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 |