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 >> > >> > > >------------------------------------------------------------------------ >> > >> > > >------------------------------------------------------------------------- >> >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
