# Jmol state version 12.0.26 2010-11-06 14:33; function _setWindowState() { # height 618; # width 779; stateVersion = 1200026; background [x000000]; axis1Color = "[xff0000]"; axis2Color = "[x008000]"; axis3Color = "[x0000ff]"; set ambientPercent 45; set diffusePercent 84; set specular true; set specularPercent 22; set specularPower 40; set specularExponent 6; set zShadePower 1; statusReporting = true; } function _setFileState() { set allowEmbeddedScripts false; set appendNew true; set appletProxy ""; set applySymmetryToBonds false; set autoBond true; set bondRadiusMilliAngstroms 150; set bondTolerance 0.45; set defaultLattice {0.0 0.0 0.0}; set defaultLoadFilter ""; set defaultLoadScript ""; set defaultVDW Auto; set forceAutoBond false; #set defaultDirectory "/Applications/jmol-12.0.26"; #set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb.gz"; #set smilesUrlFormat "http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True"; #set edsUrlFormat "http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap"; #set edsUrlCutoff "load('http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat').lines.find('MAP_SIGMA').split(' ')[2]"; set minBondDistance 0.4; set minimizationCriterion 0.0010; set minimizationSteps 100; set pdbGetHeader false; set pdbSequential false; set percentVdwAtom 23; set smallMoleculeMaxAtoms 40000; set smartAromatic true; load auto /*file*/"Benzoic_acid_DZV_VF_1.log.gz"; } function _setVariableState() { set defaultanglelabel "%VALUE %UNITS"; set defaultcolorscheme "jmol"; set defaultdistancelabel "%VALUE %UNITS"; set defaultdrawarrowscale 0.5; set defaultlattice "{0.0 0.0 0.0}"; set defaultloadfilter ""; set defaultloadscript ""; set defaulttorsionlabel "%VALUE %UNITS"; set defaulttranslucent 0.5; set defaultvdw "Auto"; set allowembeddedscripts true; set allowrotateselected false; set appletproxy ""; set applysymmetrytobonds false; set atompicking true; set atomtypes ""; set autobond true; set autofps false; set axes window; set axesmode 0; set axesscale 2.0; set bondmodeor false; set bondradiusmilliangstroms 150; set bondtolerance 0.45; set cartoonbaseedges false; set cartoonrockets false; set chaincasesensitive false; set dataseparator "~~~"; set defaultstructuredssp true; set delaymaximumms 0; set dipolescale 1.0; set disablepopupmenu false; set displaycellparameters true; set dotdensity 3; set dotscale 1; set dotsselectedonly false; set dotsurface true; set dragselected false; set drawhover false; set drawpicking false; set dsspcalculatehydrogenalways true; set dynamicmeasurements false; set ellipsoidarcs false; set ellipsoidaxes false; set ellipsoidaxisdiameter 0.02; set ellipsoidball true; set ellipsoiddotcount 200; set ellipsoiddots false; set ellipsoidfill false; set forceautobond false; set fractionalrelative false; set gestureswipefactor 1.0; set greyscalerendering false; set hbondsangleminimum 90.0; set hbondsbackbone false; set hbondsdistancemaximum 3.25; set hbondsrasmol true; set hbondssolid false; set helixstep 1; set helppath "http://chemapps.stolaf.edu/jmol/docs/index.htm"; set hermitelevel 0; set hidenameinpopup false; set hidenavigationpoint false; set highresolution false; set historylevel 0; set hoverdelay 0.5; set imagestate true; set iskiosk false; set isosurfacepropertysmoothing true; set justifymeasurements false; set loadatomdatatolerance 0.01; set logcommands false; set logfile ""; set loggestures false; set measureallmodels false; set measurementlabels true; set messagestylechime false; set minbonddistance 0.4; set minimizationcriterion 0.0010; set minimizationrefresh true; set minimizationsilent false; set minimizationsteps 100; set monitorenergy false; set multiplebondradiusfactor 0.0; set multiplebondspacing -1.0; set navigatesurface false; set navigationperiodic false; set navigationspeed 5.0; set pdbgetheader false; set pdbsequential false; set percentvdwatom 23; set pickingspinrate 10; set picklabel ""; set pointgroupdistancetolerance 0.2; set pointgrouplineartolerance 8.0; set propertyatomnumbercolumncount 0; set propertyatomnumberfield 0; set propertycolorscheme "roygb"; set propertydatacolumncount 0; set propertydatafield 0; set quaternionframe "p"; set rangeselected false; set ribbonaspectratio 16; set ribbonborder false; set rocketbarrels false; set saveproteinstructurestate true; set selectallmodels true; set selecthetero true; set selecthydrogen true; set sheetsmoothing 1.0; set showhiddenselectionhalos false; set showhydrogens true; set showkeystrokes true; set showmeasurements true; set showmultiplebonds true; set shownavigationpointalways false; set slabbyatom false; set slabbymolecule false; set smallmoleculemaxatoms 40000; set smartaromatic true; set solventprobe false; set solventproberadius 1.2; set ssbondsbackbone false; set stereodegrees -5.0; set strandcountformeshribbon 7; set strandcountforstrands 5; set strutdefaultradius 0.3; set strutlengthmaximum 7.0; set strutsmultiple false; set strutspacing 6; set testflag1 false; set testflag2 false; set testflag3 false; set testflag4 false; set tracealpha true; set usearcball false; set useminimizationthread true; set usenumberlocalization true; set vectorscale 1.0; set vibrationscale 0.5; set wireframerotation false; set zoomlarge true; # label defaults; select none; color label none; background label none; set labelOffset 4 4; set labelAlignment left; set labelPointer off; font label 13.0 SansSerif Plain; } function _setModelState() { select ({9:14 24:29 39:44 54:59 69:74 84:89 99:104 114:119 129:134 144:149 159:164 174:179 189:194 204:209 219:224 234:239 249:254 264:269 279:284 294:299 309:314 324:329 339:344 354:359 369:374 384:389 399:404 414:419 429:434 444:449 459:464 474:479 489:494 504:509 519:524 534:539 549:554 564:569 579:584 594:599 609:614 624:629 639:644 654:659 669:674}); Spacefill 0.2525; select ({0:6 15:21 30:36 45:51 60:66 75:81 90:96 105:111 120:126 135:141 150:156 165:171 180:186 195:201 210:216 225:231 240:246 255:261 270:276 285:291 300:306 315:321 330:336 345:351 360:366 375:381 390:396 405:411 420:426 435:441 450:456 465:471 480:486 495:501 510:516 525:531 540:546 555:561 570:576 585:591 600:606 615:621 630:636 645:651 660:666}); Spacefill 0.391; select ({7 8 22 23 37 38 52 53 67 68 82 83 97 98 112 113 127 128 142 143 157 158 172 173 187 188 202 203 217 218 232 233 247 248 262 263 277 278 292 293 307 308 322 323 337 338 352 353 367 368 382 383 397 398 412 413 427 428 442 443 457 458 472 473 487 488 502 503 517 518 532 533 547 548 562 563 577 578 592 593 607 608 622 623 637 638 652 653 667 668}); Spacefill 0.3495; select BONDS ({0:674}); wireframe 0.15; measures delete; select *; set measures nanometers; font measures 15.0 SansSerif Plain; select ({0:674}); Vectors 0.0015; boundBox off; font boundBox 14.0 SansSerif Plain; boundBox off; frank on; font frank 16.0 SansSerif Bold; select *; frame 1.1; moveto -1.0 {0 0 1 0} 100.0 0.36 0.0 {0.2273401 -0.003489852 -1.8500036E-4} 4.807031 {0.0 0.0 0.0} -2.0586045 -0.0456381 0.0; frame 1.41; moveto -1.0 { 1000 0 0 1.35} 100.0 0.36 0.0 {0.2273401 -0.003489852 -1.8500036E-4} 4.807031 {0.0 0.0 0.0} -2.0586085 -0.045568965 0.0; frame 1.42; moveto -1.0 { 1000 0 0 1.35} 100.0 0.36 0.0 {0.2273401 -0.003489852 -1.8500036E-4} 4.807031 {0.0 0.0 0.0} -2.0586085 -0.045568965 0.0; frame 1.43; moveto -1.0 {0 0 1 0} 100.0 0.36 0.0 {0.2273401 -0.003489852 -1.8500036E-4} 4.807031 {0.0 0.0 0.0} -2.0586045 -0.0456381 0.0; frame 1.44; moveto -1.0 {0 0 1 0} 100.0 0.36 0.0 {0.2273401 -0.003489852 -1.8500036E-4} 4.807031 {0.0 0.0 0.0} -2.0586045 -0.0456381 0.0; frame 1.45; moveto -1.0 {0 0 1 0} 100.0 0.36 0.0 {0.2273401 -0.003489852 -1.8500036E-4} 4.807031 {0.0 0.0 0.0} -2.0586045 -0.0456381 0.0; set fontScaling false; } function _setFrameState() { # frame state; # modelCount 45; # first 1.1; # last 1.45; frame RANGE 1.1 1.45; animation DIRECTION +1; animation FPS 10; animation MODE ONCE 0.0 0.0; frame 1.40; animation OFF; } function _setPerspectiveState() { set perspectiveModel 11; set scaleAngstromsPerInch 0.0; set perspectiveDepth true; set visualRange 5.0; set cameraDepth 3.0; boundbox corners {-3.2176094 -2.1634698 -8.6999906E-4} {3.6722898 2.1564898 4.9999834E-4} # volume = 0.04077672; center {0.2273401 -0.003489852 -1.8500036E-4}; moveto -1.0 {0 0 1 0} 100.0 0.36 0.0 {0.2273401 -0.003489852 -1.8500036E-4} 4.807031 {0.0 0.0 0.0} -2.0586045 -0.0456381 0.0; save orientation "default" moveto 0.0 { 1000 0 0 1.35} 100.0 0.36 0.0 {0.2273401 -0.003489852 -1.8500036E-4} 4.807031 {0.0 0.0 0.0} -2.0586085 -0.045568965 0.0;; slab 100;depth 0; set spinX 0; set spinY 30; set spinZ 0; set spinFps 30; set navX 0; set navY 0; set navZ 0; set navFps 10; set vibrationPeriod 0.5; } function _setSelectionState() { select ({0:674}); set hideNotSelected false; } function _setState() { initialize; set refreshing false; _setWindowState; _setFileState; _setVariableState; _setModelState; _setFrameState; _setPerspectiveState; _setSelectionState; set refreshing true; set antialiasDisplay false; set antialiasTranslucent true; set antialiasImages true; } _setState;