VnmrJ Command and Parameter Reference VnmrJ 2.2D

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shelli Start an interactive UNIX shell (C) ................................................ 544 shim Submit an Autoshim experiment to acquisition (C) ....................... 544 shimset Type of shim set (P) ........................................................................ 545 showconfig Show system configuration settings (M) ........................................ 546 showconsole Show system configuration settings (U)......................................... 546 showfit Display numerical results of deconvolution (M) ............................ 547 showloginbox Shows operator login dialog (M) .................................................... 547 shownumx Show x position of number (P)....................................................... 547 shownumy Show y position of number (P)....................................................... 547 showoriginal Restore first 2D spectrum in 3D DOSY experiment (M) ............... 547 showplotter Show list of currently defined plotters and printers (M) ................ 547 showplotq Display plot jobs in plot queue (M) ................................................ 547 showprintq Display print jobs in print queue (M) ............................................. 547 showprotunegui show the graphical interface while tuning (P) ................................ 548 showrfmon Show RF Monitor Button in Hardware Bar (P).............................. 548 showstat Display information about status of acquisition (M,U) .................. 548 sin Find sine value of an angle (C)....................................................... 548 sine Find values for a sine window function (M)................................... 549 sinebell Select default parameters for sinebell weighting (M)..................... 549 sinesq Find values for a sine-squared window function (M)..................... 549 size Returns the number of elements in an arrayed parameter (O)........ 550 slfreq Measured line frequencies (P) ........................................................ 550 slw Spin simulation linewidth (P) ......................................................... 550 smaxf Maximum frequency of any transition (P)...................................... 551 sminf Minimum frequency of any transition (P) ...................................... 551 smsport Sample Management System serial port connection (P) ................ 551 sn Signal-to-noise ratio (P).................................................................. 551 solppm Return ppm and peak width of solvent resonances (M) ................. 552 solvent Lock solvent (P).............................................................................. 552 solvinfo Retrieve information from solvent table (C)................................... 552 sort Sort real values of a parameter (M) ................................................ 553 sp Start of plot in directly detected dimension (P) .............................. 553 sp1 Start of plot in 1st indirectly detected dimension (P) ..................... 553 sp2 Start of plot in 2nd indirectly detected dimension (P) .................... 553 spadd Add current spectrum to add/subtract experiment (C).................... 554 spcfrq Display frequencies of rf channels (M) .......................................... 554 specdc3d 3D spectral drift correction (P) ....................................................... 555 spin Submit a spin setup experiment to acquisition (C) ......................... 555 spin Sample spin rate (P)........................................................................ 555 spincad Run SpinCAD program (C) ............................................................ 556 spingen Compile SpinCAD pulse sequence (M,U)...................................... 556 spinll Set up a slfreq array (M) ................................................................. 557 spinner Open the Spinner Control window (C) ........................................... 557 spinopt Spin automation (P) ........................................................................ 558 spins Perform spin simulation calculation (C)......................................... 558 split Split difference between two cursors (M)....................................... 560 spintype Spinner Type ((P)............................................................................ 560 spmax Take the maximum of two spectra (C)............................................ 560 spmin Take minimum of two spectra in add/subtract experiment (C)....... 560 spsm Enter spin system (M)..................................................................... 561 spsub Subtract current spectrum from add/subtract experiment (C) ........ 561 sqcosine Set up unshifted cosine-squared window function (M) .................. 562 sqdir Study queue directory (P) ............................................................... 562 sqend End a study queue (M)................................................................... 562 sqexp Load experiment from protocol (M).............................................. 562 sqfilemenu Study queue file menu commands (M).......................................... 563 sqmode Study queue mode (P).................................................................... 563 sqname Study queue parameter template (P)............................................... 563 sqpars Create study queue parameters for imaging (M) ........................... 564 sqprotocol Macro to create protocols (M) ....................................................... 564 sqreset Reset study queue parameters for imaging (M)............................. 564 sqrt Return square root of a real number (O)......................................... 564 01-999380-00 A 0808 Command and Parameter Reference for VnmrJ 2.2D 25
sqsavestudy Macro to save study parameters for imaging (M).......................... 564 sqsinebell Set up unshifted sinebell-squared window function (M)................ 565 srate Spinning rate for magic angle spinning (P) .................................... 565 sread Read converted data into VnmrJ (C) .............................................. 565 srof2 Calculate exact rof2 value for Cold Probes (M) ............................. 565 ss Steady-state transients (P)............................................................... 566 ssecho Set up solid-state echo pulse sequence (M) .................................... 566 ssecho1 Set up parameters for SSECHO1 pulse sequence (M) ................... 566 ssfilter Full bandwidth of digital filter to yield a filtered FID (P) .............. 566 sslsfrq Center of solvent-suppressed region of spectrum (P)..................... 566 ssntaps Number of coefficients in digital filter (P) ..................................... 567 ssorder Order of polynomial to fit digitally filtered FID (P)....................... 567 stack Stacking mode for processing and plotting arrayed spectra (M) ... 568 stackmode Stacking control for processing arrayed 1D spectra (P) ................. 568 startq Start a chained study queue (M) .................................................... 568 status Display status of sample changer (C,U) ......................................... 568 std1d Apptype macro for Standard 1D experiments (M) ......................... 569 stdshm Interactively create a method string for autoshimming (M) ........... 569 sth Minimum intensity threshold (P).................................................... 570 string Create a string variable (C)............................................................. 570 strtext Starting point for LP data extension in np dimension (P)............... 570 strtext1 Starting point for LP data extension in ni dimension (P)................ 570 strtext2 Starting point for LP data extension in ni2 dimension (P).............. 571 strtlp Starting point for LP calculation in np dimension (P) .................... 571 strtlp1 Starting point for LP calculation in ni dimension (P)..................... 571 strtlp2 Starting point for LP calculation in ni2 dimension (P)................... 571 studyid Study identification (P)................................................................... 572 studypar Study parameters (P)...................................................................... 572 studystatus Study status (P) .............................................................................. 572 studytime Study time (P) ................................................................................ 572 su Submit a setup experiment to acquisition (M)................................ 573 sub Subtract current FID from add/subtract experiment (C)................. 573 substr Select a substring from a string (C) ................................................ 574 suselfrq Select peak, continue selective excitation experiment (M) ............ 575 svdat Save data (C)................................................................................... 575 svf Save FIDs in current experiment (M) ............................................. 576 svfdf Save FID data in FDF format (M) .................................................. 576 svfdir Directory for non-study data (P)..................................................... 577 Svfname Create path for data storage (C)..................................................... 577 svfname Filename parameter template for non-study data ((P) .................... 579 svp Save parameters from current experiment (M)............................... 579 svs Save shim coil settings (C) ............................................................. 579 svs Spin simulation vertical scale (P) ................................................... 580 svtmp Move experiment data into experiment subfile (M) ....................... 580 sw Spectral width in directly detected dimension (P) .......................... 580 sw1 Spectral width in 1st indirectly detected dimension (P) ................. 581 sw2 Spectral width in 2nd indirectly detected dimension (P)................ 581 sw3 Spectral width in 3rd indirectly detected dimension (P)................. 581 sysgcoil System gradient coil (P).................................................................. 582 system System type (P)............................................................................... 582 systemdir VnmrJ system directory (P) ............................................................ 582 T t1 T 1 exponential analysis (M)............................................................ 584 t1s T 1 exponential analysis with short output table (M)....................... 584 t2 T 2 exponential analysis (M)............................................................ 585 t2s T 2 exponential analysis with short output table (M)....................... 585 tabc Convert data in table order to linear order (M)............................... 585 tan Find tangent value of an angle (C).................................................. 586 tape Read tapes from VXR-style system (M,U)..................................... 586 tape Control tape options of files program (P) ....................................... 587 26 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 and 22: Noesy Convert the parameter to a NO
Page 23 and 24: plcosy Plot COSY- and NOESY-type sp
Page 25 and 26: R r Recall display parameter set (M
Page 27: seqfil Pulse sequence name (P).....
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
Page 73 and 74: A Values: 'y' indicates automation
Page 75 and 76: A Description: Arguments: Examples:
Page 77 and 78: 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
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W Arguments: Examples: See also:
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W 646 Command and Parameter Referen
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X xpolar1 xy xz xz2 Set up paramete
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X xmaddreq Applicability: Descripti
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X Description: See also: Find the n
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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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