Basic VnmrJ Commands and Parameters

VnmrJ commands are entered at the vnmrJ command line. Some commands can be optionally entered with arguments or parameters enclosed in parentheses.To change a parameter value, an vnmrJ parameter is entered with the parameter name, followed by an equal sign (=), followed by the value of the parameter (real, integer, or string). A string parameter value is always enclosed in parentheses and surrounded by single quotes. Multiple command and parameter settings can be entered consecutively, separated by spaces.

Command examples:

• aph
• wft
• rl(7.25p)
• wft aph dc vsadj

Parameter setting examples:

• lb=0.2
• vp=50
• sample='tyr.2'

To check a parameter value, add a question mark (?) after the parameter:

• bs?
• lb?

Combined commands and parameter setting:

• lb=0.2 wft aph

The following lists only basic VnmrJ commands and parameters. Parameters related to 2D or higher-dimensional experiments are not included. For complete or more details of the commands and parameters, see VnmrJ Command and Parameter Reference.

Commands

Spectrometer control and data acquisition commands

• e
• eject sample
• i
• insert sample
• cexp(n)
• create new experiment from current one
• Example: cexp(2) copy current parameters and create experiment number 2 (#2 must not exist)
• jexp(n)
• join (or go to) specified experiment
• Example: jexp(2) join exp#2. exp#2 must exist.
• explib
• list experiment library. Click Process→Text Output to see list.
• time
• displays total experiment time with current parameters
• time(hours,minutes)
• displays number of scans (nt) needed if desired time of experiment is needed
• Example: time(1,10) displays number of scans needed for a one hour 10 mins experiment.
• dg
• display group of acquisition/processing parameters in Process→Text Output window.
• dps
• display pulse sequence
• go
• submit current experiment
• 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.
• aa
• abort current running experiment immediately. Recommended to use in most occasions over sa except when some experiments are queued.
• 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.
• sa('il')
• stop the experiment when the next interleaved array finishes
• ra (NOT RECOMMENDED TO USE)
• resume an experiment that has been stopped with sa command. Must be entered from the same experiment number where sa was entered.
• 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.
• 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)
• movesw
• move new spectral window to the area enclosed by the box cursor (two red cursor lines).
• 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.
• 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)

Data processing and display commands

• 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.
• ds
• display processed spectrum without preprocessing
• aph0
• automatic phasing with zero-order term only to achieve absorptive mode spectrum. Zero-order phase value (rp) is the same across the spectrum.
• aph
• automatic phasing of both zero (constant) and first-order (linear with frequency) terms.
• df
• display a single FID (default index is 1).
• Example: df displays the 1st FID or df(10) displays #10 FID in the array
• vsadj
• automatic vertical scale adjustment so that the highest peak fits the window height
• thadj(maxpks,noise_mult)
• Adjust the threshold th so that no more than maxpks number of peaks are found with a minimum of noise_mult factor above noise level.
• 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.
• f
• display the full spectrum
• 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
• centersw
• With full spectrum displayed and in single cursor mode, centers moves the cursor to the center (transmitter) of the spectrum.
• dpf
• When a threshold (with a horizontal yellow line) is set, dpf displays picked peaks above the threshold level.
• 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.
• cdc
• Turns off or cancels drift correction from dc
• 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).
• fbc
• apply baseline correction for each spectrum in an spectrum array
• 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.
• cz
• clear integral reset points
• dres
• calculates peak resolution/linewidth
• isadj
• automatic adjustment of integral vertical display height to fit page
• da
• display acquisition parameter array in Plot→Text Output window
• dli
• display list of integrals
• dll
• displays line frequency and intensities (peaks have to picked)
• dpir
• display integral values below spectrum
• dsn
• measure and display signal-to-noise ratio in region enclosed by two cursor lines.
• dssa
• display arrayed spectra in a stack plot
• Example: wft dssa
• dssh
• display arrayed spectra horizontally
• Example: wft dssh
• dssl
• Label displayed arrayed spectra with index number
• Example: wft dssh dssl
• mf
• move FID file from one experiment to another
• Example: mf(1,2) move fid from exp #1 to #2
• mp
• Move all parameters from one experiment to another
• Example: mf(1,2)
• nl
• move cursor line to nearest peak/line position
• 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.
• setref1
• Similar to setref, set reference of 1st indirect dimension by solvent H2 signal.
• adept
• Add/subtract set of DEPT data after wft to give separate pure CH, CH2 and CH3 and CH/CH2/CH3 peaks
• 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.

Plotting commands

• page
• submit plot to printer and change plotter page. Usually last command in printing command chain
• pap
• plot "all" parameters in table format
• pir
• plot integrals below spectrum
• pl
• plot spectrum
• pll
• plot frequency line list in a table format
• ppa
• plot basic parameters in plain english format
• pps
• plot pulse sequence
• ppf
• plot peak frequencies over the spectrum
• pltext
• plot user comment/notes. Not necessary if ppa command is used.

Parameters

Acquisition parameters

• at
• acquisition time in seconds.
• bs
• block size of data (number of transients) periodically read and stored on disk
• Example: bs=4 stores data every 4 scans
• nt
• number of transients or scans
• 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.
• d1
• 1st delay period in pulse sequence. Typically this is the recycle time (in seconds) between scans
• dn
• 1st decoupler nucleus
• tn
• observe transmitter nucleus
• 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.
• 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.
• 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.
• sw
• spectral width of direct detection dimension, in Hz be default.
• Example: sw=6000 or sw=15p to specify 15ppm width.
• sw1
• spectral width of 1st indirect detection dimension, in Hz be default.
• solvent
• name of solvent.
• Example: solvent='cdcl3' or solvent='c6d6'
• tof
• observe transmitter offset (center of spectrum)

Processing and display parameters

• axis
• axis label in display and plots. Values include 'h' for Hz, 'p' for ppm.
• Example: axis='p' or axis='ppm' set axis to ppm display.
• cr
• cursor position in direct detected dimension.
• Example: cr=8.0p set cursor position to 8ppm.
• 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.
• lb
• line broadening amount for exponential weighting function (Hz)
• Example: lb=0.2
• 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.
• rp
• zero order phase correction in degree, adjusted during phasing process.
• Examples: rp=45 set zero-order phase to 45 degree or rp=rp+45 to change phase by 45 degree.
• date
• date of experiment.
• ho
• horizontal offset (in mm) between a set of spectra in stacked display mode for arrayed spectra.
• intmod
• integral display mode. Value is 'off', 'full', or 'partial'
• Example: intmod='off'
• 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
• vo
• vertical offset (in mm) between a set of spectra in stacked display mode for arrayed spectra.
• vs
• vertical scale of spectrum.
• Example: vs=vs*2 (to double peak height) vs=vs*0.5 (to halve peak height)

H. Zhou updated October 2011