Menu
▾
▴
Re: [Jmol-users] bug in Jmol Version 12.0.18
|
From: Andreas P. <an...@sd...> - 2010-10-18 13:43:22
|
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 <ha...@st...> 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 <an...@sd...> 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 <ha...@st...>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 <ha...@st...>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 <an...@sd...>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 >>>>> Jmo...@li... >>>>> 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 >>> Jmo...@li... >>> 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 >> Jmo...@li... >> 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 > Jmo...@li... > 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 ----------------------------------------------------------------------- |