Hi Bob,
Just a quick follow up to confirm that this was indeed a browser caching
issue and that the new build works fine...
Thanks for your help,
Andreas
On Fri, Oct 15, 2010 at 1:44 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> Andreas, I really don't think it's Jmol.
>
> What you need to do (is this a browser?) is to completely close all windows
> of your browser, including the download window, transfer the new files into
> the directory, and then restart your browser. These aren't standard errors.
> They must be problems because you are getting different parts of the package
> from different versions (I think).
>
> If this is the Jmol application, ignore that. It's a bug. But I need to
> have the full information about what you are doing to get this exception.
>
> 12.0.18 is up at
> http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm, and you can
> see there that =3cdz loads just fine and displays just fine.
>
>
> Bob
>
>
>
> On Fri, Oct 15, 2010 at 1:00 PM, Andreas Prlic <andr...@sdsc.edu> wrote:
>
>> Thanks for the quick update,
>>
>> now I am getting a different exception. This one has been present also in
>> older versions of Jmol... (again PDB ID 3CDZ )
>>
>> Exception in thread "QueueThread1"
>> java.lang.ArrayIndexOutOfBoundsException: 7
>> at org.jmol.viewer.ColorManager.getColixAtomPalette(Unknown Source)
>> at org.jmol.viewer.Viewer.getColixAtomPalette(Unknown Source)
>> at org.jmol.shape.Shape.setColix(Unknown Source)
>> at org.jmol.shape.Shape.setColix(Unknown Source)
>> at org.jmol.shapebio.BioShape.setColix(Unknown Source)
>> at org.jmol.shapebio.BioShapeCollection.setProperty(Unknown Source)
>> at org.jmol.shape.Shape.setShapeProperty(Unknown Source)
>> at org.jmol.viewer.ShapeManager.setShapeProperty(Unknown Source)
>> at org.jmol.script.ScriptEvaluator.setShapeProperty(Unknown Source)
>> at org.jmol.script.ScriptEvaluator.colorShape(Unknown Source)
>> at org.jmol.script.ScriptEvaluator.color(Unknown Source)
>> at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown
>> Source)
>> at org.jmol.script.ScriptEvaluator.evaluateCompiledScript(Unknown Source)
>> at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
>> at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown
>> Source)
>> at
>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown
>> Source)
>> at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source)
>> at java.lang.Thread.run(Thread.java:637)
>>
>> Thanks,
>>
>> Andreas
>>
>>
>> On Fri, Oct 15, 2010 at 6:21 AM, Robert Hanson <hans...@stolaf.edu>wrote:
>>
>>> OK, I've uploaded a rebuilt copy of the binary. Works with that script
>>> for me.
>>>
>>>
>>> On Fri, Oct 15, 2010 at 8:01 AM, Robert Hanson <hans...@stolaf.edu>wrote:
>>>
>>>> I must have messed up building that. I'll rebuild it and upload the
>>>> files again.
>>>>
>>>> This should work:
>>>>
>>>> http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12_0.zip
>>>>
>>>> On Thu, Oct 14, 2010 at 6:49 PM, Andreas Prlic <andr...@sdsc.edu>wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I just tried to upgrade our Jmol installation to 12.0.18 (binary
>>>>> download), but I noticed the following problem (e.g. PDB ID 3CDZ )
>>>>>
>>>>> Exception in thread "QueueThread1" java.lang.ClassCastException:
>>>>> java.lang.String cannot be cast to java.util.BitSet
>>>>> at org.jmol.modelset.AtomCollection.getAtomBits(Unknown Source)
>>>>> at org.jmol.modelset.BondCollection.getAtomBits(Unknown Source)
>>>>> at org.jmol.modelset.ModelCollection.getAtomBits(Unknown Source)
>>>>> at org.jmol.modelset.ModelSet.getAtomBits(Unknown Source)
>>>>> at org.jmol.viewer.Viewer.getAtomBits(Unknown Source)
>>>>> at org.jmol.script.ScriptEvaluator.getAtomBits(Unknown Source)
>>>>> at org.jmol.script.ScriptEvaluator.atomExpression(Unknown Source)
>>>>> at org.jmol.script.ScriptEvaluator.lookupValue(Unknown Source)
>>>>> at org.jmol.script.ScriptEvaluator.lookupIdentifierValue(Unknown
>>>>> Source)
>>>>> at org.jmol.script.ScriptEvaluator.atomExpression(Unknown Source)
>>>>> at org.jmol.script.ScriptEvaluator.atomExpression(Unknown Source)
>>>>> at org.jmol.script.ScriptEvaluator.select(Unknown Source)
>>>>> at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown
>>>>> Source)
>>>>> at org.jmol.script.ScriptEvaluator.evaluateCompiledScript(Unknown
>>>>> Source)
>>>>> at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
>>>>> at
>>>>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown
>>>>> Source)
>>>>> at
>>>>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown
>>>>> Source)
>>>>> at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown
>>>>> Source)
>>>>> at java.lang.Thread.run(Thread.java:637)
>>>>>
>>>>> when executing the script:
>>>>>
>>>>> load
>>>>> 'http://www.rcsb.org/pdb/files/3CDZ.pdb.gz';set<http://www.rcsb.org/pdb/files/3CDZ.pdb.gz%27;set>measurementUnits
>>>>> ANGSTROMS; select all; spacefill off; wireframe off;
>>>>> backbone off; cartoon on; color cartoon structure; color structure;
>>>>> select
>>>>> ligand;wireframe 0.16;spacefill 0.5; color cpk ; select all; set
>>>>> antialiasDisplay true;
>>>>>
>>>>> Can you take a look?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Andreas
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> -----------------------------------------------------------------------
>>>>> Dr. Andreas Prlic
>>>>> Senior Scientist, RCSB PDB Protein Data Bank
>>>>> University of California, San Diego
>>>>> (+1) 858.246.0526
>>>>> -----------------------------------------------------------------------
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Download new Adobe(R) Flash(R) Builder(TM) 4
>>>>> The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly
>>>>> Flex(R) Builder(TM)) enable the development of rich applications that
>>>>> run
>>>>> across multiple browsers and platforms. Download your free trials
>>>>> today!
>>>>> http://p.sf.net/sfu/adobe-dev2dev
>>>>> _______________________________________________
>>>>> Jmol-users mailing list
>>>>> Jmol-users@lists.sourceforge.net
>>>>> 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
>>>>
>>>
>>>
>>>
>>> --
>>> 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
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Download new Adobe(R) Flash(R) Builder(TM) 4
>>> The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly
>>> Flex(R) Builder(TM)) enable the development of rich applications that run
>>> across multiple browsers and platforms. Download your free trials today!
>>> http://p.sf.net/sfu/adobe-dev2dev
>>> _______________________________________________
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>> -----------------------------------------------------------------------
>> Dr. Andreas Prlic
>> Senior Scientist, RCSB PDB Protein Data Bank
>> University of California, San Diego
>> (+1) 858.246.0526
>> -----------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>> Download new Adobe(R) Flash(R) Builder(TM) 4
>> The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly
>> Flex(R) Builder(TM)) enable the development of rich applications that run
>> across multiple browsers and platforms. Download your free trials today!
>> http://p.sf.net/sfu/adobe-dev2dev
>> _______________________________________________
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> 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
>
>
> ------------------------------------------------------------------------------
> Download new Adobe(R) Flash(R) Builder(TM) 4
> The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly
> Flex(R) Builder(TM)) enable the development of rich applications that run
> across multiple browsers and platforms. Download your free trials today!
> http://p.sf.net/sfu/adobe-dev2dev
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------
------------------------------------------------------------------------------
Download new Adobe(R) Flash(R) Builder(TM) 4
The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly
Flex(R) Builder(TM)) enable the development of rich applications that run
across multiple browsers and platforms. Download your free trials today!
http://p.sf.net/sfu/adobe-dev2dev
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