Bugman: removed Category:Software; added Category:NMR software using HotCat

2020-10-21T16:27:50Z

removed Category:Software; added Category:NMR software using HotCat

Bugman: Forced creation of a TOC - this will improve the formatting on the main page 'Did you know...' section.

2015-10-15T13:48:27Z

Forced creation of a TOC - this will improve the formatting on the main page 'Did you know...' section.

Tlinnet at 13:15, 27 August 2013

2013-08-27T13:15:45Z

Tlinnet: Created page with "== 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..."

2013-08-27T13:13:13Z

Created page with "== 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..."

New page

== 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<br>
* Join experiment X: jexp(X)
* Experiment library: explib

* Remove job from que. jexpX -> '''acqdequeue'''
<br>

== 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'''
{| class="wikitable sortable" border="1"
|-
!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 [http://nmr.chem.ucsb.edu/docs/compars.html webpage]
=== Spectrometer ===
{| class="wikitable sortable" border="1"
|-
!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)
|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.
|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
|(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.
|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 ===
{| class="wikitable sortable" border="1"
|-
!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)
|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.
|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
|display arrayed spectra in a stack plot. |Example: wft dssa
|Data
|-
|dssh
|display arrayed spectra horizontally. |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 ===
{| class="wikitable sortable" border="1"
|-
!Command
!Description
!Category
|-
|at
|Acquisition time in seconds.
|Acquisition
|-
|bs
|block size of data (number of transients) periodically read and stored on disk. |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
|spectral width of direct detection dimension, in Hz be default. |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
|name of solvent. |Example: solvent='cdcl3' or solvent='c6d6'
|Acquisition
|-
|tof
|observe transmitter offset (center of spectrum)
|Acquisition
|}

=== Display ===
{| class="wikitable sortable" border="1"
|-
!Command
!Description
!Category
|-
|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.
|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
|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.
|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
|}

[[Category:NMR]]

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	== See also ==		== See also ==
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−	[[Category:~~NMR~~]]	+
		+	== See also ==
		+	[[Category:Software]]

VnmrJ commands - Revision history

Bugman: removed Category:Software; added Category:NMR software using HotCat

Bugman: Forced creation of a TOC - this will improve the formatting on the main page 'Did you know...' section.

Tlinnet at 13:15, 27 August 2013

Tlinnet: Created page with "== 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..."