On Sun, Sep 5, 2010 at 9:12 PM, Michael Evans <evan...@illinois.edu> wrote:
> Hmm, might I suggest an orange-ish color, maybe something akin to #ffa500?
> Orange is about the farthest color away from the colors that already exist
> in that scheme right now. My second place vote goes to a deep navy blue.
I'm thinking something more subtle. Right now I've entered it as #a6a6fa,
but that's just a place-holder.
Cheers, Mike
>
> On Sun, Sep 5, 2010 at 8:20 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> Jmol users:
>>
>> We need a suitable color for carbohydrate that meshes well with other
>> STRUCTURE colors such as these:
>>
>> http://www.umass.edu/molvis/drums/codes.html
>>
>> Thanks,
>>
>> Bob
>>
>>
>> On Sun, Sep 5, 2010 at 1:48 PM, Eric Martz <ema...@microbio.umass.edu>wrote:
>>
>>> Dear Bob,
>>>
>>> The following 2 commands crash Jmol 12.0.11:
>>>
>>> load 1dlh.pdb.gz
>>> color structure
>>>
>>> The crash occurs with 1dlh.pdb.gz or 1dlh.pdb (as received from the PDB)
>>> but NOT with e.g. 1d66.pdb, 1pgb.pdb.gz, 2vaa.pdb.gz.
>>>
>>> So it seems to be related to something specific in 1dlh.pdb.
>>>
>>> Here's a clue: the following 3 commands do NOT crash Jmol:
>>>
>>> load 1dlh.pdb
>>> select (:a,:b) and protein
>>> color structure
>>>
>>> but the following 3 commands DO CRASH jmol:
>>>
>>> load 1dlh.pdb
>>> select :a,:b
>>> color structure
>>>
>>> also
>>>
>>> load 1dlh.pdb
>>> select not protein
>>> color structure
>>>
>>> The report in the java console:
>>>
>>> Exception in thread "QueueThread0"
>>> java.lang.ArrayIndexOutOfBoundsException: 7
>>> at org.jmol.viewer.ColorManager.getColixAtomPalette(Unknown
>>> Source)
>>> at org.jmol.viewer.Viewer.getColixAtomPalette(Unknown Source)
>>> at org.jmol.shape.Shape.setColix(Unknown Source)
>>> at org.jmol.shape.Balls.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.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)
>>>
>>> Thanks, -Eric
>>>
>>>
>>>
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>>
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> 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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>> This SF.net Dev2Dev email is sponsored by:
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>>
>
>
> --
> Mike Evans
> Organic Chemistry Graduate Student
> Moore Group
> University of Illinois, Urbana-Champaign
>
>
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>
> Show off your parallel programming skills.
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>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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