VnmrJ Command and Parameter Reference VnmrJ 2.2D

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paros Create additional parameters used by oversampling (M) ............... 404 parstep Parameter step size values (P) ........................................................ 404 parversion Version of parameter set (P)............................................................ 405 path3d Path to currently displayed 2D planes from a 3D data set (P)........ 405 paxis Plot horizontal LC axis (M) ............................................................ 405 Pbox Pulse shaping software (U) ............................................................. 406 pbox_bw Define excitation band (M)............................................................. 407 pbox_bws Define excitation band for solvent suppression (notch) pulses (M)407 pbox_dmf Extract dmf value from pbox.cal or Pbox shape file (M) ............... 407 pbox_dres Extract dres value from pbox.cal or Pbox shape file (M)............... 408 pbox_name Extract name of last shape generated by Pbox from pbox.cal (M). 408 pbox_pw Extract pulse length from pbox.cal or Pbox shape file (M)............ 408 pbox_pwr Extract power level from Pbox.cal or Pbox shape file (M) ............ 408 pbox_pwrf Extract fine power level from pbox.cal or Pbox shape file (M) ..... 409 pboxget Extract Pbox calibration data (M)................................................... 409 pboxpar Add parameter definition to the Pbox.inp file (M) ......................... 410 pboxrst Reset temporary Pbox variables (M) .............................................. 410 pboxunits Converts to Pbox default units (M)................................................. 410 pcon Plot contours on a plotter (C).......................................................... 410 pcss Calculate and show proton chemical shifts spectrum (M).............. 411 peak Find tallest peak in specified region (C)......................................... 411 peak2d Return information about maximum in 2D data (C)....................... 412 pen Select a pen or color for drawing (C) ............................................. 412 pexpl Plot exponential or polynomial curves (C) ..................................... 413 pexpladd Add another diffusion analysis to current plot (M) ........................ 413 pfgon Pulsed field gradient amplifiers on/off control (P) ......................... 413 pfww Plot FIDs in whitewash mode (C)................................................... 414 pge Convert parameter set to PGE pulse sequence (M) ........................ 414 pge_calib Calibrate gradient strengths for PGE pulse sequence (M).............. 414 pge_data Extract data from single element of PGE pulse sequence (M) ....... 415 pge_output Output results from PGE pulse sequence (M) ................................ 415 pge_process Automated processing of data from PGE pulse sequence (M)....... 415 pge_results Calculate diffusion constant for integral region (M) ...................... 415 pge_setup Set up gradient control parameters for PGE pulse sequence (M)... 416 ph Set phased mode in directly detected dimension (C)...................... 416 ph1 Set phased mode in 1st indirectly detected dimension (C)............. 417 ph2 Set phased mode in 2nd indirectly detected dimension (C)............ 417 phase Change frequency-independent phase rp (M)................................. 418 phase Phase selection (P) .......................................................................... 418 phase1 Phase of first pulse (P) .................................................................... 418 phase2 Phase selection for 3D acquisition (P)............................................ 418 phase3 Phase selection for 4D acquisition (P)............................................ 419 phasing Control update region during interactive phasing (P)..................... 419 phfid Zero-order phasing constant for the np FID (P) ............................. 419 phfid1 Zero-order phasing constant for ni interferogram (P)..................... 420 phfid2 Zero-order phasing constant for ni2 interferogram (P)................... 420 Phosphorus Set up parameters for 31 P experiment (M) ..................................... 420 pi3ssbsq Set up pi/3 shifted sinebell-squared window function (M)............. 420 pi4ssbsq Set up pi/4 shifted sinebell-squared window function (M)............. 421 pin Pneumatics Router Interlock ((P) ................................................... 421 pintvast Plots of integral regions (M)........................................................... 422 pir Plot integral amplitudes below spectrum (C) ................................. 422 pirn Plot normalized integral amplitudes below spectrum (M).............. 422 piv Plot integral values below spectrum (M)........................................ 422 pivn Plot normalized integral values below spectrum (M)..................... 422 pl Plot spectra (C) ............................................................................... 423 pl2d Plot 2D spectra in whitewash mode (C) ......................................... 424 plane Currently displayed 3D plane type (P) ........................................... 424 plapt Plot APT-type spectra automatically (M)........................................ 425 plarray Plotting macro for arrayed 1D spectra (M)..................................... 425 plate_glue Define a glue order for plotting and display (U) ............................ 426 plc Plot a carbon spectrum (M) ............................................................ 426 01-999380-00 A 0808 Command and Parameter Reference for VnmrJ 2.2D 19
plcosy Plot COSY- and NOESY-type spectra automatically (M) .............. 426 pldept Plot DEPT data, edited or unedited (M) ......................................... 427 plfid Plot FIDs (C)................................................................................... 427 plfit Plot deconvolution analysis (M)..................................................... 428 plgrid Plot a grid on a 2D plot (M)............................................................ 428 plh Plot proton spectrum (M)................................................................ 428 plhet2dj Plot heteronuclear J-resolved 2D spectra automatically (M).......... 429 plhom2dj Plot homonuclear J-resolved 2D spectra automatically (M) .......... 429 plhxcor Plot X,H-correlation 2D spectrum (M)........................................... 430 pll Plot a line list (M) ........................................................................... 431 pll2d Plot results of 2D peak picking (C) ................................................ 431 plockport Port number to use to lock out multiple ProTune processes (P)..... 431 plot Automatically plot spectra (M)....................................................... 432 plot1d Plotting macro for simple (non-arrayed) 1D spectra (M) ............... 432 plot2D Plot 2D spectra (M)......................................................................... 433 plotfile Plot to a file (M).............................................................................. 433 plothiresprep High resolution plot output preparation (M)................................... 434 plotmanual Plot manually (M)........................................................................... 434 plotlogo Plots a logo (M) .............................................................................. 434 plotpreview Creates temporary plots of the current plot output (M) .................. 434 plotside Plot spectrum on side (M)............................................................... 434 plotter Plotter device (P) ............................................................................ 434 plottop Plot spectrum on top (M)................................................................ 434 plottopside Plot spectrum on top and side (M).................................................. 435 plp Plot phosphorus spectrum (M)........................................................ 435 plplanes Plot a series of 3D planes (M) ........................................................ 435 plt2Darg Plot 2D arguments (P).................................................................... 436 pltext Plot text file (M) ............................................................................. 436 pltmod Plotter display mode (P) ................................................................. 436 plvast Plot VAST data in a stacked 1D-NMR matrix format (M)............. 437 plvast2d Plot VAST data in a stacked pseudo-2D format (M) ...................... 437 plww Plot spectra in whitewash mode (C) ............................................... 438 pmode Processing mode for 2D data (P) .................................................... 438 poly0 Display mean of the data in regression.inp file (M) ....................... 439 pp Decoupler pulse length (P) ............................................................. 439 ppa Plot a parameter list in plain English (M)....................................... 440 ppcal Proton decoupler pulse calibration (M) .......................................... 440 ppf Plot peak frequencies over spectrum (C)........................................ 440 pph Print pulse header (M) .................................................................... 441 ppmm Resolution on printers and plotters (P) ........................................... 441 pprofile Plot pulse excitation profile (M)..................................................... 441 pps Plot pulse sequence (C)................................................................... 442 prealfa Specify a delay for longer ring down (P)........................................ 442 prep Run prepare acquisition macro (M) ............................................... 442 Presat Set up parameters for presat 1 H experiment (M)............................ 443 prevpl Display the previous 3D plane (M)................................................. 443 prescan Study queue prescan (P)................................................................. 443 prescan_CoilTable Read or update the CoilTable File (M) ........................................... 443 prescan_tn Return tn string for a given atomic number (M)............................. 443 printer Printer device (P) ............................................................................ 444 printfile Path to the print-to-file image (P) ................................................... 444 printformat Format of saved-to-file image (P)................................................... 444 printlayout Layout of printed image (P)............................................................ 444 printoff Stop sending text to printer and start print operation (C) ............... 444 printon Direct text output to printer (C) ...................................................... 444 printregion Screen region to be printed (P) ....................................................... 445 printsize Size of printed image (P) ................................................................ 445 printsend Defines where image will print (P)................................................. 445 probe Probe type (P) ................................................................................. 445 probeConnect Specify which nucleus can be acquired on each RF channel (P).... 445 Probe_edit Edit probe for specific nucleus (U)................................................. 446 probe_edit Edit probe for specific nucleus (M) ................................................ 446 20 Command and Parameter Reference for VnmrJ 2.2D 01-999380-00 A 0808
Page 1 and 2: VnmrJ Command and Parameter Referen
Page 3 and 4: VnmrJ Command and Parameter Referen
Page 5 and 6: 2 Command and Parameter Reference f
Page 7 and 8: arraydim Dimension of experiment (P
Page 9 and 10: copy Copy a file (C) ..............
Page 11 and 12: dglc Display group of LC-NMR parame
Page 13 and 14: dsshn Display stacked spectra horiz
Page 15 and 16: gcal Gradient calibration constant
Page 17 and 18: homo3 Homodecoupling control for th
Page 19 and 20: loadcolors Load colors for graphics
Page 21: Noesy Convert the parameter to a NO
Page 25 and 26: R r Recall display parameter set (M
Page 27 and 28: seqfil Pulse sequence name (P).....
Page 29 and 30: sqsavestudy Macro to save study par
Page 31 and 32: updaterev Update after installing n
Page 33 and 34: xm1 Utility macro for study queue e
Page 35 and 36: 32 Command and Parameter Reference
Page 37 and 38: Notational Conventions md(to_exp) n
Page 39 and 40: A aph aph0 aphb aphx appdirs appmod
Page 41 and 42: A See also: parent (nested) macros
Page 43 and 44: A acosy Syntax: Description: See al
Page 45 and 46: A spin sw vp vs wp Sample spin rate
Page 47 and 48: A window should open automatically
Page 49 and 50: A See also: 595. Sample failed to i
Page 51 and 52: A spadd sub Add current spectrum to
Page 53 and 54: A Examples: See also: • 'ss' spec
Page 55 and 56: A Examples: See also: adept adept('
Page 57 and 58: A lock sample Submit an Autolock ex
Page 59 and 60: A Arguments: (3) Line containing an
Page 61 and 62: A See also: VnmrJ User Programming
Page 63 and 64: A appmode Description: Values: Appl
Page 65 and 66: A asin Find arc sine of number (C)
Page 67 and 68: A Arguments: Examples: When called
Page 69 and 70: A go_ load loc lock method sample s
Page 71 and 72: A Aufindz0 Automatic adjustment of
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A Values: 'y' indicates automation
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A Description: Arguments: Examples:
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A Examples: Examples: See also: >9
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A See also: NMR Spectroscopy User G
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A Examples: See also: number_argume
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A dscale pscale Display scale below
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B Arguments: Examples: See also: me
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B This command should rarely be use
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B See also: NMR Spectroscopy User G
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B 88 Command and Parameter Referenc
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C contact_time MAS cross-polarizati
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C Description: See also: Calculates
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C See also: 127 for imaging attenua
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C See also: NMR Spectroscopy User G
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C Description: checkstring is used
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C clfreq Description: See also: Cal
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C it runs in interactive mode; if n
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C Arguments: Examples: See also:
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C Description: Arguments: See also:
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C Examples: See also: • -dxxx, wh
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C Dqcosy relayh Set up parameters f
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C Related: apptype Application type
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C cr2 Description: See also: Cursor
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C crl Description: See also: Clear
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C See also: NMR Spectroscopy User G
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C 120 Command and Parameter Referen
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D delta Cursor difference in direct
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D dosygamma dosytimecubed dot1 dotf
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D See also: If d0='n', the software
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D daslp Description: Values: See al
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D dc Description: See also: Calcula
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D Arguments: Examples: See also: ds
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D ft2d imconi wft2d Fourier transfo
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D Syntax: Description: ddrcr= Sets
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D dm2 dm3 Decoupler mode for second
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D Description: Arguments: Examples:
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D deptproc Description: See also: P
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D dfid Syntax: Description: See als
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D ho plfid pfww sc vo vpf wc Horizo
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D Arguments: Examples: See also: te
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D See also: NMR Spectroscopy User G
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D Examples: in these directories. T
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D nli z Find integral values (C) Ad
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D Values: See also: 5 Hz to 2 MHz i
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D Description: Arguments: Examples:
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D See also: outside of the acqi pro
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D dnode Applicability: Description:
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D Examples: See also: max_width is
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D Values: See also: deltaf (if the
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D See also: dpf('top','noll') dpf('
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D dplane Syntax: Description: Argum
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D Arguments: See also: The pulse pa
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D CAUTION: See also: Decoupling pow
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D Examples: See also: • 'xor','no
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D ds Syntax: Description: Arguments
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D Examples: See also: ds2dn ds2dn('
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D dseq4 Applicability: Description:
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D Values: See also: the digital fil
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D dsp Applicability: Description: V
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D Arguments: Examples: See also: Th
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D step is the increment for the spe
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D dsww ft1d ho intmod pl plww sc sc
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D dsvast2d Display VAST data in a p
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D homorof3 tn Delay between setting
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E See also: NMR Spectroscopy User G
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E enter Applicability: Syntax: Desc
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E ewrite Applicability: Syntax: Des
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E keyword 'maclib' 'command' 'ascii
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E exit Description: CAUTION: Call t
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E Arguments: Examples: See also: (3
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E Syntax: Description: Arguments: E
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F foldcc foldj foldt fontselect for
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F make3dcoef par2d Make 3D coeffici
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F Examples: See also: v1, v2... is
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F fiddleu Perform reference deconvo
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F Arguments: Examples: See also: st
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F slfreq sp usemark wp Measured lin
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F Arguments: Examples: See also: nf
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F focus Description: See also: Send
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F See also: format($snum,3,1):$rval
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F Examples: See also: type of tree
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F Examples: See also: start is the
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F See also: NMR Spectroscopy User G
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F • 'noop' is a keyword to not pe
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F See also: • 'ni2' is a keyword
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F Arguments: ft3d Entered from UNIX
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F make3dcoef ptspec3d set3dproc spe
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G gHSQC_d213 Ghsqctoxy gilson gin g
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G examined for signal level. If the
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G See also: Be aware that if an old
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G Examples: See also: extension is
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G Examples: See also: • 'xall' is
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G Arguments: Examples: See also: A
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G See also: detected dimension. Thi
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G gilson Syntax: Description: See a
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G Values: 'n' disable spinning duri
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G gmax Description: See also: Maxim
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G go seqfil usergo Submit experimen
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G grayctr Gray level window adjustm
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G gtnroesy Applicability: Descripti
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G 274 Command and Parameter Referen
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H homo2 homo3 homo4 HOMODEC homo2d
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H See also: j2r is the reduced coup
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H Examples: See also: hcdept hcdept
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H homo homorof1 homorof2 homorof3 t
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H Examples: See also: hdwshimlist='
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H HMQC_d2 Description: Set up param
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H Related: dm3 Decoupler mode for t
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hoult Set parameters alfa and rof2
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H hsqctoxySE Description: Set up pa
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H htss1 Description: Values: See al
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H 296 Command and Parameter Referen
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I ihwinfo Syntax: Description: Argu
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I Examples: See also: dir_flag imag
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I See also: fn. The insref paramete
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I See also: NMR Spectroscopy User G
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I category type gettype returns str
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I 308 Command and Parameter Referen
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J Arguments: Examples: See also: ex
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J jviewports Viewport layout (P) De
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K See also: NMR Spectroscopy User G
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K 316 Command and Parameter Referen
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L lp1 lp2 lpalg lpalg1 lpalg2 lpext
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L Values: See also: A positive valu
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L legrelay Description: Values: See
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L See also: in Hz, analogous to sfr
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L Examples: See also: • 'comment'
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L Examples: See also: ln(.5) ln(val
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L Values: See also: 1, 2, 3, or 4 (
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L See also: User Guide: Solid-State
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L See also: lookup('delimiter',' ,\
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L strtlp strtext Starting point for
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L lpfilt ni LP coefficients to calc
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L lpprint Description: Values: See
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L Arguments: Examples: directory is
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L lsfrq1 Description: Values: Frequ
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L 346 Command and Parameter Referen
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M movetof mp mqcosy mrev8 mrfb mref
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M Arguments: Examples: See also: ov
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M make3dcoef Syntax: Description: A
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M element_number and format argumen
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M Description: Arguments: (5) mark
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M Values: See also: Note that the V
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M mf Syntax: Description: Arguments
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M mfopen mftrace rfblk rftrace Memo
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M mlabel Description: See also: Men
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M Examples: See also: mp(4) mp(2,3)
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M Description: Examples: An array o
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M CAUTION: See also: One special ca
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N newmenu Syntax: Description: Argu
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N ni3 Description: See also: Number
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N Arguments: Examples: See also: 'p
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N r6 returns the percentage channel
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N ntrig Applicability: Description:
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N 382 Command and Parameter Referen
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O Arguments: Examples: See also: %d
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O paros sw Create additional parame
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O 'n' causes normal acquisition to
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P pboxpar pboxrst pboxunits pcon pc
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P prescan_CoilTable prescan_tn prin
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P Description: Values: See also: Sp
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P See also: The pa1 command is only
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P page Description: Name of page (P
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P Description: See also: Creates th
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P See also: The quality of filterin
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P See also: User Programming Relate
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P See also: NMR Spectroscopy User G
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P pboxpar Syntax: Description: Argu
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P See also: User Programming Relate
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P Values: See also: A three-charact
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P Examples: See also: reference_reg
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P phase Syntax: Description: Argume
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P phfid1 Description: Values: See a
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P pintvast Applicability: Syntax: D
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P ft1d ho intmod plww pshr pslw sc
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P plate_glue Applicability: Descrip
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P vpf wc Current vertical position
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P • Negative or positive contours
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P Related: protune Macro to start P
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P plothiresprep High resolution plo
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P p1 pw First pulse width (P) Pulse
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P Examples: See also: pprofile ppro
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P Examples: str is a string that ca
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P See also: VnmrJ User Programming
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P See also: proc1d does not work wi
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P Description: Arguments: Examples:
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P Third case: exec — keyword that
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P Examples: See also: C3 sets lb1=-
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P See also: searched for when an ex
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P sw sw1 sw2 Spectral width in dire
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P See also: point are used in the s
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P Arguments: Examples: See also: fi
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P 466 Command and Parameter Referen
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Q ? Display the value of an individ
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R rfband rfblk rfchannel rfchtype r
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R See also: experiment with the rt
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R Examples: The par1 and par2 param
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R Examples: See also: readhw('z1c',
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R Description: Produces 2D images (
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R record Syntax: Description: Argum
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R Related: reff1 Reference f2 Indir
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R See also: if it is a heteronuclea
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R the current tree, if it exists th
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R vnmrjcmd() wp Commands to invoke
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R Arguments: Examples: See also: us
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R Values: See also: The values of r
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R rfp Description: Values: See also
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R rfwg Description: Values: See als
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R rl rl2 scalesw1 sfrq Set ref. lin
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R See also: NMR Spectroscopy User G
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R See also: NMR Spectroscopy User G
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R Examples: See also: noabort — k
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S setcolor setdecpars setdec2pars s
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S spincad Run SpinCAD program (C) s
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S Description: Saves a copy of the
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S See also: NMR Spectroscopy User G
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S sd2 Applicability: Description: S
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S Examples: See also: • 'f1f3', '
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S Arguments: Examples: See also: se
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S See also: initialization, etc.).
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S See also: User Programming Relate
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S See also: Pulsed Field Gradient M
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S Arguments: Examples: Syntax 5 eje
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S Step Value Parameter setting Argu
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S sw rof2 Spectral width in directl
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S sw tpwr Spectral width in directl
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S Arguments: Examples: See also: re
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S See also: flushing mode. In the l
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S Examples: See also: trev time rev
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S See also: (e.g.: multiselective)
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S See also: and radial shims x1, y1
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S Arguments: See also: shift sets t
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S testsn testct Test signal-to-nois
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S spadd Syntax: Description: Argume
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S See also: If the spinning speed i
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S dsp initialize_iterate iterate ni
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S sqdir sqname studyid Svfname Stud
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S ss Steady-state transients (P) De
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S ssfilter sslsfrq ssntaps wft Full
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S shim wshim Submit an Autoshim exp
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S See also: sub('new') sub('trace',
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S Examples: See also: where numgray
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S Percent sign (%) substitution spe
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S Examples: See also: The svs comma
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S See also: variable evolution time
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T tpwrm Observe transmitter linear
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T Arguments: Examples: See also: 2D
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T Arguments: Examples: See also: 1
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T Syntax: Values: status of the cur
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T textis Syntax: Description: Argum
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T nt sw1 sw2 Number of transients (
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T tnroesy Description: See also: Se
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T tpwr tpwrm Observe transmitter po
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T Examples: See also: the 1 H, the
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T tupwr Description: See also: Tran
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U See also: NMR Spectroscopy User G
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U See also: NMR Spectroscopy User G
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U 608 Command and Parameter Referen
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V vast1d Applicability: Description
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V vf Description: Values: See also:
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V Examples: See also: Changing sele
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V See also: vnmr2sc('gcosy',2,3) nt
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V Examples: See also: file is the n
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V See also: NMR Spectroscopy User G
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V See also: NMR Spectroscopy User G
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V See also: VnmrJ Installation and
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W wp wp1 wp2 write writefid writepa
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W Values: Width, in mm. See also: N
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W wet Description: Flag to turn on
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W Examples: See also: before each o
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W Description: Arguments: See also:
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W See also: NMR Spectroscopy User G
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W wp2 Description: See also: Width
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W writefid Syntax: Description: Arg
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W See also: 'e' or 'exp' sets that
Page 647 and 648:
W Arguments: Examples: See also:
Page 649 and 650:
W 646 Command and Parameter Referen
Page 651 and 652:
X xpolar1 xy xz xz2 Set up paramete
Page 653 and 654:
X xmaddreq Applicability: Descripti
Page 655 and 656:
X Description: See also: Find the n
Page 657 and 658:
X Description: See also: A macro th
Page 659 and 660:
X Description: See also: Sets up th
Page 661 and 662:
Y Values: See also: If shimset is 1
Page 663 and 664:
Z Arguments: Examples: See also: be
Page 665 and 666:
Z See also: NMR Spectroscopy User G
Page 667 and 668:
Z See also: NMR Spectroscopy User G
Page 669 and 670:
Z 666 Command and Parameter Referen
Page 671 and 672:
Index type of data processing, 447
Page 673 and 674:
Index analysis of DEPT data, 70 car
Page 675 and 676:
Index parameters in a parameter tre
Page 677 and 678:
Index contour plot, 130 contour plo
Page 679 and 680:
Index FDM program, running, 219 FID
Page 681 and 682:
Index gradient calibration pulse se
Page 683 and 684:
Index linear modulator power, 179,
Page 685 and 686:
Index Oxford-Sorenson VT controller
Page 687 and 688:
Index Hewlett-Packard, 648 maximum
Page 689 and 690:
Index recording keyboard entries, 4
Page 691 and 692:
Index create parameters, 401 filter
Page 693 and 694:
Index t 2 dimension in, 343 tablib
Page 695:
Index WETPWXCAL pulse sequence, 631
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VnmrJ Command and Parameter Reference VnmrJ 2.2D

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