VnmrJ Command and Parameter Reference VnmrJ 2.2D

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VnmrJ Command and Parameter Reference Varian, Inc. Inova and MercuryPlus NMR Systems With VnmrJ 2.2D Software Pub. No. 01-999380-00, Rev. A 0808
VnmrJ Command and Parameter Reference Varian, Inc. Inova and MercuryPlus NMR Systems With VnmrJ 2.2D Software Pub. No. 01-999380-00, Rev. A 0808 Revision history: Rev A – Initial release for VnmrJ 2.2D Technical writer and editor: Everett Schreiber Copyright ©2008 by Varian, Inc. 3120 Hansen Way, Palo Alto, California 94304 1-800-356-4437 www.varianinc.com All rights reserved. Printed in the United States. The information in this document has been carefully checked and is believed to be entirely reliable. However, no responsibility is assumed for inaccuracies. Statements in this document are not intended to create any warranty, expressed or implied. Specifications and performance characteristics of the software described in this manual may be changed at any time without notice. Varian reserves the right to make changes in any products herein to improve reliability, function, or design. Varian does not assume any liability arising out of the application or use of any product or circuit described herein; neither does it convey any license under its patent rights nor the rights of others. Inclusion in this document does not imply that any particular feature is standard on the instrument. UNITY INOVA, MERCURY-VX, MERCURY-PLUS, MERCURY, Varian, Inc. NMR Spectrometer Systems, VnmrJ, VNMR, MAGICAL II, Magnex, AutoLock, AutoShim, AutoPhase, limNET, ASM, and SMS are registered trademarks or trademarks of Varian, Inc. . Dell, the Dell logo, Precision, Dimension, Inspiron and Axim are registered trademarks or trademarks of Dell Computer Corporation. Red Hat is a registered trademark of Red Hat, Inc. Linux is a registered trademark of Linus Torvalds in the United States and in other countries. Ethernet is a registered trademark of Xerox Corporation. VxWORKS and VxWORKS POWERED are registered trademarks of WindRiver Inc. Other product names in this document are registered trademarks or trademarks of their respective holders.
Page 1: 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 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
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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
Page 85 and 86:
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
Page 101 and 102:
C Description: checkstring is used
Page 103 and 104:
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
Page 117 and 118:
C cr2 Description: See also: Cursor
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C crl Description: See also: Clear
Page 121 and 122:
C See also: NMR Spectroscopy User G
Page 123 and 124:
C 120 Command and Parameter Referen
Page 125 and 126:
D delta Cursor difference in direct
Page 127 and 128:
D dosygamma dosytimecubed dot1 dotf
Page 129 and 130:
D See also: If d0='n', the software
Page 131 and 132:
D daslp Description: Values: See al
Page 133 and 134:
D dc Description: See also: Calcula
Page 135 and 136:
D Arguments: Examples: See also: ds
Page 137 and 138:
D ft2d imconi wft2d Fourier transfo
Page 139 and 140:
D Syntax: Description: ddrcr= Sets
Page 141 and 142:
D dm2 dm3 Decoupler mode for second
Page 143 and 144:
D Description: Arguments: Examples:
Page 145 and 146:
D deptproc Description: See also: P
Page 147 and 148:
D dfid Syntax: Description: See als
Page 149 and 150:
D ho plfid pfww sc vo vpf wc Horizo
Page 151 and 152:
D Arguments: Examples: See also: te
Page 153 and 154:
D See also: NMR Spectroscopy User G
Page 155 and 156:
D Examples: in these directories. T
Page 157 and 158:
Page 159 and 160:
D nli z Find integral values (C) Ad
Page 161 and 162:
D Values: See also: 5 Hz to 2 MHz i
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D Description: Arguments: Examples:
Page 165 and 166:
D See also: outside of the acqi pro
Page 167 and 168:
Page 169 and 170:
D dnode Applicability: Description:
Page 171 and 172:
D Examples: See also: max_width is
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D Values: See also: deltaf (if the
Page 175 and 176:
D See also: dpf('top','noll') dpf('
Page 177 and 178:
D dplane Syntax: Description: Argum
Page 179 and 180:
D Arguments: See also: The pulse pa
Page 181 and 182:
D CAUTION: See also: Decoupling pow
Page 183 and 184:
D Examples: See also: • 'xor','no
Page 185 and 186:
D ds Syntax: Description: Arguments
Page 187 and 188:
D Examples: See also: ds2dn ds2dn('
Page 189 and 190:
D dseq4 Applicability: Description:
Page 191 and 192:
D Values: See also: the digital fil
Page 193 and 194:
D dsp Applicability: Description: V
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D Arguments: Examples: See also: Th
Page 197 and 198:
D step is the increment for the spe
Page 199 and 200:
D dsww ft1d ho intmod pl plww sc sc
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D dsvast2d Display VAST data in a p
Page 203 and 204:
D homorof3 tn Delay between setting
Page 205 and 206:
E See also: NMR Spectroscopy User G
Page 207 and 208:
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
Page 217 and 218:
E Syntax: Description: Arguments: E
Page 219 and 220:
F foldcc foldj foldt fontselect for
Page 221 and 222:
F make3dcoef par2d Make 3D coeffici
Page 223 and 224:
F Examples: See also: v1, v2... is
Page 225 and 226:
F fiddleu Perform reference deconvo
Page 227 and 228:
F Arguments: Examples: See also: st
Page 229 and 230:
F slfreq sp usemark wp Measured lin
Page 231 and 232:
F Arguments: Examples: See also: nf
Page 233 and 234:
F focus Description: See also: Send
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F See also: format($snum,3,1):$rval
Page 237 and 238:
F Examples: See also: type of tree
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F Examples: See also: start is the
Page 241 and 242:
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
Page 247 and 248:
F Arguments: ft3d Entered from UNIX
Page 249 and 250:
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
Page 255 and 256:
G See also: Be aware that if an old
Page 257 and 258:
G Examples: See also: extension is
Page 259 and 260:
G Examples: See also: • 'xall' is
Page 261 and 262:
G Arguments: Examples: See also: A
Page 263 and 264:
G See also: detected dimension. Thi
Page 265 and 266:
G gilson Syntax: Description: See a
Page 267 and 268:
G Values: 'n' disable spinning duri
Page 269 and 270:
G gmax Description: See also: Maxim
Page 271 and 272:
G go seqfil usergo Submit experimen
Page 273 and 274:
G grayctr Gray level window adjustm
Page 275 and 276:
G gtnroesy Applicability: Descripti
Page 277 and 278:
G 274 Command and Parameter Referen
Page 279 and 280:
H homo2 homo3 homo4 HOMODEC homo2d
Page 281 and 282:
H See also: j2r is the reduced coup
Page 283 and 284:
H Examples: See also: hcdept hcdept
Page 285 and 286:
H homo homorof1 homorof2 homorof3 t
Page 287 and 288:
H Examples: See also: hdwshimlist='
Page 289 and 290:
H HMQC_d2 Description: Set up param
Page 291 and 292:
H Related: dm3 Decoupler mode for t
Page 293 and 294:
hoult Set parameters alfa and rof2
Page 295 and 296:
H hsqctoxySE Description: Set up pa
Page 297 and 298:
H htss1 Description: Values: See al
Page 299 and 300:
H 296 Command and Parameter Referen
Page 301 and 302:
I ihwinfo Syntax: Description: Argu
Page 303 and 304:
I Examples: See also: dir_flag imag
Page 305 and 306:
I See also: fn. The insref paramete
Page 307 and 308:
I See also: NMR Spectroscopy User G
Page 309 and 310:
I category type gettype returns str
Page 311 and 312:
I 308 Command and Parameter Referen
Page 313 and 314:
J Arguments: Examples: See also: ex
Page 315 and 316:
J jviewports Viewport layout (P) De
Page 317 and 318:
K See also: NMR Spectroscopy User G
Page 319 and 320:
K 316 Command and Parameter Referen
Page 321 and 322:
L lp1 lp2 lpalg lpalg1 lpalg2 lpext
Page 323 and 324:
L Values: See also: A positive valu
Page 325 and 326:
L legrelay Description: Values: See
Page 327 and 328:
L See also: in Hz, analogous to sfr
Page 329 and 330:
L Examples: See also: • 'comment'
Page 331 and 332:
L Examples: See also: ln(.5) ln(val
Page 333 and 334:
L Values: See also: 1, 2, 3, or 4 (
Page 335 and 336:
L See also: User Guide: Solid-State
Page 337 and 338:
L See also: lookup('delimiter',' ,\
Page 339 and 340:
L strtlp strtext Starting point for
Page 341 and 342:
L lpfilt ni LP coefficients to calc
Page 343 and 344:
L lpprint Description: Values: See
Page 345 and 346:
L Arguments: Examples: directory is
Page 347 and 348:
L lsfrq1 Description: Values: Frequ
Page 349 and 350:
L 346 Command and Parameter Referen
Page 351 and 352:
M movetof mp mqcosy mrev8 mrfb mref
Page 353 and 354:
M Arguments: Examples: See also: ov
Page 355 and 356:
M make3dcoef Syntax: Description: A
Page 357 and 358:
M element_number and format argumen
Page 359 and 360:
M Description: Arguments: (5) mark
Page 361 and 362:
M Values: See also: Note that the V
Page 363 and 364:
M mf Syntax: Description: Arguments
Page 365 and 366:
M mfopen mftrace rfblk rftrace Memo
Page 367 and 368:
M mlabel Description: See also: Men
Page 369 and 370:
M Examples: See also: mp(4) mp(2,3)
Page 371 and 372:
M Description: Examples: An array o
Page 373 and 374:
M CAUTION: See also: One special ca
Page 375 and 376:
N newmenu Syntax: Description: Argu
Page 377 and 378:
N ni3 Description: See also: Number
Page 379 and 380:
N Arguments: Examples: See also: 'p
Page 381 and 382:
N r6 returns the percentage channel
Page 383 and 384:
N ntrig Applicability: Description:
Page 385 and 386:
N 382 Command and Parameter Referen
Page 387 and 388:
O Arguments: Examples: See also: %d
Page 389 and 390:
O paros sw Create additional parame
Page 391 and 392:
O 'n' causes normal acquisition to
Page 393 and 394:
P pboxpar pboxrst pboxunits pcon pc
Page 395 and 396:
P prescan_CoilTable prescan_tn prin
Page 397 and 398:
P Description: Values: See also: Sp
Page 399 and 400:
P See also: The pa1 command is only
Page 401 and 402:
P page Description: Name of page (P
Page 403 and 404:
P Description: See also: Creates th
Page 405 and 406:
P See also: The quality of filterin
Page 407 and 408:
P See also: User Programming Relate
Page 409 and 410:
P See also: NMR Spectroscopy User G
Page 411 and 412:
Page 413 and 414:
P pboxpar Syntax: Description: Argu
Page 415 and 416:
P See also: User Programming Relate
Page 417 and 418:
P Values: See also: A three-charact
Page 419 and 420:
P Examples: See also: reference_reg
Page 421 and 422:
P phase Syntax: Description: Argume
Page 423 and 424:
P phfid1 Description: Values: See a
Page 425 and 426:
P pintvast Applicability: Syntax: D
Page 427 and 428:
P ft1d ho intmod plww pshr pslw sc
Page 429 and 430:
P plate_glue Applicability: Descrip
Page 431 and 432:
P vpf wc Current vertical position
Page 433 and 434:
P • Negative or positive contours
Page 435 and 436:
P Related: protune Macro to start P
Page 437 and 438:
P plothiresprep High resolution plo
Page 439 and 440:
Page 441 and 442:
Page 443 and 444:
P p1 pw First pulse width (P) Pulse
Page 445 and 446:
P Examples: See also: pprofile ppro
Page 447 and 448:
P Examples: str is a string that ca
Page 449 and 450:
P See also: VnmrJ User Programming
Page 451 and 452:
P See also: proc1d does not work wi
Page 453 and 454:
P Description: Arguments: Examples:
Page 455 and 456:
P Third case: exec — keyword that
Page 457 and 458:
P Examples: See also: C3 sets lb1=-
Page 459 and 460:
P See also: searched for when an ex
Page 461 and 462:
P sw sw1 sw2 Spectral width in dire
Page 463 and 464:
Page 465 and 466:
P See also: point are used in the s
Page 467 and 468:
P Arguments: Examples: See also: fi
Page 469 and 470:
P 466 Command and Parameter Referen
Page 471 and 472:
Q ? Display the value of an individ
Page 473 and 474:
R rfband rfblk rfchannel rfchtype r
Page 475 and 476:
R See also: experiment with the rt
Page 477 and 478:
R Examples: The par1 and par2 param
Page 479 and 480:
R Examples: See also: readhw('z1c',
Page 481 and 482:
R Description: Produces 2D images (
Page 483 and 484:
R record Syntax: Description: Argum
Page 485 and 486:
R Related: reff1 Reference f2 Indir
Page 487 and 488:
R See also: if it is a heteronuclea
Page 489 and 490:
R the current tree, if it exists th
Page 491 and 492:
R vnmrjcmd() wp Commands to invoke
Page 493 and 494:
R Arguments: Examples: See also: us
Page 495 and 496:
R Values: See also: The values of r
Page 497 and 498:
R rfp Description: Values: See also
Page 499 and 500:
R rfwg Description: Values: See als
Page 501 and 502:
R rl rl2 scalesw1 sfrq Set ref. lin
Page 503 and 504:
R See also: NMR Spectroscopy User G
Page 505 and 506:
R See also: NMR Spectroscopy User G
Page 507 and 508:
R Examples: See also: noabort — k
Page 509 and 510:
S setcolor setdecpars setdec2pars s
Page 511 and 512:
S spincad Run SpinCAD program (C) s
Page 513 and 514:
S Description: Saves a copy of the
Page 515 and 516:
S See also: NMR Spectroscopy User G
Page 517 and 518:
Page 519 and 520:
S sd2 Applicability: Description: S
Page 521 and 522:
S Examples: See also: • 'f1f3', '
Page 523 and 524:
S Arguments: Examples: See also: se
Page 525 and 526:
S See also: initialization, etc.).
Page 527 and 528:
S See also: User Programming Relate
Page 529 and 530:
S See also: Pulsed Field Gradient M
Page 531 and 532:
S Arguments: Examples: Syntax 5 eje
Page 533 and 534:
S Step Value Parameter setting Argu
Page 535 and 536:
S sw rof2 Spectral width in directl
Page 537 and 538:
S sw tpwr Spectral width in directl
Page 539 and 540:
S Arguments: Examples: See also: re
Page 541 and 542:
S See also: flushing mode. In the l
Page 543 and 544:
Page 545 and 546:
S Examples: See also: trev time rev
Page 547 and 548:
S See also: (e.g.: multiselective)
Page 549 and 550:
S See also: and radial shims x1, y1
Page 551 and 552:
Page 553 and 554:
S Arguments: See also: shift sets t
Page 555 and 556:
S testsn testct Test signal-to-nois
Page 557 and 558:
S spadd Syntax: Description: Argume
Page 559 and 560:
Page 561 and 562:
S See also: If the spinning speed i
Page 563 and 564:
S dsp initialize_iterate iterate ni
Page 565 and 566:
Page 567 and 568:
S sqdir sqname studyid Svfname Stud
Page 569 and 570:
S ss Steady-state transients (P) De
Page 571 and 572:
S ssfilter sslsfrq ssntaps wft Full
Page 573 and 574:
S shim wshim Submit an Autoshim exp
Page 575 and 576:
Page 577 and 578:
S See also: sub('new') sub('trace',
Page 579 and 580:
S Examples: See also: where numgray
Page 581 and 582:
S Percent sign (%) substitution spe
Page 583 and 584:
S Examples: See also: The svs comma
Page 585 and 586:
S See also: variable evolution time
Page 587 and 588:
T tpwrm Observe transmitter linear
Page 589 and 590:
T Arguments: Examples: See also: 2D
Page 591 and 592:
T Arguments: Examples: See also: 1
Page 593 and 594:
T Syntax: Values: status of the cur
Page 595 and 596:
T textis Syntax: Description: Argum
Page 597 and 598:
T nt sw1 sw2 Number of transients (
Page 599 and 600:
T tnroesy Description: See also: Se
Page 601 and 602:
T tpwr tpwrm Observe transmitter po
Page 603 and 604:
T Examples: See also: the 1 H, the
Page 605 and 606:
T tupwr Description: See also: Tran
Page 607 and 608:
U See also: NMR Spectroscopy User G
Page 609 and 610:
U See also: NMR Spectroscopy User G
Page 611 and 612:
U 608 Command and Parameter Referen
Page 613 and 614:
V vast1d Applicability: Description
Page 615 and 616:
V vf Description: Values: See also:
Page 617 and 618:
V Examples: See also: Changing sele
Page 619 and 620:
V See also: vnmr2sc('gcosy',2,3) nt
Page 621 and 622:
V Examples: See also: file is the n
Page 623 and 624:
V See also: NMR Spectroscopy User G
Page 625 and 626:
V See also: NMR Spectroscopy User G
Page 627 and 628:
V See also: VnmrJ Installation and
Page 629 and 630:
W wp wp1 wp2 write writefid writepa
Page 631 and 632:
W Values: Width, in mm. See also: N
Page 633 and 634:
W wet Description: Flag to turn on
Page 635 and 636:
W Examples: See also: before each o
Page 637 and 638:
W Description: Arguments: See also:
Page 639 and 640:
W See also: NMR Spectroscopy User G
Page 641 and 642:
W wp2 Description: See also: Width
Page 643 and 644:
W writefid Syntax: Description: Arg
Page 645 and 646:
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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