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*<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*<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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