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;