Hi again Bob --
I've been able to test Jmol 11.6RC4 and I'm sorry to say that I get the same
behavior.... Is there any other information I can provide you to help track
this down??
-Tom
FileManager.openFile(../../struct/protein1_aligned.pdb)
//../../struct/protein1_aligned.pdb
FileManager opening
http://comte/struct/protein1_aligned.pdb<http://comte/struct/EphB4/02252331/EphB4_02252331_aligned.pdb>
The Resolver thinks Pdb
openFile(../../struct/protein1_aligned.pdb): 156 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/structures3/sandbox_11.6RC4/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 8/10/08, Thomas Stout <[EMAIL PROTECTED]> wrote:
>
>
> 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
>> > >
>> >
>> >------------------------------------------------------------------------
>> > >
>> >
>> >-------------------------------------------------------------------------
>> > >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
>> > >http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> > <http://moblin-contest.org/redirect.php?banner_id=100&url=/>
>> > >
>> >
>> >------------------------------------------------------------------------
>> > >
>> > >_______________________________________________
>> > >Jmol-users mailing list
>> > >Jmol-users@lists.sourceforge.net
>>
>> > <mailto:Jmol-users@lists.sourceforge.net>
>> > >https://lists.sourceforge.net/lists/listinfo/jmol-users
>> > >
>> > >
>> >
>> >
>> > --
>> > 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
>> >
>> >
>> >
>> >
>> -------------------------------------------------------------------------
>> > 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
>> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> > <http://moblin-contest.org/redirect.php?banner_id=100&url=/>
>> > _______________________________________________
>> > Jmol-users mailing list
>> > Jmol-users@lists.sourceforge.net
>>
>> > <mailto:Jmol-users@lists.sourceforge.net>
>> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>> >
>> >
>> >------------------------------------------------------------------------
>> >
>> >-------------------------------------------------------------------------
>> >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
>> >http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> >
>> >------------------------------------------------------------------------
>> >
>> >_______________________________________________
>> >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
>> 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
>>
>>
>>
>> -------------------------------------------------------------------------
>> 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
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
-------------------------------------------------------------------------
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
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
