File:Protein L1TD1 PDB 3soo.png

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

1. Jmol state version 12.0.41 2011-02-04 14:47;

 # fullName = "jmolApplet0__720407745873318__";
 # documentBase = "http://www.pdb.org/pdb/explore/jmol.do?structureId=3SOO&opt=3";
 # codeBase = "http://www.pdb.org/pdb/Viewers/jmol-12.0.41/";

function _setWindowState() {

1. height 818;
2. width 1259;

 stateVersion = 1200041;
 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 "";
 #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 /*file*/"http://www2.rcsb.org/pdb/files/3SOO.pdb.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 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 1.0;
 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() {

 select ({0:18 27:162 172:313 323:363 373:396 402:436 446:519 529:559 569:580 598:622 632:666 672:690 699:834 840:981 987:1027 1033:1056 1062:1096 1106:1179 1189:1219 1229:1240 1254:1278 1284:1318 1324:1338 1347:1475 1485:1626 1636:1676 1686:1709 1719:1753 1763:1836 1842:1872 1882:1893 1907:1931 1937:1971 1977:2016});
 color atoms opaque structure;
 select ({19:26 163:171 314:322 364:372 397:401 437:445 520:528 560:568 581:597 623:631 667:671 691:698 835:839 982:986 1028:1032 1057:1061 1097:1105 1180:1188 1220:1228 1241:1253 1279:1283 1319:1323 1339:1346 1476:1484 1627:1635 1677:1685 1710:1718 1754:1762 1837:1841 1873:1881 1894:1906 1932:1936 1972:1976 2017});
 Spacefill 0.5;
 select ({0:18 27:162 172:313 323:363 373:396 402:436 446:519 529:559 569:580 598:622 632:666 672:690 699:834 840:981 987:1027 1033:1056 1062:1096 1106:1179 1189:1219 1229:1240 1254:1278 1284:1318 1324:1338 1347:1475 1485:1626 1636:1676 1686:1709 1719:1753 1763:1836 1842:1872 1882:1893 1907:1931 1937:1971 1977:2016});
 Spacefill 0.0;
 select BONDS ({1:4 6:8 10:17 20:27 30:37 40:43 46:53 56:63 66:73 76:91 94:101 104:107 109:112 114:116 118:121 124:127 130:133 136:139 142:149 152:159 162:169 172:183 186:189 192:195 197:200 202:204 206:213 216:223 226:233 236:243 246:253 256:259 262:269 272:283 286:289 292:295});
 wireframe 0.16;
 select BONDS ({0 5 9 18 19 28 29 38 39 44 45 54 55 64 65 74 75 92 93 102 103 108 113 117 122 123 128 129 134 135 140 141 150 151 160 161 170 171 184 185 190 191 196 201 205 214 215 224 225 234 235 244 245 254 255 260 261 270 271 284 285 290 291 296:2035});
 wireframe 0.0;

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

 select ({0:1976});
 Cartoon on;
 color Cartoon opaque structure;

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

 unitcell off;
 font unitcell 14.0 SansSerif Plain;
 unitcell off;

 hover "%U";

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

}

function _setPerspectiveState() {

 set perspectiveModel 11;
 set scaleAngstromsPerInch 0.0;
 set perspectiveDepth true;
 set visualRange 5.0;
 set cameraDepth 3.0;
 boundbox corners {-57.578003 2.836998 -3.5429993} {2.7729988 64.644 56.898} # volume = 225451.83;
 center {-27.4025 33.740498 26.6775};
 moveto -1.0 {0 0 1 0} 100.0 0.0 0.0 {-27.4025 33.740498 26.6775} 43.332287 {0.0 0.0 0.0} 28.957264 35.654873 0.0;
 save orientation "default";
 moveto 0.0 { 827 537 167 16.57} 80.44 0.0 0.0 {-27.4025 33.740498 26.6775} 43.332287 {0.0 0.0 0.0} 20.055058 32.099434 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 ({0:2017});
 set hideNotSelected false;

}

function _setState() {

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

}

_setState;

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