File:PDB GAD67.jpg

1. Jmol state version 11.8.4 2009-08-11 23:55;

 # fullName = "jmolApplet0__121253383540451__";
 # documentBase = "http://www.pdb.org/pdb/explore/jmol.do?structureId=2OKJ&bionumber=1%22;
 # codeBase = "http://www.pdb.org/pdb/Viewers/jmol-11.8.4/%22;

function _setWindowState() {

1. height 550;
2. width 550;

 stateVersion = 1108004;
 backgroundColor = "[xffffff]";
 axis1Color = "[xff0000]";
 axis2Color = "[x008000]";
 axis3Color = "[x0000ff]";
 ambientPercent = 45;
 diffusePercent = 84;
 specular = true;
 specularPercent = 22;
 specularPower = 40;
 specularExponent = 6;
 statusReporting  = true;

}

function _setFileState() {

 set allowEmbeddedScripts false;
 set autoBond true;
 set appendNew true;
 set appletProxy "";
 set applySymmetryToBonds false;
 set bondRadiusMilliAngstroms 150;
 set bondTolerance 0.45;
 set defaultLattice {0.0 0.0 0.0};
 set defaultLoadScript "";
 set defaultVDW Jmol;
 set forceAutoBond false;
 set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb%22;
 set minBondDistance 0.4;
 set pdbSequential false;
 set pdbGetHeader false;
 set percentVdwAtom 20;
 set smartAromatic true;
 load /*file*/"http://www.rcsb.org/pdb/files/2OKJ.pdb1.gz%22;

}

function _setVariableState() {

  set defaultanglelabel "%VALUE %UNITS";
  set defaultcolorscheme "Jmol";
  set defaultdistancelabel "%VALUE %UNITS";
  set defaultdrawarrowscale 0.5;
  set defaultlattice "{0 0 0}";
  set defaultloadscript "";
  set defaulttorsionlabel "%VALUE %UNITS";
  set defaulttranslucent 0.5;
  set defaultvdw "Jmol";
 set allowembeddedscripts true;
 set allowkeystrokes false;
 set allowrotateselected false;
 set appletproxy "";
 set applysymmetrytobonds false;
 set atompicking true;
 set atomtypes "";
 set autobond true;
 set autofps false;
 set autoloadorientation false;
 set axes window;
 set axesmode 0;
 set axesscale 2.0;
 set bondmodeor false;
 set bondpicking false;
 set bondradiusmilliangstroms 150;
 set bondtolerance 0.45;
 set cartoonrockets false;
 set chaincasesensitive false;
 set dataseparator "~~~";
 set delaymaximumms 0;
 set dipolescale 1.0;
 set disablepopupmenu false;
 set displaycellparameters true;
 set dotdensity 3;
 set dotsselectedonly false;
 set dotsurface true;
 set dragselected false;
 set drawhover false;
 set drawpicking false;
 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 fontcaching true;
 set forceautobond false;
 set greyscalerendering false;
 set hbondsangleminimum 90.0;
 set hbondsbackbone false;
 set hbondsdistancemaximum 3.25;
 set hbondssolid false;
 set helixstep 1;
 set helppath "http://chemapps.stolaf.edu/jmol/docs/index.htm%22;
 set hermitelevel 0;
 set hidenameinpopup false;
 set hidenavigationpoint false;
 set highresolution false;
 set historylevel 0;
 set hoverdelay 0.5;
 set imagestate true;
 set isosurfacepropertysmoothing true;
 set justifymeasurements false;
 set loadatomdatatolerance 0.01;
 set loadformat "http://www.rcsb.org/pdb/files/%FILE.pdb%22;
 set measureallmodels false;
 set measurementlabels true;
 set messagestylechime false;
 set minbonddistance 0.4;
 set navigatesurface false;
 set navigationperiodic false;
 set navigationspeed 5.0;
 set pdbgetheader false;
 set pdbsequential false;
 set percentvdwatom 20;
 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 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 smartaromatic true;
 set solventprobe false;
 set solventproberadius 1.2;
 set ssbondsbackbone false;
 set stereodegrees -5;
 set strandcountformeshribbon 7;
 set strandcountforstrands 5;
 set testflag1 false;
 set testflag2 false;
 set testflag3 false;
 set testflag4 false;
 set tracealpha true;
 set useminimizationthread true;
 set usenumberlocalization true;
 set vectorscale 1.0;
 set vibrationperiod 1.0;
 set vibrationscale 1.0;
 set wireframerotation false;
 set zoomlarge true;
 set zshade false;

1. user-defined variables;

 @site_1 ({2675:2682 4717:4747 7689:7699 7933:7954});
 @site_ac1 ({779:801 3737:3747 6615:6626});
 @site_ac2 ({2675:2682 4717:4747 7689:7699 7933:7954});
 @site_ac3 ({953:963 2839:2848 4725:4747 5196:5208 5502:5511 5921:5924 5932:5938 6139:6146 6152:6156 6368:6375 6383:6416 7926:7932 8160 8165});
 site_ac1 = ["[GLN]190:A", "[LEU]191:A", "[SER]192:A", "[ARG]567:A", "[TYR]434:B"];
 site_ac2 = ["[LEU]435:A", "[ASN]189:B", "[GLN]190:B", "[LEU]191:B", "[SER]192:B", "[ARG]567:B", "[PLZ]2001:B"];
 site_ac3 = ["[PHE]214:A", "[CYS]455:A", "[GLY]456:A", "[GLN]190:B", "[LEU]191:B", "[SER]192:B", "[GLY]251:B", "[GLY]252:B", "[ALA]253:B", "[HIS]291:B", "[GLY]346:B", "[THR]348:B", "[ASP]373:B", "[ALA]375:B", "[ASN]402:B", "[HIS]404:B", "[LLP]405:B", "[ABU]1002:B", "[HOH]2030:B", "[HOH]2035:B"];
 site_list = ["site_AC1", "site_AC3", "site_AC2"];

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() {

 select ({2444:2467 6393:6416 7919:7954});
 Spacefill 0.5;
 select ({0:2443 2468:6392 6417:7918 7955:8313});
 Spacefill 0.0;
 select BONDS ({0:35 1573:1596 5616:5624 5626:5640});
 wireframe 0.16;
 select BONDS ({36:1572 1597:5615 5625 5641:8143});
 wireframe 0.0;

 measures delete;
 select *; set measures nanometers;
 font measures 15.0 SansSerif Plain;
 select measures ({null});

 select ({0:7918});
 Cartoon on;
 color Cartoon opaque chain;

 boundBox off;

 hover "%U";

 frank on;
 font frank 16.0 SansSerif Bold;
 set fontScaling false;

}

function _setPerspectiveState() {

 set perspectiveModel 11;
 set scaleAngstromsPerInch 0.0;
 set perspectiveDepth true;
 set visualRange 5.0;
 set cameraDepth 3.0;
 boundbox corners {-71.367004 -31.439999 -56.352997} {27.567001 38.684002 12.543999} # volume = 477983.12;
 center {-21.900002 3.6220007 -21.9045};
 moveto 0.0 { -55 -87 995 149.21} 115.0 0.0 0.0 {-21.900002 3.6220007 -21.9045} 55.248177 {0.0 0.0 0.0} -22.243408 -12.745966 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 ({0:8313});
 set hideNotSelected false;

}

function _setState() {

 initialize;
 set refreshing false;
 _setWindowState;
 _setFileState;
 _setVariableState;
 _setModelState;
 _setPerspectiveState;
 _setSelectionState;
 set refreshing true;
 set antialiasDisplay false;
 set antialiasTranslucent true;
 set antialiasImages true;

}

_setState;

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