exit; # BEGINOFOPTIONS # Options for the scene # caption: Overview of the 1HEW secondary structure: Alpha Helices, 3-10 helix, Beta Strands, with loops in white and disulfide bonds in yellow. Arrow tips point towards the C-terminal end. # spinState: on # doModelReload: false # savePSpeed: -1 # killMove: 1 # killZoom: 0 # animationDirection: 0 # animationMode: PALINDROME # loopPause: 1 # ENDOFOPTIONS # Jmol state version 14.29.16 2018-06-03 23:13; # fullName = "jmolApplet0__853515731279615__"; # documentBase = "http://proteopedia.org/wiki/index.php?title=Hen_Egg-White_(HEW)_Lysozyme&action=edit"; # codeBase = "http:/wiki/extensions/jsmol/j2s/"; function _setWindowState() { # width 350; # height 350; stateVersion = 1429016; 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 celShading false; set celShadingPower 10; set zShadePower 3; } 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 "https://files.rcsb.org/download/%FILE.pdb"; # set loadLigandFormat "https://files.rcsb.org/ligands/download/%FILE.cif"; # set smilesUrlFormat "https://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=true"; # set nihResolverFormat "https://cactus.nci.nih.gov/chemical/structure/%FILE"; # set pubChemFormat "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d"; set bondingVersion 1; set legacyAutoBonding false; set legacyAutoBonding false; set legacyHAddition false; set legacyJavaFloat true; set minBondDistance 0.4; set minimizationCriterion 0.001; set minimizationSteps 100; set multipleBondBananas false; set pdbAddHydrogens false; set pdbGetHeader false; set pdbSequential false; set percentVdwAtom 20; set smallMoleculeMaxAtoms 40000; set smartAromatic true; reloadfile = false; if (loadedfileprev != "2f267243b1cf263a27c03cd5ce051b66"); load /*file*/"/cgi-bin/getfrozenstructure?2f267243b1cf263a27c03cd5ce051b66"; loadedfileprev = "2f267243b1cf263a27c03cd5ce051b66"; 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 atomtypes ""; set autobond true; set autofps false; set axes window; set axesmode 0; set axesoffset 0.0; set axesscale 2.0; set bondmodeor false; set bondradiusmilliangstroms 150; set bondtolerance 0.45; set cartoonbaseedges false; set cartoonblockheight 0.5; set cartoonblocks false; set cartoonfancy false; set cartoonladders false; set cartoonrockets false; set cartoonsfancy false; set cartoonsteps 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 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 hbondsbackbone false; set hbondsrasmol true; set hbondssolid false; set helixstep 1; set helppath "http://chemapps.stolaf.edu/jmol/docs/index.htm"; set hermitelevel 0; set hiddenlinesdashed false; set hidenameinpopup false; set hidenavigationpoint false; set highresolution false; set hoverdelay 0.5; set infofontsize 20; set isosurfacekey false; set isosurfacepropertysmoothing true; set isosurfacepropertysmoothingpower 7; set jmolinjspecview true; 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 multiplebondbananas false; set multiplebondradiusfactor 0.0; set multiplebondspacing -1.0; set navigationperiodic false; set navigationspeed 5.0; set nbocharges true; set nmrpredictformat "http://www.nmrdb.org/service/predictor?POST?molfile="; set nmrurlformat "http://www.nmrdb.org/new_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 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 selecthetero true; set selecthydrogen true; set sheetsmoothing 1.0; set showhiddenselectionhalos false; set showhydrogens true; set showmeasurements true; set showmodulationvectors false; set showmultiplebonds true; set shownavigationpointalways false; set showunitcelldetails 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 tracealpha true; set translucent true; set twistedsheets false; set usenumberlocalization true; set vectorscale 1.0; set vectorscentered false; set vectorsymmetry false; set vectortrail 0; 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; @~anomalous_atoms ({}); @~backbone_invisible ({}); @~hydroxy_unchained_nucs ({}); @~nobackbone_aas ({}); @~nophosphorus_nucs ({}); @~protein ({0:1000}); @~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 off; halos off; color cpk; hbonds off; select ({0:1000}); color atoms opaque structure; select ({0:1146}); Spacefill 0; select BONDS ({0:3}); color bonds opaque [xffff30]; select BONDS ({4:1069}); wireframe 0; select BONDS ({0:3}); wireframe 0.25; measures delete; select *; set measures angstroms; font measures 15 SansSerif Plain; Backbone ({0:1000}); Backbone 0.0; select ({326:345}); color Backbone opaque [x00ffa0]; select ({429:461}); color Backbone opaque [x00ff20]; select ({31:64}); color Backbone opaque [x0020ff]; select ({146:172}); color Backbone opaque [x00a0ff]; select ({883:908}); color Backbone opaque [xff6000]; select ({762:787}); color Backbone opaque [xffe000]; select ({636:662}); color Backbone opaque [xc0ff00]; select ({291:325}); color Backbone opaque [x00ffc0]; select ({405:428}); color Backbone opaque [x00ff40]; select ({238:256}); color Backbone opaque [x00ffff]; select ({529:557}); color Backbone opaque [x40ff00]; select ({257:290}); color Backbone opaque [x00ffe0]; select ({380:404}); color Backbone opaque [x00ff60]; select ({507:528}); color Backbone opaque [x20ff00]; select ({65:79}); color Backbone opaque [x0040ff]; select ({173:202}); color Backbone opaque [x00c0ff]; select ({346:379}); color Backbone opaque [x00ff80]; select ({839:882}); color Backbone opaque [xff8000]; select ({685:709}); color Backbone opaque [xf0f000]; select ({971:1000}); color Backbone opaque [xff0000]; select ({663:684}); color Backbone opaque [xe0ff00]; select ({203:237}); color Backbone opaque [x00e0ff]; select ({80:117}); color Backbone opaque [x0060ff]; select ({558:586}); color Backbone opaque [x60ff00]; select ({933:970}); color Backbone opaque [xff2000]; select ({813:838}); color Backbone opaque [xffa000]; select ({738:761}); color Backbone opaque [xfff000]; select ({118:145}); color Backbone opaque [x0080ff]; select ({609:635}); color Backbone opaque [xa0ff00]; select ({710:737}); color Backbone opaque [xffff00]; select ({0:30}); color Backbone opaque [x0000ff]; select ({909:932}); color Backbone opaque [xff4000]; select ({788:812}); color Backbone opaque [xffc000]; select ({587:608}); color Backbone opaque [x80ff00]; select ({462:506}); color Backbone opaque [x00ff00]; select ({0:1000}); Cartoon on; set echo off; hover "%n %r, Chain=%c, Element=%e"; frank on; font frank 16 SansSerif Bold; 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 {-18.918 0.7589989000000017 0.32400129999999905} {22.033 39.8 40.871998} # volume = 64826.84104966273; if (reloadfile) { center {-0.33203837 20.866533 19.55904}; } # removed moveto -1.0 {0 0 1 0} 100.0 0.0 0.0 {1.557500000000001 20.2795 20.598} 30.896765908230314 {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 ({1001:1043}); set hideNotSelected false; } function _setState() { # # initialize; # update caption ppdiaCaptionCmd = "changeCaption('Overview of the 1HEW secondary structure: Alpha Helices, 3-10 helix, Beta Strands, with loops in white and disulfide bonds in yellow. Arrow tips point towards the C-terminal end.');"; javascript @ppdiaCaptionCmd; 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; SelectionHalos OFF; delay 1.0; moveto 1.0 { -430 -10 903 146.05} 100.0 0.0 0.0 {-0.33203837 20.866533 19.55904} 31.371292 {0 0 0} 0 0 0 3.0 0.0 0.0;; moveto 1.0 { -430 -10 903 146.05} 150.0 0.0 0.0 {-0.33203837 20.866533 19.55904} 31.371292 {0 0 0} 0 0 0 3.0 0.0 0.0;; set refreshing true; if (antialiasDisplayFlag) { antialiasDisplay = true } else { antialiasDisplay = false }; set antialiasTranslucent true; set antialiasImages true; spin on; } _setState;