Re: [Jmol-users] Renew State Issue

Otis Rothenberger Sun, 26 Sep 2010 21:42:21 -0700

Bob,

In my second note, I was only referring to the extracted file approach. With state saving, I still have the bond issue. I should mention that I'm using the following to "restore:"

jmolScript("script ../temp/" + "555556565656" + ".txt")

The basic idea is that two users "checks out" a modelkit identified by a unique 12 digit number. Changes to this model are recorded in a server text file, and the remote users see these changes via the shared number and the above script. The state file below (end of email) should be 2-butyne that started from an ethene molfile load. The model kit edit shows 2-butyne, but here is what the above script produces from the state file:

# Jmol state version 12.1.11_dev 2010-09-05 20:18;
# fullName = "jmolApplet0__721296650030216__";
# documentBase = "http://localhost:8080/web_molecules/script_page_large.aspx";
# codeBase = "" class="moz-txt-link-rfc2396E" href="http://localhost:8080/code/jmol/">"http://localhost:8080/code/jmol/";

function _setWindowState() {
# height 460;
# width 450;
stateVersion = 1201011;
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 false;
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;
load /*file*/"http://localhost:8080/models/ethene.txt";
set allowEmbeddedScripts false;
set appendNew false;
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;
load data "append inline"
3
Viewer.AddHydrogens#noautobond
H 1.1692474 -1.803469 -1.0238824 - - - - 7
H 1.1692474 -1.9308412 0.7678584 - - - - 8
H 2.5095618 -1.0795374 -0.07202141 - - - - 9
end "append inline" ;
set allowEmbeddedScripts false;
set appendNew false;
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 35;
set pdbGetHeader false;
set pdbSequential false;
set percentVdwAtom 23;
set smallMoleculeMaxAtoms 40000;
set smartAromatic true;
load data "append inline"
3
Viewer.AddHydrogens#noautobond
H -1.152512 1.9360499 -0.769462 - - - - 10
H -1.1511153 1.8175426 1.0228863 - - - - 11
H -2.5008903 1.1038758 0.0766591 - - - - 12
end "append inline" ;

}

function _setVariableState() {

   set defaultanglelabel "%VALUE %UNITS";
   set defaultcolorscheme "jmol";
   set defaultdistancelabel "%VALUE %UNITS";
   set defaultdrawarrowscale 0.5;
   set defaultlattice "{0.0 0.0 0.0}";
   set defaultloadfilter "";
   set defaultloadscript "";
   set defaulttorsionlabel "%VALUE %UNITS";
   set defaulttranslucent 0.5;
   set defaultvdw "Auto";
set allowembeddedscripts false;
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 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 false;
set minimizationsilent false;
set minimizationsteps 35;
set monitorenergy false;
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 -5.0;
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 usearcball false;
set useminimizationthread false;
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;
chrg = [-0.1062, -0.1062, 0.053099997, 0.053099997, 0.053099997, 0.053099997];
pickingmode = "ident";

# 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 _setDataState() {

DATA "atomName set"
2 ;
Jmol Property Data Format 1 -- Jmol 12.1.11_dev 2010-09-05 20:18;
4 C [SUBUNIT]1:A.C4_#4 C4 ;
6 C [SUBUNIT]1:A.C6_#6 C6 ;
end "atomName set";

DATA "coord set"
10 ;
Jmol Property Data Format 1 -- Jmol 12.1.11_dev 2010-09-05 20:18;
1 C [SUBUNIT]1:A.C1_#1 -0.54984075 0.24622107 0.018003711 ;
2 C [SUBUNIT]1:A.C2_#2 0.5521053 -0.2399553 -0.01460026 ;
4 C [SUBUNIT]1:A.C4_#4 -1.4881593 1.3583729 0.09207648 ;
6 C [SUBUNIT]1:A.C6_#6 1.4954495 -1.3478783 -0.08854454 ;
7 H H7_#7 1.3319885 -1.9035021 -1.0328846 ;
8 H H8_#8 1.3328092 -2.023396 0.77426726 ;
9 H H9_#9 2.5341158 -0.9546968 -0.06292417 ;
10 H H10_#10 -1.3230828 2.0329626 -0.7709833 ;
11 H H11_#11 -1.3219352 1.9135363 1.0362012 ;
12 H H12_#12 -2.528371 0.9698703 0.06707128 ;
end "coord set";

DATA "element set"
2 ;
Jmol Property Data Format 1 -- Jmol 12.1.11_dev 2010-09-05 20:18;
4 C [SUBUNIT]1:A.C4_#4 6 ;
6 C [SUBUNIT]1:A.C6_#6 6 ;
end "element set";

DATA "partialCharge set"
6 ;
Jmol Property Data Format 1 -- Jmol 12.1.11_dev 2010-09-05 20:18;
1 C [SUBUNIT]1:A.C1_#1 -0.1062 ;
2 C [SUBUNIT]1:A.C2_#2 -0.1062 ;
3 H [SUBUNIT]1:A.H3_#3 0.053099975 ;
4 C [SUBUNIT]1:A.C4_#4 0.053099975 ;
5 H [SUBUNIT]1:A.H5_#5 0.053099975 ;
6 C [SUBUNIT]1:A.C6_#6 0.053099975 ;
end "partialCharge set";
}

function _setModelState() {
connect ({0}) ({2}) delete;
connect ({1}) ({4}) delete;
data "connect_atoms"
0    1    3    0.3    0.0    triple;
6    5    1    0.3    0.0    single;
7    5    1    0.3    0.0    single;
8    5    1    0.3    0.0    single;
9    3    1    0.3    0.0    single;
10    3    1    0.3    0.0    single;
11    3    1    0.3    0.0    single;
end "connect_atoms";

select ({2 4});
Spacefill 0.2525;
select ({0 1 3 5});
Spacefill 0.391;
select ({6:11});
Spacefill 0.253;
select BONDS ({0:8});
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 1 3 5:11});
center {0.0028723478 0.0047832727 0.0016583204};
moveto -1.0 {0 0 1 0} 100.0 0.0 0.0 {0.0 -5.0008297E-5 0.0} 2.7502866 {0.0 0.0 0.0} 0.0 -9.05576E-4 0.0;
save orientation "default"
moveto 0.0 { 499 859 -114 7.8} 100.0 0.0 0.0 {0.0028723478 0.0047832727 0.0016583204} 3.9663374 {0.0 0.0 0.0} -0.040259466 0.05803979 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() {
delete ({2 4});
select ({0 1 3 5:11});
set hideNotSelected false;
}

function _setState() {
initialize;
set refreshing false;
_setWindowState;
_setFileState;
_setVariableState;
_setDataState;
_setModelState;
_setPerspectiveState;
_setSelectionState;
set refreshing true;
set antialiasDisplay false;
set antialiasTranslucent true;
set antialiasImages true;
}

_setState;

Otis Rothenberger
chemagic.com

On 9/25/2010 9:51 AM, Robert Hanson wrote:

Otis, anytime you find that save/restore does not work, I'm interested. It indicates a flaw in the save state business.

I see your second message. My checking suggests, like you say, the double bond issue seems fine.

What's the story on partial bonds?

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Re: [Jmol-users] Renew State Issue

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