/****** Jmol Embedded Script ****

1. Jmol state version 12.0.40 2011-02-04 14:47;

function _setWindowState() {

1. height 491;
2. width 954;

 stateVersion = 1200040;
 background [xffffff];
 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 "C:/Windows/system32";
 #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 legacyAutoBonding false;
 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*/"./2J5H.pdb.gz";

}

function _setVariableState() {

  set defaultanglelabel "%VALUE %UNITS";
  set defaultcolorscheme "Jmol";
  set defaultdistancelabel "%VALUE %UNITS";
  set defaultdrawarrowscale 0.5;
  set defaultlattice "{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 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;
 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;

1. 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() {

 structure none ({0:523})    	# model=1.1;
 structure turn ({126:142})    	# model=1.1 & (10 - 11);
 structure turn ({478:498})    	# model=1.1 & (36 - 37);
 structure none ({524:1047})    	# model=1.2;
 structure turn ({667:711})    	# model=1.2 & (12 - 14);
 structure turn ({848:868})    	# model=1.2 & (24 - 25);
 structure none ({1048:1571})    	# model=1.3;
 structure turn ({1209:1235})    	# model=1.3 & (13 - 14);
 structure turn ({1372:1392})    	# model=1.3 & (24 - 25);
 structure turn ({1472:1496})    	# model=1.3 & (32 - 33);
 structure turn ({1526:1546})    	# model=1.3 & (36 - 37);
 structure none ({1572:2095})    	# model=1.4;
 structure turn ({1600:1628})    	# model=1.4 & (2 - 3);
 structure turn ({1715:1759})    	# model=1.4 & (12 - 14);
 structure none ({2096:2619})    	# model=1.5;
 structure turn ({2257:2283})    	# model=1.5 & (13 - 14);
 structure turn ({2588:2604})    	# model=1.5 & (37 - 38);
 structure none ({2620:3143})    	# model=1.6;
 structure turn ({2781:2807})    	# model=1.6 & (13 - 14);
 structure none ({3144:3667})    	# model=1.7;
 structure turn ({3287:3353})    	# model=1.7 & (12 - 15);
 structure turn ({3468:3488})    	# model=1.7 & (24 - 25);
 structure turn ({3636:3652})    	# model=1.7 & (37 - 38);
 structure none ({3668:4191})    	# model=1.8;
 structure turn ({3811:3855})    	# model=1.8 & (12 - 14);
 structure turn ({3992:4012})    	# model=1.8 & (24 - 25);
 structure none ({4192:4715})    	# model=1.9;
 structure turn ({4657:4690})    	# model=1.9 & (35 - 37);
 structure none ({4716:5239})    	# model=1.10;
 structure turn ({4877:4903})    	# model=1.10 & (13 - 14);

 select ({6:520 530:1044 1054:1568 1578:2092 2102:2616 2626:3140 3150:3664 3674:4188 4198:4712 4722:5236});
 color atoms opaque structure;
 Spacefill 0.0;
 select BONDS ({2 6:9 12 16:19 22 26:29 32 36:39 42 46:49 52 56:59 62 66:69 72 76:79 82 86:89 92 96:625 628:1153 1156:1681 1684:2209 2212:2737 2740:3265 3268:3793 3796:4321 4324:4849 4852:5377});
 wireframe 0.0;

 measures delete;
 select *; set measures nanometers;
 font measures 15.0 SansSerif Plain;

 select ({6:520 530:1044 1054:1568 1578:2092 2102:2616 2626:3140 3150:3664 3674:4188 4198:4712 4722:5236});
 Cartoon on;

 boundBox off;
 font boundBox 14.0 SansSerif Plain;
 boundBox off;

 hover "%U";

 frank on;
 font frank 16.0 SansSerif Bold;
 select *;

}

function _setFrameState() {

1. frame state;
2. modelCount 10;
3. first 1.1;
4. last 1.10;

 frame RANGE 1.1 1.10;
 animation DIRECTION  1;
 animation FPS 10;
 animation MODE ONCE 0.0 0.0;
 frame 1.1;
 animation OFF;

}

function _setPerspectiveState() {

 set perspectiveModel 11;
 set scaleAngstromsPerInch 0.0;
 set perspectiveDepth true;
 set visualRange 5.0;
 set cameraDepth 3.0;
 boundbox corners {-14.823999 -17.135 -17.839} {18.031 22.205 11.193001} # volume = 37524.32;
 center {1.6034999 2.5349998 -3.323};
 moveto -1.0 {0 0 1 0} 100.0 0.0 0.1 {1.6034999 2.5349998 -3.323} 24.430798 {0.0 0.0 0.0} 0.0 0.0 0.0;
 save orientation "default";
 moveto 0.0 { 904 180 -389 58.93} 100.0 0.0 0.0 {1.6034999 2.5349998 -3.323} 24.430798 {0.0 0.0 0.0} -5.2485275 14.446587 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;

}

function _setSelectionState() {

 select ({0:5 521:523});
 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;

• • /