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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--
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
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