Re: [Jmol-users] State and Inline Load

Otis Rothenberger Mon, 27 Sep 2010 09:57:34 -0700

  Bob,

I may have complicated the issue with the example of duplicating a 
model. The problem seems to exist in any single model (no append) using 
load from string. Appended to this email is the state code for a model 
of acetic acid loaded with a string using data returned from NIH 
Resolver. I can save the state, but attempts to restore state lead to 
"cannot find string data."


Otis

# Jmol state version 12.1.14_dev  2010-09-17 15:12;
   # fullName = "jmolApplet0__699979344321214__";
   # documentBase = 
"http://localhost:8080/web_molecules/script_page_large.aspx";;
   # codeBase = "http://localhost:8080/code/jmol/";;


function _setWindowState() {
# height 460;
# width 450;
   stateVersion = 1201014;
   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 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 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;
   {
var mod1 = "C2H4O2\nAPtclcactv09271012363D 0   0.00000     0.00000\n \n  
8  7  0  0  0  0  0  0  0  0999 V2000\n    1.4183    0.4213   -0.0000 
C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.2518   -1.2408   -0.0000 
O   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.0161    0.8327   -0.0000 
O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0108   -0.0568   -0.0000 
C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.9331    0.5259    0.0000 
H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.7629    0.5365    1.0277 
H   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0452   -0.3075   -0.5138 
H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4806    1.3805   -0.5138 
H   0  0  0  0  0  0  0  0  0  0  0  0\n  3  4  1  0  0  0  0\n  2  4  
2  0  0  0  0\n  1  4  1  0  0  0  0\n  3  5  1  0  0  0  0\n  1  6  1  
0  0  0  0\n  1  7  1  0  0  0  0\n  1  8  1  0  0  0  0\nM  END\n$$$$\n\n";
   load
}
  "@mod1";

}

function _setVariableState() {

    set defaultanglelabel "%VALUE %UNITS";
    set defaultcolorscheme "Jmol";
    set defaultdistancelabel "%VALUE %UNITS";
    set defaultdrawarrowscale 0.5;
    set defaultlattice "{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 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 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 isosurfacepropertysmoothingpower 7;
   set justifymeasurements false;
   set loadatomdatatolerance 0.01;
   set logcommands false;
   set logfile "";
   set loggestures false;
   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;
   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 zdepth 0;
   set zoomlarge true;
   set zslab 0;

#user-defined variables;
   mod1 = "C2H4O2\nAPtclcactv09271012363D 0   0.00000     0.00000\n \n  
8  7  0  0  0  0  0  0  0  0999 V2000\n    1.4183    0.4213   -0.0000 
C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.2518   -1.2408   -0.0000 
O   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.0161    0.8327   -0.0000 
O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0108   -0.0568   -0.0000 
C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.9331    0.5259    0.0000 
H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.7629    0.5365    1.0277 
H   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0452   -0.3075   -0.5138 
H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4806    1.3805   -0.5138 
H   0  0  0  0  0  0  0  0  0  0  0  0\n  3  4  1  0  0  0  0\n  2  4  
2  0  0  0  0\n  1  4  1  0  0  0  0\n  3  5  1  0  0  0  0\n  1  6  1  
0  0  0  0\n  1  7  1  0  0  0  0\n  1  8  1  0  0  0  0\nM  END\n$$$$\n\n";

# 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 3});
   Spacefill 0.391;
   select ({1 2});
   Spacefill 0.3495;
   select ({4:7});
   Spacefill 0.253;
   select BONDS ({0:6});
   wireframe 0.15;

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

   set echo off;

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

   hover "";

   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 ({0:7});
   center {0.056050003 0.06984997 0.25694996};
   moveto -1.0 {0 0 1 0} 100.0 0.0 0.0 {0.056050003 0.06984997 
0.25694996} 3.380128 {0.0 0.0 0.0} 0.0 0.0 0.0;
   save orientation "default"
   moveto 0.0 {0 0 1 0} 100.0 0.0 0.0 {0.056050003 0.06984997 
0.25694996} 3.380128 {0.0 0.0 0.0} -0.8347846 1.0177015 0.0;;
   slab 100;depth 0;
   set slabRange 0.0;
   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 ({0:7});
   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;


Otis Rothenberger
chemagic.com






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Re: [Jmol-users] State and Inline Load

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