is a field/frequency lock?
What does "shimming" mean?
What is the significance of "gain" and "Autogain"
What is the ADC (analog-to-digital converter, digitizer)? ;
- Transferring Files Via Unix
I have received a lot of requests for help with transferring files via UNIX
terminal or command line. The old way to do this is via simple FTP using
get and put statements. The problem with FTP is that it isn't secure,
so it has not been enabled on our Sun workstations. Instead, I most
often use SCP. Included at the bottom is a link that describes how to
use secure copy.
On our spectrometers, Varian data is typically stored in either your home
directory or in the vnmrsys folder in your home directory. For example,
if my login is jpeavy in Prof. Bochy's lab, my data can be found in either:
Lets assume that in my home directory, I have a data directory named
ethylbenzene.fid on the 300. To copy this into the directory I am
presently in on MY computer, I would go to a terminal command line and type:
scp -r firstname.lastname@example.org:/export/home/bochy/jpeavy/ethylbenzene.fid .
The -r flag means "recursive copy" and the "." at the end of the statement
I should then be prompted for a password and my data
will begin to transfer. Variations of the SCP command are discussed in
the link. Note that this works on just about any UNIX style command line.
Sun, Mac, etc. For Windows, you can download PuTTY, which is a free
implementation of Telnet and SSH for Win32 platforms.
there are several programs that will allow you to copy files to a
Windows machine in a very convenient drag and drop method. You should,
however, make sure you get these types of programs from a reliable source.
All the best,
Computing services - SCP
- Generating a PostScript plot file
We have added a new menu selection to easily generate a postscript plot
file of your spectrum.
- Diaplay your spectrum and set up vertical scaling, expansion, etc.
desired for your plot, as usual.
- Click on the "Return" (far right) menu button; or click on "Main Menu",
then on "Display".
- Click on the "PlotPS" button. Choose your desired plot components by
clicking on the appropriate button; "Plot" corresponds to the "pl" command,
"Scale" is the equivalent of "pscale", etc.
- Once you have selected everything you want on your plot, click on
"Write File". You will be prompted to type in a name; if the name you
type in already existe, you will be prompted to try another name.
- You will find your newly created .ps file in your home directory.
How can I control the temperature?
First of all, make sure that the
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.
- 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.
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'
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.
- What (and why) is a field/frequency lock?
First of all, it has nothing to do with "locking/unlocking an experiment",
which is a mechanism to prevent two people running Vnmr from trying
to use the same space at the same time.
In order to resolve closely spaced peaks, it is desirable that the
peaks in an NMR spectrum be as sharp (narrow) as possible. This
means that the magnetic field must be as stable and homogeneous
throughout the sample volume as possible. Spec for the narrowest
lineshape achievable on our NMR instruments (with a suitable sample)
is better than 0.3 Hz
(linewidth measured halfway up the peak). At a proton frequency
of 300 - 400 Mhz, that corresponds to stablity and homogeneity
better than one part per billion (1 part in 109)
.There are several
factors that can contribute to instability of the magnetic
field. Due to imperfections in the joints between the various
sections of the superconducting wire in the magnet, the magnetic
field decays at a very slow but significant rate, typically a few
proton Hertz per hour. It is also susceptable to changes from
movement of nearby ferromagnetic objects (someone walks by with
a pocket full of keys, or moves a nearby chair with some metal
components, or someone moves a gas cylinder in the lab next door, etc.)
In order to compensate for these changes, the magnetic field is
monitored by observing the deuterium NMR resonance of the solvent.
Any change in the magnetic field would result in a shift of the
deuterium resonance frequency. The lock circuitry is so arranged that
when the lock is engaged, this results in a change in the
current through a room-temperature compensating coil (the Z0 coil)
that is exactly the amount needed to keep the field from deviating from
the value it had when the lock was engaged. Thus, the magnetic field
is "locked" to the value that keeps constant the resonance frequency
of a particular nucleus, in this case the deuterium in your solvent.
What does "shimming" mean?
A great deal of care is taken in the design, construction, choice
of materials, etc., of the magnet itself, the probe, and the
structures that support them, to make the magnetic field as
homogeneous as possible throughout the sample volume. However,
there is an unavoidable perturbation of this homogeneity whenever
a different sample is introduced into the probe. Because the magnetic
susceptiblity of organic solvents differs substantially from that
of atmospheric air, the value of the magnetic field within the
solution is different from its value outside the solution. This
introduces regions of inhomogeneity at the top and bottom of the
liquid sample, where the field is changing value. This sample-induced
inhomogeneity depends on the exact geometric dimensions of the
sample, particularly its height. This is why it is quite important
to use a sufficient volume of solution (recommended 0.5 ml minimum,
better 0.6 ml) and to position your nmr tube correctly in the spinner.
Because of this dependence on exact semple gemomtery and composition,
it is necessary to make some adjustments every time the sample is
changed to correct for changes in the shape of the field. In
mechanics, a shim is a piece of thin material used to level something
or improve a fit. Here, shimming refers to adjusting the currents
through a set of coils surrounding the sample area that are arranged
so as to be able to make small changes in the shape of the magnetic
field. The goal is to adjust the currents in these coils to cancel the
inhomogeneity in magnetic field throughout the sample volume.
What is the significance of "gain" and "Autogain"?
The very weak NMR signal coming out of the probe must be amplified by the
pre-amplifier and the receiver to a value suitable for the
The amount of amplification necessary depends on the strength of the original
signal, and is controlled by the parameter 'gain'. If the amplitude of
the input to the digitizer exceeds the limit that can be accurately
represented, the result is
, which leads to distortions and artifacts
in the NMR spectrum that can range from subtle to gross, depending on
how far the signal amplitude exceeds the digitizers range. On the other
hand, for the digitizer output to accurately represent the NMR signal,
the amplitude cannot be too small. "Autogain" is a procedure
by which the software attempts to optimize the gain parameter by
repeatedly acquiring the NMR signal, then increasing the gain if
the amplitude is to small, or decreasing it if the signal is too large.
In the standard parameter sets for the Varian NMRs, Autogain is turned
on by default. This is done by setting the 'gain' parameter to
inactive ("gain='n'"), and the Autogain procedure is
performed each time you type 'go'. If the signal is still too large
after 'gain' has been reduced to zero,
the acquisition is aborted with the "Autogain Failure" message.
('gain = 0' does not mean zero gain; it means that the gain has been
reduced to the lowest possible value with the existing hardware.)
What is the ADC?
The ADC (analog-to-digital converter, or digitizer) is in
essence a digital voltmeter that can measure and store the amplitude
of the NMR signal very rapidly (typically every few tens of
microseconds to hundreds of microseconds), As an illustration, consider
a three (decimal) digit voltmeter with a full-scale
range of +/- one volt; it can accurately represent values from - 0.999
volt to + 0.999 volt. Any values outside these limits will not be accurately
represented; for instance, an input of + 2 volts will still result in an
output of 0.999. Further, if the amplitude of the signal is too low (for
example, only +/- 0.001 volt), it will also not be represented accurately.
Although the output of the ADC is in binary instead of
decimal, the same principles apply. When the input to the ADC goes
beyond the maximum or minimum value that can be represented,
the the ADC is said to "overflow".