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