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 >> > >> > > >------------------------------------------------------------------------ >> > >> > > >------------------------------------------------------------------------- >> >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 >> > >> > >> >> >> -- >> 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=/> >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>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
