USEFUL COMMANDS AND PARAMETERS, Nov. 1995 edition
acqi / 3 / “acquisition” This command brings up the acquisition window used to lock and shim samples.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 “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.
btune / 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 13C 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.
d1, d2 / 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).
deptproc / 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.
dgs / 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.
dp / 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).
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.
fn / 154 / “fourier number” This command sets up the number of points to be transformed. It must be a power of two (i.e., 2n) 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.
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.
lb / 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).