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
