Right. I fixed that, too, I think. No?
This:
{
var mod1 = "C2H4O2 ...";
load
}
"@mod1";
should be this:
{
var mod1 = "C2H4O2\nAPtclcactv09271012363D 0 ...."
load "@mod1";
}
Try the latest* *I uploaded.
Bob
On Mon, Sep 27, 2010 at 11:56 AM, Otis Rothenberger
<[email protected]>wrote:
> 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(<http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat%27%29.lines.find%28%27MAP_SIGMA%27%29.split%28>
> '
> ')[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
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
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