exit; # Jmol state version 14.0.17_2014.06.09 2014-06-09 22:55; # fullName = "jmolApplet0__201656100273533__"; # documentBase = "http://proteopedia.org/wiki/index.php?title=Green_Fluorescent_Protein&action=edit"; # codeBase = "http:/wiki/extensions/jsmol/j2s/"; function _setWindowState() { # width 350; # height 350; stateVersion = 1400017; background [x000000]; axis1Color = "[xff0000]"; axis2Color = "[x008000]"; axis3Color = "[x0000ff]"; set ambientPercent 45; set diffusePercent 84; set specular true; set specularPercent 22; set specularPower 40; set celShading false; set celShadingPower 10; set specularExponent 6; set zShadePower 3; 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}; set defaultLoadFilter ""; set defaultLoadScript ""; set defaultStructureDssp true; set defaultVDW Jmol; set forceAutoBond false; # set defaultDirectory ""; # set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb"; # set loadLigandFormat "http://www.rcsb.org/pdb/files/ligand/%FILE.cif"; # set smilesUrlFormat "http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True"; # set nihResolverFormat "http://cactus.nci.nih.gov/chemical/structure/%FILE"; # set pubChemFormat "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d"; # set edsUrlFormat "http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap"; # set edsUrlCutoff "http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat"; set bondingVersion 0; set legacyAutoBonding false; set legacyHAddition false; set minBondDistance 0.4; set minimizationCriterion 0.001; set minimizationSteps 100; set pdbAddHydrogens false; set pdbGetHeader false; set pdbSequential false; set percentVdwAtom 20; set smallMoleculeMaxAtoms 40000; set smartAromatic true; reloadfile = false; if (loadedfileprev != "c633a54d03b8b50318876fc5555cdc4c"); load /*file*/"/cgi-bin/getfrozenstructure?c633a54d03b8b50318876fc5555cdc4c"; loadedfileprev = "c633a54d03b8b50318876fc5555cdc4c"; reloadfile = true; endif; } function _setParameterState() { set defaultanglelabel "%VALUE %UNITS"; set defaultcolorscheme "jmol"; set defaultdistancelabel "%VALUE %UNITS"; set defaultdrawarrowscale 0.5; set defaultlabelpdb "%m%r"; set defaultlabelxyz "%a"; set defaultlattice "{0 0 0}"; set defaultloadfilter ""; set defaultloadscript ""; set defaulttorsionlabel "%VALUE %UNITS"; set defaulttranslucent 0.5; set defaultvdw "Jmol"; set allowembeddedscripts true; set allowmoveatoms false; set allowrotateselected false; set animationmode "ONCE"; 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 backbonesteps false; set bondmodeor false; set bondradiusmilliangstroms 150; set bondtolerance 0.45; set cartoonbaseedges false; set cartoonfancy false; set cartoonladders 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 drawfontsize 14.0; set drawhover false; set drawpicking false; set dsspcalculatehydrogenalways true; set ellipsoidarcs false; set ellipsoidarrows false; set ellipsoidaxes false; set ellipsoidaxisdiameter 0.02; set ellipsoidball true; set ellipsoiddotcount 200; set ellipsoiddots false; set ellipsoidfill false; set energyunits "kJ"; set forceautobond 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://www.stolaf.edu/academics/chemapps/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 isosurfacekey false; set isosurfacepropertysmoothing true; set isosurfacepropertysmoothingpower 7; set justifymeasurements false; set loadatomdatatolerance 0.01; set measureallmodels false; set measurementlabels true; set meshscale 1; set messagestylechime false; set minbonddistance 0.4; set minimizationcriterion 0.001; set minimizationrefresh true; set minimizationsilent false; set minimizationsteps 100; set minpixelselradius 6; set modulationscale 1.0; set monitorenergy false; set multiplebondradiusfactor 0.0; set multiplebondspacing -1.0; set navigationperiodic false; set navigationspeed 5.0; set nmrpredictformat "http://www.nmrdb.org/service/predictor?POST?molfile="; set nmrurlformat "http://www.nmrdb.org/predictor?POST?molfile="; set partialdots false; set particleradius 20.0; set pdbaddhydrogens false; 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 "c"; 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 showunitcelldetails true; set showunitcellinfo true; set slabbyatom false; set slabbymolecule false; set smallmoleculemaxatoms 40000; set smartaromatic true; set solventprobe false; set solventproberadius 1.2; set ssbondsbackbone true; set starwidth 0.05; 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 translucent true; set twistedsheets false; set useminimizationthread true; set usenumberlocalization true; set vectorscale 1.0; set vectorscentered false; set vectorsymmetry false; set vibrationscale 1.0; set waitformoveto true; set wireframerotation false; set zdepth 0; set zoomheight false; set zoomlarge true; set zslab 50; # user-defined atom sets; @chromophore ({465:486}); @~anomalous_atoms ({}); @~backbone_invisible ({}); @~hydroxy_unchained_nucs ({}); @~nobackbone_aas ({}); @~nophosphorus_nucs ({}); @~protein ({0:464 487:1770}); @~unbondable_aas ({}); @~unchained_aas ({}); @~unchained_nucs ({}); # label defaults; select none; color label none; background label none; set labelOffset 4 4; set labelAlignment left; set labelPointer off; font label 13 SansSerif Plain; } function _setModelState() { calculate hbonds; select all; wireframe off; spacefill off; dots off; backbone off; trace off; ribbon off; cartoon off; strands off; rocket off; meshribbon off; isosurface /*file*/"/scripts/10/100139/Green_fluorescent_protein/1.iso"; # isosurface off; halos off; color cpk; hbonds off; structure none ({0:1865}) # model=1.1; structure HELIX ({15:52}) # model=1.1 & (4 - 8); structure SHEET ({71:151}) # model=1.1 & (12 - 22); structure SHEET ({164:249}) # model=1.1 & (25 - 36); structure SHEET ({278:343}) # model=1.1 & (41 - 48); structure HELIX ({397:432}) # model=1.1 & (57 - 60); structure HELIX ({494:519}) # model=1.1 & (69 - 71); structure HELIX ({620:656}) # model=1.1 & (83 - 86); structure SHEET ({690:774}) # model=1.1 & (92 - 100); structure SHEET ({803:897}) # model=1.1 & (105 - 115); structure SHEET ({910:989}) # model=1.1 & (118 - 128); structure SHEET ({1143:1187}) # model=1.1 & (148 - 152); structure SHEET ({1230:1320}) # model=1.1 & (160 - 170); structure SHEET ({1356:1454}) # model=1.1 & (176 - 187); structure SHEET ({1532:1602}) # model=1.1 & (199 - 207); structure SHEET ({1699:1758}) # model=1.1 & (220 - 227); select ({0:464 487:1865}); color atoms opaque [x00ff00]; select ({0:1865}); Spacefill 0; select BONDS ({1:15 17:24 1336:1338 1346 1347 1349}); wireframe 0.36; select BONDS ({0 16 25:1335 1339:1345 1348 1350:1814}); wireframe 0; measures delete; select *; set measures nanometers; font measures 15 SansSerif Plain; select ({0:464 487:1770}); Cartoon on; color Cartoon translucent 0.5 [x00ff00]; # isosurface delete chromophoresurf select(chromophore) ignore(not chromophore) molecular translucent 200 [Xcbbe8a]; # isosurface ID "chromophoresurf" fill noMesh noDots notFrontOnly frontlit; color isosurface opaque [xffa500]; hover "%U"; frank on; font frank 16 SansSerif Plain; select *; set fontScaling false; } function _setPerspectiveState() { if (reloadfile) { set perspectiveModel 11; } set scaleAngstromsPerInch 0; set perspectiveDepth true; set visualRange 5; set cameraDepth 3; boundbox corners {6.008000000000003 5.7790000000000035 12.229999999999997} {45.09 55.552 62.725} # volume = 98224.30735106999; if (reloadfile) { center {25.549000000000003 30.6655 37.4775}; } # removed moveto -1.0 {0 0 1 0} 100.0 0.0 0.0 {25.549000000000003 30.6655 37.4775} 31.160713373915442 {0 0 0} 0 0 0 3.0 0.0 0.0; # removed save orientation "default"; slab 100;depth 0; set slabRange 0.0; set spinX = 0; set spinY = 5; set spinZ = 0; spinFps = 20; spin axisangle {0.0 1.0 0.0} 10.0; } function _setSelectionState() { select ({0:464 487:1770}); set hideNotSelected false; } function _setState() { # initialize; zoomto 1.0 100; delay 0.5; select all; labels off; measurements off; set refreshing false; _setWindowState; _setFileState; _setParameterState; _setModelState; _setPerspectiveState; _setSelectionState; set refreshing true; delay 1.0; moveto 1.0 { 952 304 17 121.29} 100.0 0.0 0.0 {25.549000000000003 30.6655 37.4775} 31.160713373915442 {0 0 0} 0 0 0 3.0 0.0 0.0;; moveto 1.0 { 952 304 17 121.29} 230.0 0.0 0.0 {25.549000000000003 30.6655 37.4775} 31.160713373915442 {0 0 0} 0 0 0 3.0 0.0 0.0;; if (antialiasDisplayFlag) { antialiasDisplay = true } else { antialiasDisplay = false } set antialiasTranslucent true; set antialiasImages true; spin on; } _setState;