Dear Bob,
I downloaded Jmol-12.0.11_dev today 9/1 about 10 AM.
The VERY good news: It works fine in both my under-development
tutorial on MHC in the JTAT shell, and in FirstGlance in Jmol
(limited testing).
-------------
I found 1 Bug. This bug has been present since 11.6.RC12. I was
hoping this version would not have it. I can run many script files
just fine, but, on the SECOND attempt to run one particular script
named labelm1.spt, it reproducibly crashes Jmol:
FileManager opening file:/Volumes/JTAT/mhc/chapter04/labelm1.spt
Exception in thread "QueueThread0" java.lang.NullPointerException
at org.jmol.shape.Labels.setColix(Unknown Source)
at org.jmol.shape.Labels.setProperty(Unknown Source)
at org.jmol.shape.Shape.setShapeProperty(Unknown Source)
at org.jmol.viewer.ShapeManager.setShapeProperty(Unknown Source)
at org.jmol.script.ScriptEvaluator.setShapeProperty(Unknown Source)
at org.jmol.script.ScriptEvaluator.colorShape(Unknown Source)
at org.jmol.script.ScriptEvaluator.color(Unknown Source)
at
org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown Source)
at org.jmol.script.ScriptEvaluator.script(Unknown Source)
at
org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown Source)
at
org.jmol.script.ScriptEvaluator.evaluateCompiledScript(Unknown Source)
at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
at
org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown Source)
at
org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown Source)
at
org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source)
at java.lang.Thread.run(Thread.java:613)
I have narrowed it down to this.
Start Jmol.jar.
In the console, enter "set antialiasdisplay"
Load any PDB file (it must contain an atom with the number specified,
e.g. 3053 below, which occurs in 2vaa or 2hu4; for 1d66, use e.g. 1549).
Now execute the following script TWICE:
select all
set fontsize 16
set labelfront
color labels none
select atomno=3053
label Beta-2 Mic.
On the second execution, Jmol will crash.
It does not seem to be a single command, but perhaps two. I haven't
narrowed it down further.
The antialiasdisplay can be entered before or after loading the molecule.
-Eric
At 8/31/10, Robert Hanson wrote:
>I would appreciate those recently requesting bug fixes to take a
>look at this version prior to our releasing it. The changes I made
>were rather involved, and I'm not sure I have all the files here to
>test it. I would appreciate your testing both 12.1.9 and 12.0.11
>(and especially 12.0.11).
>
>Thank you.
>
>12.1.9
><http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip>http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
>12.0.11 http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12_0.zip
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