General Command Structure
- OVJ commands are entered at the command line. Some commands require arguments or parameters, which can enclosed in parentheses.
- To change a parameter value, the parameter is entered followed by an equal sign (=), followed by the value of the parameter (real, integer, or string).
- String values are always enclosed in parentheses and surrounded by single quotes.
- Multiple command and parameter settings can be entered consecutively, separated by spaces.
Command Examples:
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Example of Setting a Parameter Value:
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Commonly Used OVJ Parameters
The following sections provide a list of commonly OVJ commands and parameters. For a complete list of commands see the VnmrJ Command and Parameter Reference.
Commands
Spectrometer Control and Data Acquisition Parameters
| Command | Description/Example |
|---|---|
| aa | abort current running experiment immediately. Recommended to use in most occasions over sa except when some experiments are queued |
| cexp(n) | create new experiment from current one Example: cexp(2) copy current parameters and create experiment number 2 (#2 must not exist) |
| dg | display group of acquisition/processing parameters in Process→Text Output window |
| dps | display pulse sequence |
| ga | start experiment and autoprocess the data when data are available |
| go | start experiment using acquisition parameters |
| jexp(n) | join (or go to) specified experiment Example: jexp(2) join exp#2. exp#2 must exist |
| movesw | move new spectral window (sw) to the area enclosed by the two red cursors |
| movetof | move transmitter offset freqeuency (tof) to the cursor position |
| su | setup experiment. Force hardware to changes according to current parameter settings Example: load=‘MySpectrum’ su - change shims to current values in parameter file Example: tn=‘C13’ su - change direct detection to C13 |
| time | displays total experiment time with current parameters |
| time(hours,minutes) | displays number of scans (nt) required for a given time of experiment Example: time(1,10) - displays number of scans needed for a one hour 10 mins experiment |
| 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 |
Data Processing and Display Commands
| Command | Description/Example |
|---|---|
| aph | automatic phasing of both zero (constant) and first-order (linear with frequency) terms |
| aph0 | automatic phasing with zero-order term only to achieve absorptive mode spectrum. Zero-order phase value (rp) is the same across the spectrum |
| 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 |
| 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) |
| centersw | With full spectrum displayed and in single cursor mode, centers moves the cursor to the center (transmitter) of the spectrum |
| cz | clear integral reset points |
| da | display acquisition parameter array in Plot→Text Output window |
| 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 |
| df | display a single FID (default index is 1) Example: df displays the 1st FID or df(10) displays #10 FID in the array |
| dli | display list of integrals |
| dll | displays line frequency and intensities (peaks have to picked) |
| dpir | display integral values below spectrum |
| 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 |
| dres | calculates peak resolution/linewidth |
| ds | display processed spectrum without preprocessing |
| 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 |
| dsn | measure and display signal-to-noise ratio in region enclosed by two cursor lines |
| f | display the full spectrum |
| fbc | apply baseline correction for each spectrum in an spectrum array |
| 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 |
| fp | find peaks in arrayed dataset according to the refrence peaks found by dll |
| isadj | automatic adjustment of integral vertical display height to fit page |
| 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: mp(1,2) |
| nl | move cursor line to nearest peak/line position |
| th | set a threshold for peaks in dll command |
| 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) |
| peak | Find tallest peak in current display region Example: peak - display tallest peak position and height in current displayed spectrum region Example: 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 |
| vsadj | automatic vertical scale adjustment so that the highest peak fits the window height |
| 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 |
| 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 |
Plotting Commands
| Command | Description/Example |
|---|---|
| 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 |
| pltext | plot user comment/notes. Not necessary if ppa command is used |
| ppa | plot basic parameters in plain english format |
| pps | plot pulse sequence |
| ppf | plot peak frequencies over the spectrum |
Parameters
Acquisition parameters
| Parameter | Description/Example |
|---|---|
| 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 |
| 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 |
| 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 |
| nt | number of transients or scans |
| 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 |
| rattn | receiver attenuation, the attenuation can be set from 0 to 95, a too high value will attenuate all signals. A too small value will increase noise without increasing the signal strength. |
| 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’ |
| tn | observe transmitter nucleus |
| tof | observe transmitter offset (center of spectrum) |
Processing and display parameters
| Parameter | Description/Example |
|---|---|
| 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 |
| date | date of experiment |
| 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 |
| 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’ |
| 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 |
| vo | vertical offset (in mm) between a set of spectra in stacked display mode for arrayed spectra |
| vp | vertical position of spectrum, in mm Example: vp=60 sets spectrum baseline roughly in the middle of the display along Y-axis Example: vp=vp+20 moves the spectrum up by 20 mm |
| vs | vertical scale of spectrum Example: vs=vs*2 - set vertical scale to double peak height Example: vs=vs*0.5 - set vertical scale to halve peak height |