Thanks, Bob! You are truly the man.
On Nov 26, 2012, at 6:39 PM, Robert Hanson
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>>
wrote:
On Mon, Nov 26, 2012 at 4:57 PM, Evans, Michael James
<evan...@illinois.edu<mailto:evan...@illinois.edu>> wrote:
Jmol'ers,
I'm having some trouble with state scripts in JSmol (generated by the latest
version of JSmol). Comparable state scripts in Jmol proper work fine. To test,
see these two pages, which are identical except for the use of JSmol in the
latter. Did I miss a memo? I'm having a tough time debugging this since JSmol
lacks a console.
The console is by issuing the following JavaScript, for applet named
jmolApplet0:
jmolApplet0._showInfo(true)
Here's your console report:
Jmol applet jmol_object__918579045542545__ ready
script 2 started
FileManager.getAtomSetCollectionFromFile(http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/sildenafil/SDF?record_type=3d)
starting HoverWatcher_2
FileManager opening
http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/sildenafil/SDF?record_type=3d
The Resolver thinks Mol
5212
-OEChem-11261219223D
Time for
openFile(http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/sildenafil/SDF?record_type=3d):
2345 ms
reading 63 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty
"auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Babel
63 atoms created
ModelSet: not autobonding; use forceAutobond=true to force automatic bond
creation
call loadScript ..\..\..\..\lib\jsmol\org\jmol\symmetry\Symmetry.js
call loadScript ..\..\..\..\lib\jsmol\org\jmol\api\SymmetryInterface.js --
required by org.jmol.symmetry.Symmetry
call loadScript ..\..\..\..\lib\jsmol\org\jmol\symmetry\PointGroup.js
call loadScript ..\..\..\..\lib\jsmol\org\jmol\symmetry\SpaceGroup.js
call loadScript ..\..\..\..\lib\jsmol\org\jmol\symmetry\HallInfo.js
call loadScript ..\..\..\..\lib\jsmol\org\jmol\symmetry\HallRotation.js
call loadScript ..\..\..\..\lib\jsmol\org\jmol\symmetry\HallTranslation.js
call loadScript ..\..\..\..\lib\jsmol\org\jmol\symmetry\SymmetryOperation.js
call loadScript ..\..\..\..\lib\jsmol\org\jmol\symmetry\SymmetryInfo.js
call loadScript ..\..\..\..\lib\jsmol\org\jmol\symmetry\UnitCell.js
ColorManager: color "roygb" range 0 0
slabRange = 0
spinX = 0
spinY = 30
spinZ = 0
spinFPS = 30
navX = 0
navY = 0
navZ = 0
navFPS = 10
Script completed
Jmol script terminated
Application loaded.
http://www.metallacycle.com/play/netmol/assets/userfiles/mevans/Sildenafil_test_2/
http://www.metallacycle.com/play/netmol/assets/userfiles/mevans/Sildenafil_test_2/?use=html5
If state scripts shouldn't be working because of lack of support for a
particular command, that would be helpful information. I can simply cut the
offending command out of my state scripts. Thanks for the help!
I'll look into that. An interesting thing about this is that you have total
access to the entire Java and Jmol code, so I can look into that and find that:
jmol._applet.viewer.refreshing
is "false", and that prevents any refreshing of the screen. It's something that
is set false in a state script and then set true at the end. If it is not set
true, you see nothing. I did this:
jmol._applet.viewer.refreshing = true; jmol._script("load ''")
from the developer window, and I see sildenifil. So I'll track down what's
going on there. I think it's the two moveto commands.
Bob
Cheers, Mike
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
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SAP, cloud infrastructure, etc. Download 30-day Free Trial.
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