Terrific - looking forward to it!
Thanks Bob,
Tom
On Sun, Aug 10, 2008 at 12:14 AM, Bob Hanson <[EMAIL PROTECTED]> wrote:
> I found it. That's fixed for 11.6RC4
>
> Thomas Stout wrote:
>
> >
> > Hi Bob --
> >
> > It looks like 11.6RC2 behaves the same way. I had bigger problems
> > with 11.6RC3, so I can't evaluate that version with respect to this.
> > Here's the bottom of the java console dump:
> >
> > FileManager.openFile(../../struct/protein1_aligned.pdb)
> > //../../struct/protein1_aligned.pdb
> > FileManager opening
> http://comte.exelixis.com/struct/protein1_aligned.pdb
> > The Resolver thinks Pdb
> > openFile(../../struct/protein1_aligned.pdb): 94 ms
> > ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
> > 1 models in this collection. Use getProperty "modelInfo" or
> > getProperty "auxiliaryInfo" to inspect them.
> > ModelSet: autobonding; use autobond=false to not generate bonds
> > automatically
> > FileManager opening
> > http://comte.exelixis.com/structures3/sandbox_11.6RC2/color_models.spt
> > java.lang.ClassCastException: java.util.BitSet cannot be cast to
> > java.lang.String
> > at org.jmol.viewer.Eval.expression(Unknown Source)
> > at org.jmol.viewer.Eval.expression(Unknown Source)
> > at org.jmol.viewer.Eval.select(Unknown Source)
> > at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source)
> > at org.jmol.viewer.Eval.script(Unknown Source)
> > at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source)
> > at org.jmol.viewer.Eval.runEval(Unknown Source)
> > at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
> > at org.jmol.viewer.Viewer.scriptWait(Unknown Source)
> > at org.jmol.applet.Jmol.scriptProcessor(Unknown Source)
> > at org.jmol.applet.Jmol.scriptWait(Unknown Source)
> > at JmolApplet.scriptWait(Unknown Source)
> > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> > at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
> > at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
> > at java.lang.reflect.Method.invoke(Unknown Source)
> > at sun.plugin.javascript.JSInvoke.invoke(Unknown Source)
> > at sun.reflect.GeneratedMethodAccessor8.invoke(Unknown Source)
> > at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
> > at java.lang.reflect.Method.invoke(Unknown Source)
> > at sun.plugin.javascript.JSClassLoader.invoke(Unknown Source)
> > at sun.plugin.com.MethodDispatcher.invoke(Unknown Source)
> > at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source)
> > at sun.plugin.com.DispatchImpl$1.run(Unknown Source)
> > at java.security.AccessController.doPrivileged(Native Method)
> > at sun.plugin.com.DispatchImpl.invoke(Unknown Source)
> > java.lang.Exception: java.lang.ClassCastException: java.util.BitSet
> > cannot be cast to java.lang.String
> > at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source)
> > at sun.plugin.com.DispatchImpl$1.run(Unknown Source)
> > at java.security.AccessController.doPrivileged(Native Method)
> > at sun.plugin.com.DispatchImpl.invoke(Unknown Source)
> >
> >
> >
> > On 8/8/08, *Bob Hanson* <[EMAIL PROTECTED]
> > <mailto:[EMAIL PROTECTED]>> wrote:
> >
> > I'm pretty sure I found that and fixed it last week. Please try
> > 11.6.RC2
> >
> > Thomas Stout wrote:
> >
> > >
> > > When running Jmol 11.5.37, the following script (color_models.spt)
> > > works fine:
> > >
> > > n_models = getProperty("modelInfo","modelCount");
> > >
> >
> clist=array("green","palevioletred","lightblue","coral","yellow","cyan",\
> > > "dodgerblue","aqua","salmon","greenyellow","lavender",\
> > > "lightgoldenrodyellow","lightseagreen","lightskyblue",\
> > >
> > "lime","limegreen","mistyrose","olive","orange","peachpuff",\
> > >
> > "sandybrown","seagreen","tan","teal","wheat","yellowgreen");
> > >
> > > ini = 2;
> > > fin = n_models;
> > > for (var i = ini; i <= fin; i = i + 1)
> > > m = "*/"+i+".1";
> > > select @m and :Z and *.C??;
> > > print clist[i];
> > > s = clist[i];
> > > color @s;
> > > end for
> > >
> > >
> > > This results in different colors for the carbons of multiple chains
> > > "Z" from superimposed PDB files. Unfortunately in Jmol 11.5.51,
> I'm
> > > finding that this same script causes a java exception and locks
> > up the
> > > Jmol applet graphics.
> > >
> > > Here is the output to the Java console when it works (Jmol
> 11.5.37):
> > >
> > > *FileManager.openFile(../../struct/protein1_aligned.pdb)
> > > //../../struct/protein1_aligned.pdb
> > > FileManager opening
> > > **http://comte.exelixis.com/struct/protein1_aligned.pdb*
> > > *The Resolver thinks Pdb
> > > openFile(../../struct/protein1_aligned.pdb): 32 ms
> > > ModelSet: haveSymmetry:false haveUnitcells:true
> > haveFractionalCoord:false
> > > 1 models in this collection. Use getProperty "modelInfo" or
> > > getProperty "auxiliaryInfo" to inspect them.
> > > ModelSet: autobonding; use autobond=false to not generate bonds
> > > automatically
> > > FileManager opening
> > >
> > **
> http://comte.exelixis.com/structures3/bin-release/color_models.spt*
> > > *flowContextfor 10
> > > end flowContextfor
> > > palevioletred
> > > *
> > > And here is the same output from Jmol 11.5.51:
> > > FileManager.openFile(../../struct/protein1_aligned.pdb)
> > > //../../struct/protein1_aligned.pdb
> > > FileManager opening
> > http://comte.exelixis.com/struct/protein1_aligned.pdb
> > > The Resolver thinks Pdb
> > > openFile(../../struct/protein1_aligned.pdb): 31 ms
> > > ModelSet: haveSymmetry:false haveUnitcells:true
> > haveFractionalCoord:false
> > > 1 models in this collection. Use getProperty "modelInfo" or
> > > getProperty "auxiliaryInfo" to inspect them.
> > > ModelSet: autobonding; use autobond=false to not generate bonds
> > > automatically
> > > FileManager opening
> > >
> >
> http://comte.exelixis.com/structures3/sandbox_11.5.51/color_models.spt
> > > java.lang.ClassCastException: java.util.BitSet cannot be cast to
> > > java.lang.String
> > > at org.jmol.viewer.Eval.expression(Eval.java:1467)
> > > at org.jmol.viewer.Eval.expression(Eval.java:1391)
> > > at org.jmol.viewer.Eval.select(Eval.java:5338)
> > > at org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:991)
> > > at org.jmol.viewer.Eval.script(Eval.java:5073)
> > > at org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:973)
> > > at org.jmol.viewer.Eval.runEval(Eval.java:280)
> > > at org.jmol.viewer.Viewer.evalStringWaitStatus(Viewer.java:3495)
> > > at org.jmol.viewer.Viewer.scriptWait(Viewer.java:3441)
> > > at org.jmol.applet.Jmol.scriptProcessor(Jmol.java:689)
> > > at org.jmol.applet.Jmol.scriptWait(Jmol.java:717)
> > > at JmolApplet.scriptWait(JmolApplet.java:185)
> > > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> > > at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
> > > at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
> > > at java.lang.reflect.Method.invoke(Unknown Source)
> > > at sun.plugin.javascript.JSInvoke.invoke(Unknown Source)
> > > at sun.reflect.GeneratedMethodAccessor8.invoke(Unknown Source)
> > > at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
> > > at java.lang.reflect.Method.invoke(Unknown Source)
> > > at sun.plugin.javascript.JSClassLoader.invoke(Unknown Source)
> > > at sun.plugin.com.MethodDispatcher.invoke(Unknown Source)
> > > at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source)
> > > at sun.plugin.com.DispatchImpl$1.run(Unknown Source)
> > > at java.security.AccessController.doPrivileged(Native Method)
> > > at sun.plugin.com.DispatchImpl.invoke(Unknown Source)
> > > java.lang.Exception: java.lang.ClassCastException: java.util.BitSet
> > > cannot be cast to java.lang.String
> > > at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source)
> > > at sun.plugin.com.DispatchImpl$1.run(Unknown Source)
> > > at java.security.AccessController.doPrivileged(Native Method)
> > > at sun.plugin.com.DispatchImpl.invoke(Unknown Source)
> > >
> > >
> > > Might anything have changed between these versions that would cause
> > > this? Can I infer from the java error stream that there is
> > something
> > > about string handling that has gone awry?
> > >
> > > Thanks,
> > > Tom
> > >
> >
> >------------------------------------------------------------------------
> > >
> >
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> >------------------------------------------------------------------------
> > >
> > >_______________________________________________
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> > >
> >
> >
> > --
> > Robert M. Hanson
> > Professor of Chemistry
> > 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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> >
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> >Build the coolest Linux based applications with Moblin SDK & win great
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> >Grand prize is a trip for two to an Open Source event anywhere in the
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>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> 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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> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
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