I don't know if this is a bug or a feature, but my script to display a model
of benzene ends up with all double bonds. Here is a snippet of the script
(the structure is defined via an inline data file):
set autobond false;
data "model benzene" | ... (atom coordinates here) ... |end "model benzene";
show data;
connect (atomno=1) (atomno=2) AROMATIC create;
connect (atomno=2) (atomno=3) AROMATIC create;
connect (atomno=3) (atomno=4) AROMATIC create;
connect (atomno=4) (atomno=5) AROMATIC create;
connect (atomno=5) (atomno=6) AROMATIC create;
connect (atomno=6) (atomno=1) AROMATIC create;
This produces all double bonds. When I play around with the console, the
only way I can get what I want (and expect) is to say:
connect;
connect (atomno=1) (atomno=2) AROMATIC modify;
...etc. for all the remaining bonds
I've attached a state file.
Dean
# Jmol state version 11.6.RC17 2008-09-20 13:06;
# fullName = "jmolApplet0__18749094039234__";
# documentBase =
"http://dhj-macbook.local/~djohnston/symmetry/tutorial/benzene.html";;
# codeBase = "http://dhj-macbook.local/~djohnston/symmetry/common/Jmol/";;
function _setWindowState();
# height 591;
# width 591;
stateVersion = 1106000;
backgroundColor = "[xffffff]";
axis1Color = "[xff0000]";
axis2Color = "[x008000]";
axis3Color = "[x0000ff]";
ambientPercent = 45;
diffusePercent = 84;
specular = true;
specularPercent = 22;
specularPower = 40;
specularExponent = 6;
statusReporting = true;
end function;
function _setFileState();
set allowEmbeddedScripts false;
set autoBond false;
set appendNew true;
set appletProxy "";
set applySymmetryToBonds false;
set bondRadiusMilliAngstroms 150;
set bondTolerance 0.45;
set defaultDirectory "";
set defaultLattice {0.0 0.0 0.0};
set defaultLoadScript "";
set defaultVDW Jmol;
set forceAutoBond false;
set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb";;
set minBondDistance 0.4;
set pdbSequential false;
set pdbGetHeader false;
set percentVdwAtom 20;
set smartAromatic true;
data "model inline"
12
benzene
C -1.2125 -0.7000 0.0000
C -1.2125 0.7000 0.0000
C 0.0000 1.4000 0.0000
C 1.2124 0.7000 0.0000
C 1.2124 -0.7000 0.0000
C 0.0000 -1.4000 0.0000
H -2.1478 -1.2400 0.0000
H -2.1478 1.2400 0.0000
H 0.0000 2.4800 0.0000
H 2.1477 1.2400 0.0000
H 2.1477 -1.2400 0.0000
H 0.0000 -2.4800 0.0000
end "model inline";;
end function;
function _setVariableState();
set defaultanglelabel "%VALUE %UNITS";
set defaultcolorscheme "Jmol";
set defaultdirectory "";
set defaultdistancelabel "%VALUE %UNITS";
set defaultdrawarrowscale 0.5;
set defaultlattice "{0 0 0}";
set defaultloadscript "";
set defaulttorsionlabel "%VALUE %UNITS";
set defaulttranslucent 0.5;
set defaultvdw "Jmol";
set allowembeddedscripts true;
set allowrotateselected false;
set appletproxy "";
set applysymmetrytobonds false;
set atompicking true;
set autobond false;
set autofps false;
set axes window;
set axesmode 0;
set axesscale 2.0;
set bondmodeor false;
set bondpicking false;
set bondradiusmilliangstroms 150;
set bondtolerance 0.45;
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 dotsselectedonly false;
set dotsurface true;
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 greyscalerendering false;
set hbondsbackbone false;
set hbondssolid false;
set helppath "http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm";;
set hermitelevel 0;
set hidenameinpopup false;
set hidenavigationpoint false;
set highresolution false;
set historylevel 0;
set hoverdelay 0.5;
set isosurfacepropertysmoothing true;
set justifymeasurements false;
set loadformat "http://www.rcsb.org/pdb/files/%FILE.pdb";;
set measureallmodels false;
set measurementlabels true;
set messagestylechime false;
set minbonddistance 0.4;
set navigationperiodic false;
set navigationspeed 5.0;
set pdbgetheader false;
set pdbsequential false;
set percentvdwatom 20;
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 "c";
set rangeselected false;
set ribbonaspectratio 16;
set ribbonborder false;
set rocketbarrels false;
set selectallmodels true;
set selecthetero true;
set selecthydrogen true;
set sheetsmoothing 1.0;
set showhiddenselectionhalos false;
set showhydrogens true;
set showmeasurements true;
set showmultiplebonds true;
set shownavigationpointalways false;
set smartaromatic true;
set solventprobe false;
set solventproberadius 1.2;
set ssbondsbackbone false;
set stereodegrees 5;
set strandcountformeshribbon 7;
set strandcountforstrands 5;
set testflag1 false;
set testflag2 false;
set testflag3 false;
set testflag4 false;
set tracealpha true;
set usenumberlocalization true;
set vectorscale 1.0;
set vibrationperiod 1.0;
set vibrationscale 1.0;
set wireframerotation false;
set zoomlarge true;
set zshade false;
#user-defined variables;
# --none--;
# 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;
end function;
function _setModelState();
connect ({0}) ({1}) aromatic;
connect ({1}) ({2}) aromatic;
connect ({2}) ({3}) aromatic;
connect ({3}) ({4}) aromatic;
connect ({4}) ({5}) aromatic;
connect ({5}) ({0}) aromatic;
connect ({0}) ({6}) single;
connect ({1}) ({7}) single;
connect ({2}) ({8}) single;
connect ({3}) ({9}) single;
connect ({4}) ({10}) single;
connect ({5}) ({11}) single;
measures delete;
select *; set measures nanometers;
font measures 15.0 SansSerif Plain;
select measures ({null});
boundBox off;
frank on;
font frank 16.0 SansSerif Bold;
set fontScaling false;
end function;
function _setPerspectiveState();
set perspectiveModel 11;
set scaleAngstromsPerInch 0.0;
set perspectiveDepth false;
set visualRange 5.0;
set cameraDepth 3.0;
boundbox corners {-2.1478 -2.48 0.0} {2.1476998 2.48 0.0} # volume = 0.0;
center {-3.3318996E-5 9.934108E-9 0.0};
moveto 0.0 {0 0 1 0} 100.0 0.08 0.08 {-3.3318996E-5 9.934108E-9 0.0}
3.6800203 {0.0 0.0 0.0} 4.4924353E-4 0.0 50.0;;
slab 100;depth 0;
set spinX 0; set spinY 30; set spinZ 0; set spinFps 30;
end function;
function _setSelectionState();
select ({0:11});
set hideNotSelected false;
end function;
function _setState();
initialize;
set refreshing false;
_setWindowState;
_setFileState;
_setVariableState;
_setModelState;
_setPerspectiveState;
_setSelectionState;
set refreshing true;
set antialiasDisplay false;
set antialiasTranslucent true;
set antialiasImages true;
end function;
_setState;-------------------------------------------------------------------------
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