# VnmrJ commands

## Useful commands

• Create experiment number X: cexp(X)
• Move parameters from experiment X to experiment Y: mp(X,Y)
• Save shims: svs('name')
• Retrieve shims: rts('name') and type su
• Join experiment X: jexp(X)
• Experiment library: explib
• Remove job from que. jexpX -> acqdequeue

## VnmrJ-nmrPipe dictionary

### General parameters

#Gyromagnetic ratios (gamma)
y_H1=+2.675*10^8 rad s^{-1} T^{-1} -
y_N15=-2.713*10^7 rad s^{-1} T^{-1}
y_C13=+6.728*10^7 rad s^{-1} T^{-1}

#Field strength of v750
B0 = - (nu_0 * 2pi)/y_H1 = (750.0614408 *10^6 Hz * 2pi) / 2.675*10^8 rad s^{-1} T^{-1} = 17.6178 T    (Keeler, p.32)

#Field strength of v800
B0 = - (nu_0 * 2pi)/y_H1 = (799.7773975 *10^6 Hz * 2pi) / 2.675*10^8 rad s^{-1} T^{-1} = 18.7856 T    (Keeler, p.32)

#PPM scale (Keeler, p.6)
ppm=10^6*((v-v_ref)/(v_ref))  => v=ppm*v_ref*10^{-6}+v_ref


Parameters related to gNHSQC

VnmrJ nmrPipe Desc. grep in procpar
sw xSW Spectral width in directly detected dimension. [Hz] grep -A 1 "sw " procpar
sw1 ySW Spectral width in 1st indirectly detected dimension. [Hz] grep -A 1 "sw1 " procpar
np xN Number of data points. Calculated automatically from sw. Including complex points. grep -A 1 "np " procpar
xT Number of data points in real. Half of xN np/2
ni yT Number of increments in 1st indirectly detected dimension. Not including complex phase. grep -A 1 "ni " procpar
yN Total Number of increments in 1st indirectly detected dimension. Including complex phase. 2*yT for Rance-Kay
sfrq xOBS Transmitter frequency of observe nucleus grep -A 1 "sfrq " procpar
dfrq2 yOBS Observe frequence of indirect nucleus. xOBS*(y_N15/y_H1)
dn2 yLAB Nucleus for second decoupler grep -A 1 "dn2 " procpar
reffrq Reference frequency, in MHz, of the reference line. Directly detected dimension. grep -A 1 "reffrq " procpar
reffrq2 Reference frequency, in MHz, of the reference line. In-directly detected dimension. grep -A 1 "reffrq2 " procpar
xCAR Carrier Position ppm in H1. tof in ppm =1*10^6*(sfrq-reffrq)/reffrq
yCAR Carrier Position ppm in N15. See DSS_referencing Use calcOffset procpar,option [2], to find it. It depends on the gyromagnetic ratios, and is easiest to calculate via script.

## VnmrJ Commands

Taken from this webpage

### Spectrometer

Command Description Category
e eject sample Spectrometer
i insert sample Spectrometer
cexp(n) create new experiment from current one. Example: cexp(2) copy current parameters and create experiment number 2 (#2 must not exist) Spectrometer
jexp(n) join (or go to) specified experiment. Example: jexp(2) join exp#2. exp#2 must exist. Spectrometer
explib list experiment library. Click Process→Text Output to see list. Spectrometer
time displays total experiment time with current parameters Spectrometer
time(hours,minutes) Example: time(1,10) displays number of scans needed for a one hour 10 mins experiment. Spectrometer
dg / dg2 display group of acquisition/processing parameters in Process→Text Output window. Spectrometer
dps display pulse sequence Spectrometer
go submit current experiment Spectrometer
ga submit current experiment and autoprocess the data when data are available. NOTE: It fails to autoprocess in our version of software. Same as go. Spectrometer
aa abort current running experiment immediately. Recommended to use in most occasions over sa except when some experiments are queued. Spectrometer
sa abort current experiment regardless if it is running or is queued. That is, if the current displayed experiment is #2 and #2 is running, it is stopped. If #1 is running and #2 is in the queue after #1, #2 is stopped and removed from the queue and #1 is left untouched. sa has no effect on experiments that are neither actively running or in the queue. Spectrometer
sa('il') stop the experiment when the next interleaved array finishes Spectrometer
ra If you load an older data into vnmrJ, ra will not work. |NOTE: NOT recommended to use. Resuming a stopped experiment may introduce artifacts and line broadening because the experiment condition may have changed over time. It is better to collect a separate experiment and use the add/subtract features of vnmrJ or another program to sum the results. Spectrometer
su setup experiment. Force hardware to changes according to current parameter settings. Example: load='y' su (change shims to current values in parameter file). tn='C13' su (change direct detection to C13) Spectrometer
movesw move new spectral window to the area enclosed by the box cursor (two red cursor lines). Spectrometer
movetof move transmitter (center of spectrum) to the cursor position. With test spectrum displayed, set single cursor to desired position, enter movetof to set new center, followed by acquisition. Spectrometer
unlock(exp_number) remove interactive lock and join an experiment. Useful to remove lockup of an experiment, sometimes due to user failure to exit vnmrJ before logging out Linux. Example: unlock(1) Spectrometer
unlock(exp_number,'force') remove interactive lock and join an experiment by force. Example: unlock(1,'force') Spectrometer

### Data

Command Description Category
wft Weighted Fourier transform (FT). Weighting is applying a window function to the profile of the FID to enhance resolution or signal-to-noise and to reduce truncation artifacts from finite data collection. Data
ds display processed spectrum without preprocessing Data
aph0 automatic phasing with zero-order term only to achieve absorptive mode spectrum. Zero-order phase value (rp) is the same across the spectrum. Data
aph automatic phasing of both zero (constant) and first-order (linear with frequency) terms. Data
df display a single FID (default index is 1). Example: df displays the 1st FID or df(10) displays #10 FID in the array Data
vsadj automatic vertical scale adjustment so that the highest peak fits the window height Data
thadj(maxpks,noise_mult) Example: "thadj(20,5) dpf". Adjust threshold and display peaks so that a maximum 20 highest peaks are found and the minimum height cutoff is 5 times above noise level. Data
f display the full spectrum Data
full display spectrum with full window size. The range of the spectrum is not changed. Example: "f full" display the full spectrum with full window size Data
centersw With full spectrum displayed and in single cursor mode, centers moves the cursor to the center (transmitter) of the spectrum. Data
dpf When a threshold (with a horizontal yellow line) is set, dpf displays picked peaks above the threshold level. Data
dc Apply a simple drift correction (with a straight line function) so that the spectrum baseline is close to zero. Level (lvl) and tilt (tlt) parameters are adjusted. Data
cdc Turns off or cancels drift correction from dc Data
bc 1D or 2D baseline correction with a spline or 2nd to 20th order polynomial function. Needs to define baseline regions (regions in between the integral areas covering peaks). Data
fbc apply baseline correction for each spectrum in an spectrum array Data
peak Find tallest peak in current display region. Example: "peak" display tallest peak position and height in current displayed spectrum region. peak:"$height,$freq" find tallest peak in current displayed region and save height and frequency in the variables $height and$freq. $heigt? or$freq? shows the values. Data
cz clear integral reset points Data
dres calculates peak resolution/linewidth Data
isadj automatic adjustment of integral vertical display height to fit page Data
da display acquisition parameter array in Plot→Text Output window Data
dli display list of integrals Data
dll displays line frequency and intensities (peaks have to picked) Data
dpir display integral values below spectrum Data
dsn measure and display signal-to-noise ratio in region enclosed by two cursor lines. Data
dssa Example: wft dssa Data
dssh Example: wft dssh Data
dssl Label displayed arrayed spectra with index number Example: wft dssh dssl Data
mf move FID file from one experiment to another Example: mf(1,2) move fid from exp #1 to #2 Data
mp Move all parameters from one experiment to another Example: mf(1,2) Data
nl move cursor line to nearest peak/line position Data
setref set reference ppm of any nucleus by the chemical shift of the deuterium signal from the solvent, according to IUPAC standard indirect referencing to TMS 1H signal. Data
setref1 Similar to setref, set reference of 1st indirect dimension by solvent H2 signal. Data
adept Add/subtract set of DEPT data after wft to give separate pure CH, CH2 and CH3 and CH/CH2/CH3 peaks Data
array Enter this command to set an arrayed experiment where a parameter is varied and an experiment is collected with each parameter. Enter parameter name, initial value, number of steps, and stepsize. All other parameters are kept constant. Data

### Acquisition

Command Description Category
at Acquisition time in seconds. Acquisition
bs Example: bs=4 stores data every 4 scans Acquisition
nt number of transients or scans Acquisition
ct current transient (or scan) number. ct is displayed at the bottom of vnmrJ screen during a running experiment. If the experiment is stopped before all transients are done, ct (stored in the parameter file procpar) is the number of scans completed. Acquisition
d1 1st delay period in pulse sequence. Typically this is the recycle time (in seconds) between scans Acquisition
dn 1st decoupler nucleus Acquisition
tn observe transmitter nucleus Acquisition
gain receiver gain. If gain='n', auto-gain adjustment is set before data acquisition. Autogain cannot be used for arrayed experiment. Gain values go from 0 to 60. Too high a gain setting causes receiver overflow, leading to severe artifacts in the spectrum. Example: gain=36 sets gain to 36. Acquisition
pad preacquisition delay (in seconds). pad is the additional delay time set before the 1st recycle delay (d1) before the start of an experiment. If pad=60, the experiment will start after 60 secs. Acquisition
ss number of steady-state transients or dummy scans before start of experiment. It's used to establish a steady-state for the spins before data collection. Acquisition
sw Example: sw=6000 or sw=15p to specify 15ppm width. Acquisition
sw1 spectral width of 1st indirect detection dimension, in Hz be default. Acquisition
solvent Example: solvent='cdcl3' or solvent='c6d6' Acquisition
tof observe transmitter offset (center of spectrum) Acquisition

### Display

Command Description Category
axis Example: axis='p' or axis='ppm' set axis to ppm display. Display
cr cursor position in direct detected dimension. Example: cr=8.0p set cursor position to 8ppm. Display
delta In two-cursor (box cursor) mode, delta stores the width in Hz between the two cursors. Example: delta=1000 sets the separation between two cursors to 1000 Hz, or delta? to see the cursor separation value. Display
lb line broadening amount for exponential weighting function (Hz). Example: lb=0.2 Display
lp 1st order (or linear) phase in directly detected dimension, adjusted during phasing process. Example: lp=0 sets linear phase correction to zero, useful to reset linear phase to zero to correct accidental introduction of large lp value during manual phasing. Display
rp Examples: rp=45 set zero-order phase to 45 degree or rp=rp+45 to change phase by 45 degree. Display
date date of experiment. Display
ho horizontal offset (in mm) between a set of spectra in stacked display mode for arrayed spectra. Display
intmod integral display mode. Value is 'off', 'full', or 'partial' Example: intmod='off' Display
vp vertical position of spectrum, in mm. Example: vp=60 sets spectrum baseline roughly in the middle of the display along Y-axis. vp=vp+20 moves the spectrum up by 20 mm Display
vo vertical offset (in mm) between a set of spectra in stacked display mode for arrayed spectra. Display
vs vertical scale of spectrum. Example: vs=vs*2 (to double peak height) vs=vs*0.5 (to halve peak height) Display