Hurrah! I think that's done it -- no exceptions at all.....
Thank you again, Bob, for your incredible efforts on Jmol -- I, for one, am
very grateful!
-Tom
On Mon, Aug 11, 2008 at 9:35 PM, Bob Hanson <[EMAIL PROTECTED]> wrote:
> Oh, I think it's fixed. The following works at
> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
>
> load 1crn.pdb
> m = "2,3,4"
> print m
> select @m
>
> It was the @m in the select command that was the problem in earlier
> versions.
>
> 1) Make sure ALL your browsers windows have been closed. This generally
> flushes the Java cache and allows a new Jmol version to load.
> 2) Use the jar files in
> http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.zip
> 3) If it still does not work, send me the full console report, including
> the line that shows what Jmol version was loaded. Also, if you can,
> please send me the model and the script so I can try it here myself.
>
> Bob
>
>
> Thomas Stout wrote:
>
> >
> > 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]
> > <mailto:[EMAIL PROTECTED]>> wrote:
> >
> >
> > Terrific - looking forward to it!
> >
> > Thanks Bob,
> > Tom
> >
> >
> > On Sun, Aug 10, 2008 at 12:14 AM, Bob Hanson <[EMAIL PROTECTED]
> > <mailto:[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]>
> >
> >> <mailto:[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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> >> the world
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> > <http://moblin-contest.org/redirect.php?banner_id=100&url=/>
> >>
> > <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>
> >
> >> <mailto: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=/>
> >>
> > <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>
> >
> >> <mailto: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=/
> > <http://moblin-contest.org/redirect.php?banner_id=100&url=/>
> >>
> >>------------------------------------------------------------------------
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> >>_______________________________________________
> >>Jmol-users mailing list
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> >>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
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> >
> >------------------------------------------------------------------------
> >
> >_______________________________________________
> >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=/
> _______________________________________________
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>
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