On Mon, Nov 26, 2012 at 4:57 PM, Evans, Michael James
<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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web console. Get in-depth insight into apps, servers, databases, vmware,
SAP, cloud infrastructure, etc. Download 30-day Free Trial.
Pricing starts from $795 for 25 servers or applications!
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