USEFUL COMMANDS AND PARAMETERS, November 1995 Edition
Command
Page Description
**
“acquisition” This command brings up the acquisition window used to lock and shim samples.
acqi
3
aph
17
“auto phase” This command carries out an automatic phasing. May fail when you have a low signal to noise ratio.
aph0
17
“auto phase the zero order term” This command autophases the frequency independent term, rp, only.
apt
19
“attached proton test” This command sets up the spectrometer to do an attached proton test. (Used to indicate which carbons
have even and which have odd numbers of attached hydrogens).
aptaph
19
“attached proton tests auto phase” This command auto phases apt data.
array
21
“array” This parameter is used to set up a sequence of experiments where some variable is systematically incremented.
at
23
“acquisition time” This parameter sets the length of time you collect the FID. The signal is strongest at the very start of the
FID and rapidly drops off in intensity until it is lost in the background noise, therefore you get the best signal to noise ratio by
using the early part of the FID. The longer the FID you collect the better the digital resolution you will get in the final
spectrum (i.e., resolution is proportional to one over the at). However, after a certain acquisition time the signal is down to
zero and all you are collecting is noise. Therefore, short acquisition times give the best signal to noise ratio but poor
resolutions while long acquisition times give poor signal to noise ratios but excellent resolution: a classic trade off. Setting
“at” at values just slightly longer than the end of the FID signal gives a good compromise for signal to noise and resolution,
while minimizing total data collection time. This is especially important for long data collections. Note: as “at” increases
**The page numbers are from the Varian Manual “Commands and Parameter Reference, VNMR 5.1”, the preliminary version.
D:\106747310.doc
-1-
Command
Page Description
**
the “np” (number of points) increases as well. Example: at = 3.75 sets the acquisition time at 3.75 seconds.
atex
23
“append text” This command adds a line of text to the file. Example atext (‘bug eyes’) would print bug eyes on the data file.
au
24
“automatic acquisition and processing” This command is like ga but also checks shims, lock, etc. for 1-D and 2-D equipment.
autodept
26
“automatic dept” This command automatically processes dept data.
axis
31
“axis” This command defines the identify of the axis. Example” axis = ‘h’ and axis = ‘p’ sets the axis in Hz and ppm,
respectively.
bc
34
“baseline correct” This command corrects the baseline. Examples: bc and bc(3) does 1st and 3rd order baseline corrections,
respectively.
bs
37
“block size” This parameter gives the number of transients to be collected before each set of data is written to disk in a long
data collection. Its value is such that if you are on a overnight acquisition set for 30,000 transient (i.e., nt = 30,000) and it
crashes at 29,999 with bs = n then you lose all the data. If bs is too small you waste some collection time and if it is too large
a crash will cost more data. In practice though, its exact value is not critical and values of 16 or 64 are probably the most
commonly used (use values of 2n). Example: bs = 16 sets the number of transients in each block as 16.
D:\106747310.doc
-2-
Command
btune
Page Description
**
37
“broadband tune” This command sets the spectrometer to pulsing at the frequency of the observe nucleus in the current
experiment. This command is used so that you can minimize the feedback for that nucleus (i.e., tune the probe). This
command should be done after the cables are moved to the tune meter and the quarter wavelength cables are changed (if
required). “tuneoff” cancels “btune”.
capt
40
“carbon and APT” This command prepares parameters for a 13C followed by an APT spectrum. Example: capt (‘dmso’) nt =
1,000 au would automatically collect 1,000 scans of
13
C and APT and would be processed, in turn, by rttmp(‘C13’) and
rttmp(‘apt’).
cdc
41
“cancel drift correction” This command cancels the dc.
cdept
42
“carbon and dept” This command prepares parameters for a 13C followed by a dept. Example: cdept(‘benzene’) nt = 1,000
au followed by rttmp(‘C13’) and rttmp(‘dept’) to process the spectra.
cosy
55
“cosy” This command sets up the parameters for a cosy experiment.
cosyps
55
“phase sensitive cosy” This command sets up a phase sensitive cosy experiment.
ct
61
“collected transients” This parameter indicates the number of transients that were actually collected.
ctext
62
“clear text” This command clears the text from the current experiment.
cz
64
“clear integral reset points” This command removes currently defined integral reset points.
D:\106747310.doc
-3-
Command
d1, d2
Page Description
**
64
“delay” These commands set the first and second delay times. These are used in nontrivial experiments to allow/prevent
NOE effects, to allow spin evolution, etc. They are only needed for gated decoupling and “named” experiments.
da
66
“display arrays of acquisition parameters” This command displays the arrayed acquisition parameters. Example: pw = 20,
40, 60, 80 ga da would yield an array of four stacked spectra differing in the pulse widths used.
dc
67
“drift correct” This command levels the baseline with the lvl and tlt parameters, (i.e., a liner baseline correction).
dconi
69
“display interactive contour plot” This command displays an interactive contour plot.
delta
77
This parameter measures the frequency difference between the two cursors. Example: delta? asks what the delta value is.
dept
77
“DEPT” This command sets up the parameters for a Distortionless Enhancement by Polarization Transfer experiment (used
to distinguish CH3 from CH2 from CH groups).
78
“DEPT process” This command automatically processes DEPT data.
df
79
“display fid” This command displays the current FID. [dfid is the same command.]
dg
85
“display group of parameters” This command updates the parameter list and presents it as a window.
dga
85
“display group of spin simulation parameters” This command displays the table of spin simulation parameters.
deptproc
D:\106747310.doc
-4-
Command
dgs
Page Description
**
86
“display group of special parameters” This command presents the list of special parameters which includes the shim settings,
etc.
dli
89
“display list of integrals” This command lists integrals and their reset points.
dll
90
“display list of lines” This command displays a list of line frequencies and amplitude above the threshold.
dm
91
“decoupler mode” This command turns the decoupler on or off. It is set at y or yyy or n or nnn if decoupler is always on or
off. For “gated” experiments, dm = nny, nyn, yyn, etc.
dmf
93
“decoupler modulation frequency” This command sets the modulation frequency for the WALTZ decoupling (i.e., broadband
decoupling, dmm = W) DON’T PLAY WITH THIS PARAMETER!.
dmm
97
“decoupler modulation mode” This command sets the type of decoupling. dmm = c for continuous wave (selective)
decoupling, = W for broadband (WALTZ) decoupling, and = f and = r for swept square wave and square wave decoupling,
respectively. dmm = C or W are all we use.
dn
100
“decoupler nucleus” This command sets up to decouple the specified nucleus (e.g., 1H, 19F, 31P) by looking up drfq and dof
from lookup tables.
dof
101
“decoupled offset” This command sets the decoupler offset (i.e., the center of the frequency to be decoupled). Use the sd
command to set dof to the cursor position.
D:\106747310.doc
-5-
Command
dp
Page Description
**
104
“double precision” This command can be set at ‘y’ of ‘n’. You should always have dp = ‘y’ to give the maximum wordlength
and quality of data.
dpf
105
“display peak frequencies” This command displays the peak maxima.
dps
107
“display pulse sequence” This command displays the pulse sequence.
dpwr
107
“decoupler power” This command sets the decoupler power. Has values of 0 to 63 in steps of 0.5 dB. Typical values are 8
dB for Waltz decoupling of 1H and 32 to 38 dB for selective homonuclear decoupling of 1H. Never use dpwr of greater than
49 for dmm = ‘c’, ‘f’, or ‘r’. It can damage probe.
dqcosy
111
“double quantum filtered cosy” This command sets up the parameters for this experiment.
dres
113
“display resolution” This command displays the peak width at half-height of the peak on which the cursor is positioned.
ds
114
“display spectrum” This command displays the current spectrum.
dscale
117
“display scale” This command puts the scale on the screen. Examples: dscale and dscale(30) puts scale on screen at bottom
and with a vp = 30, respectively.
dsn
120
“display signal to noise” This command gives the S/N ratio between the largest peak in the window and the noise between the
cursors (delta should = 200 Hz).
D:\106747310.doc
-6-
Command
Page Description
**
dssa
123
“display stacked spectra offset” This command displays stacked spectra with an incremental offset.
dssh
125
“display stacked spectra horizontal” This command displays a “normal” stacked plot.
e
129
“eject” This command ejects the sample currently in the NMR.
ernst
136
“calculate ernst angle pulse width” This command calculates the optimum pulse width to use to get the best S/N in a set time,
the ernst angle. This value is always less than a 90 pulse and depending on T1 is usually for a 10-45 pulse. The correct
value for this allows you to pulse as quickly as possible with the best balance of relaxation between pulses.
exit
138
“exit” This command exits VNMR.
f19
144
“automated 19F” This command automatically sets up the parameter for 19F data acquisition
FID
“free induction decay” This term describes the “raw” NMR data set (i.e., in the time domain) and looks like series of
superimposed sine waves. It is a measure of the magnetization perpendicular to the magnetic field. It has “real”: and
“imaginary” components that can be displayed separately and can be thought of as the magnetization in the x and y
dimensions. An FID is fourier transformed to give a “spectrum” of frequencies.
D:\106747310.doc
-7-
Command
fn
Page Description
**
154
“fourier number” This command sets up the number of points to be transformed. It must be a power of two (i.e., 2 n) but it
will round itself up to the correct value, (e.g. 32,000 to 32,768). For fn = np, all the points are transformed. For fn < np only
fn points are transformed. For fn> np, fn - np zeros are added to the data before it’s transformed. Such zero filling yields
increased resolution with no increase in signal to noise. A typical setting for zero filling is fn = 2np.
ft
159
“fourier transform” This command says Fourier transform the current FID.
ga
175
“ga” This command says go collect the experiment then wft the result.
gain
175
“gain” This command sets the amplifier gain. Gain values range from 0 to 30 dB in steps of 2. Examples: gain = 20 and
gain = ‘n’ sets the gain at 30 and as autogain, respectively.
gf
183
“gausion function” This parameter in seconds, sets the Gausian apodization, “fudge factor,” for peak width often a wft.
Examples: gf = ‘n’ and gf = 1 sets the data processing parameter off and to 1 second, respectively. Normally, gf = ‘n’.
gfs
184
“gausian shift” This parameter shifts the center of the Gausian apodization function into the spectrum. Examples: gfs = ‘n’
and gfs = 1 sets the gausian shift at off and 1 second, respectively.
go
186
“go” This command says go and collect the experiment.
h1
195
“automated 1H” This command automatically sets up the parameters for 1H data acquisition
hc
197
“automated 1H and 13C” This command combines automated 1H and 13C data acquisition setup.
D:\106747310.doc
-8-
Command
Page Description
**
hcapt
197
“automated 1H, 13C and APT” This command sets up for collection of all three parameters.
hccorr
198
“automated 1H, 13C, and HETCOR” This command sets up the parameters for carrying out all three experiments.
hcdept
198
“automated 1H, 13C, and Dept” This command sets up the parameters for automated running of all three experiments.
hcosy
199
“automated 1H and COSY” This command sets up parameters for automated 1H and COSY collection
hetcor
200
“HETCOR” This command sets up the parameters for a 1H-13C HETCOR experiment. You must already have collected a 1H
spectrum.
ho
201
“horizontal offset” This parameter sets the horizontal offsets of stacked plot. vo sets vertical offsets of 1-D data.
homadj
202
“homonuclear 2-D J-resolved” This command sets up the parameters for homonuclear 2-D J-resolved spectra.
i
207
“insert” This command inserts the sample into the NMR.
inset
215
“inset” This command displays the part of the spectrum between two cursors as an inset.
integrate
215
“automatically integrate” This command automatically integrates the spectrum.
jexpx
jumps to experiment x
killplot
219
“kill plot” This command kills all plots in the queue.
killprint
219
“kill print” This command kills all print jobs in the queue.
D:\106747310.doc
-9-
Command
lb
Page Description
**
222
“line broadening”
This parameter is the number one “fudge factor,” apodization function, used in weighted fourier
transforms. A lb value equal to 1 Hz is conventional and “hides” small shiming errors. lb = ‘n’ turns it off.
lock
229
“lock” This command performs an automatic lock.
lp
233
“1st order phase” This parameter sets the frequency dependent component of the phasing (rp is the consant component). lp
has no effect at the right hand edge of the spectrum.
lsfid
241
“left shift fid” This parameter left shifts the FID. In other words, which points in the FID won’t be fourier transformed.
Example: lsfid = 50 does not transform the first 50 complex points of the spectrum. (i.e., left shift 50 points).
lvl
244
“level” This parameter specifies the amount of the linear baseline correction (turned on by dc).
movesw
257
“move sweep width” This command moves the transmitter offset frequency, tof, to the middle of the window defined by the
two cursors and changes the sweep width, sw, to the difference between the two cursors. In practice if you use the left and
right hand cursors to mark the edges of a spectral window you’d like to collect data from then type movesw the sw and tof
values will be automatically set to do this. It is good, or at least “neat”, practice to manually change sw to some even multiple
of ppm (i.e., 10 ppm or 100 ppm). To do this type sw = 10 p or sw = 100 p, respectively.
movetof
257
“move transmitter offset frequency” This command moves the transmitter offset frequency, tof, to the current position of the
cursor.
D:\106747310.doc
-10-
Command
Page Description
**
“move parameter” This command moves the experimental parameters from experiment x to y.
mp(x,y)
nl
264
“nearest line” This command moves the cursor to the top of the nearest peak.
noesy
266
“NOESY” This command sets up the NOESY experiment.
np
268
“number of points” This parameter is the product of the acquisition time and the scan width (np = 2 x at x sw). It has a
maximum value of 32 K for single precision and 64 K for double precision due to hardware and software limits on the data
system. Its value changes automatically as you change at and sw. Example: np = 64,000 sets at and sw to conform the
64,000 maximum.
nt
269
“number of transients” This parameter sets the maximum number of transients to be collected in a spectrum. The signal to
noise ratio increases proportional to the square root of the number of transients (really, it is even slower than this and a value
of .7 (nt)0.5 is not unreasonable). Example: nt = 32 sets the number of transients as 32.
p31
276
“31P” This command sets up normal31P NMR parameters.
page
278
“page” This command says print the previous list of stuff all on one page and do it now, sends data to the printer. Example:
pl pscale pap page would print a spectrum, its scale, and parameters on one page.
pap
279
“print all parameters” This command tells the system to print all the parameters (i.e., those given by dg). Requires a “page”
command.
D:\106747310.doc
-11-
Command
pl
Page Description
**
296
“plot” This command sets up the current spectrum to plot. Requires a “page” command to print. Examples: pl and pl (80)
would plot a spectrum at the page bottom and with a vp of 80, respectively.
plapt
200
“plot apt” This command plots apt spectrum (can do this on same page as 13C spectrum).
plarray
300
“plot array” This command plots an array of 1-D spectra.
plc
300
“plot 13C” This command plots 13C spectra.
plcosy
301
“plot cosy and noesy” This command plots 2-D homocorelation spectra.
pldept
302
“plot dept” This command plots dept data.
plfid
302
“plot FID” This command plots the current FID. Requires a page command.
plh
303
“plot 1H” This command plots 1H spectra.
plhxcor
303
“plot HETCOR” This command plots hetcor spectra.
pll
305
“plot line list” This command plots the line list.
plot
306
“generic plot” This command calls up the correct plot macro.
ppa
311
“plot parameters” This command plots all parameters in plain English (cf pap).
ppf
312
“plot peak frequencies” This command plots these positions over the peaks.
D:\106747310.doc
-12-
Command
Page Description
**
pps
313
“plot plus sequence” This command plots the pulse sequence (cf dps).
procarray
317
“process array” This command processes arrayed FIDs.
process
318
“generic automatic processing” This command automatically picks the correct data processing macro and does it.
pscale
320
“print scale” This command tells the system to print a scale. It requires a “page” command. Examples: pscale and pscale
(80) request scales to be printed on the bottom of the page and with a vp of 80, respectively.
pwd
326
“print working directory” This command displays where you are in your hierarchy of files.
ra
332
“resume acquisition” This command resumes data acquisition where it left off.
resolu
338
“set resolution enhancement” This command calculates default resolution enhancement functions (e.g., lb and gr) including
zero filling.
rl
344
“reference line” This command defines the current cursor position as the reference line. It is used to “zero” the scale, usually
on the peak of TMS or the solvent. Examples: rl(2.32p) and rl(487) define the two cursor positions as 2.32 ppm and 487 Hz,
respectively.
rp
D:\106747310.doc
347
“right phase parameter” This parameter in the phase term that is frequency independent. (lp is the frequency dependent part.)
-13-
Command
Page Description
**
“retrieve shims” This command retrieves the shim settings recorded in the shims menu. You are promoted to name the
rts
specific shim settings to use. On the 5 mm probe these are usually stored as “best” or “best5”. Example: rts return best 5
return retrieve the shim settings in “best5” and loads them into the spectrometer.
rttmp
349
“retrieve data from a subfile” This command retrieves subfiles. Examples: rttmp(‘H1’) and rttmp(‘dept’) would retrieve the
1
s
351
H and dept data, respectively.
“save screen setup s1, s2, s3, etc.” These commands save the current screen set ups as 1, 2, 3, etc. r1 retrieves the set up
defined by s1.
sa
352
“stop acquisition” This command temporarily stops data acquisition. ra resumes it and aa permanently stops it.
sb
353
“sinebell” This parameter is for the sinebell apodization correction, “fudge factor,” for the wft. Typically, sb = ‘n’. Normally
used in absolute value 2-D experiments only.
sbs
354
“shift sinebell” This parameter is the shift of the sinebell apodization, “fudge factor”.
sc
355
“start of chart in x axis” This parameter positions the start of the plotting position on the paper with respect to its right edge.
sc2
355
“start of chart in y axis” This parameter sets sc for th y axis of the paper (from the bottom?).
sd
357
“set decoupler” This command sets the decoupler offset, dof, to the current cursor position.
D:\106747310.doc
-14-
Command
sda
Page Description
**
358
“set decoupler array” This command sets up an array of decoupler offsets (use sd for first position and sda for subsequent
positions).
sf
373
“start of FID” This parameter gives the start of the displayed portion of the FID.
sfrg
373
“sweep frequency” This parameter is chosen by the computer to correspond to the selected observe nucleus.
shim
374
“autoshim” This command runs an autoshim experiment.
sp
382
“start of plot” This parameter gives the starting position, on the right hand side, of the spectrum on the display window.
Examples: sp = 231 or sp = 1.13p sets the starting point at 231 Hz or 1.13 ppm, respectively.
ss
389
“steadystate” This command causes data to be accumulated only for the steady state pulses.
su
395
“set up” This command resets the communication between the host computer and the NMR console. Do this every time you
change the observe nucleus, decoupling procedures, pulse sequence, etc. It ensures that both the host computer and the NMR
console are “in sinc”.
svf
397
“save FID” This command tells the system to save the current FID data. The system prompts you for a name.
svp
398
“save parameters” This command tells the system to save the current parameters as a defined experiment. It will prompt you
for a name.
D:\106747310.doc
-15-
Command
svs
Page Description
**
398
“saves shim settings” This command saves the current shim settings in the shim menu. The system prompts you to name the
current set of shims.
sw
400
“sweep width” This parameter sets the width of the window that the spectrometer will observe centered around the
transmitter offset frequency (tof). When you don’t know exactly how wide a spectrum will be or where it will be centered,
collect a quick spectrum at a wide sw to be sure it includes all the peaks. Then, transform it and use the cursors and movesw
to set a window that just includes all the peaks. This gives a minimum sw which, in turn, yields a minimum np and so allows
you to get the longest at and hence the best resolution. Example: sw = 34,000 sets the sweep width at 34,000 Hz.
“temperature” This command sets the temperature of a variable temperature run. It shouldn’t be changed more than 20
temp
degrees at a time. Example: temp = -20 and temp = ‘n’ sets variable temperature at -20C and off, respectively.
th
410
“threshold” This command sets the threshold for peak picking
time
412
This parameter asks how long the current experiment will take to collect. Example: time? asks how long it will take.
tn
413
“transmitter nucleus” This command indicates the selected transmitter nucleus.
D:\106747310.doc
-16-
Command
tof
Page Description
**
414
“transmitter offset frequency” This parameter sets the center of the transmitter window (i.e., the center of the sweep width,
sw). This is the frequency at which the observe nucleus is pulsed. The compound movetof is used to move the transmitter
frequency, tof, to the position of the cursor. The tof is sometimes observable in the middle of the spectrum as a weak
“unphased” signal. If it overlaps with a signal of interest, it should be moved away. Example: tof = -486 means the
transmitter is offset -486 Hz from the default value (defined by the software for a given solvent with respect to its deuterium
lock signal).
tuneoff
421
“tuning off” This command stops the pulsing used during tuning. The cables are moved back from the meter after this
command is used. “btune” starts tuning.
vp
431
“vertical position” This command established the height of the baseline. It is usually at zero for conventional 1-D spectra.
Example: vp = 80 positions the baseline in the middle of the page.
“unlock” This command unlocks experiments, e.g., unlock(2) unlocks experiment #2
unlock
vs
431
“vertical scale” This parameter sets the “height” of the spectrum. A vertical scale of 160 is just right to keep all peaks on the
screen. Example: vs = 160 sets the vertical scale at 160.
wc
436
“width of chart” This parameter sets the width of the paper, the plotter area.
wc2
436
“width of chart in y” This parameter = wc for y axis.
D:\106747310.doc
-17-
Command
Page Description
**
wf
438
“width of fid” This parameter gives the width of FID to be displayed.
wft
438
“weighted fourier transform” This command weights the FID with various “fudge factors” prior to fourier transforming them.
wp
443
“width of plot” This parameter gives the width of the spectrum on the display window. You should always use standard
values for this parameter (e.g., 8 ppm, 4 ppm, 2 ppm, 0.5 ppm, 40 Hz, 20 Hz, 10 Hz, 5 Hz) to make later comparison of
spectra much more convenient. Examples: wp = 40 or wp = 2p sets the width of plot at 40 Hz or 2 ppm, respectively.
D:\106747310.doc
-18-