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.
Now for the real reason for my e-mail: I want to make sure I understand
"write state REMOTEPATH" and "write state LOCALPATH." Can I specify, for
instance, "../structures" to replace all the file references in a state file
to a directory called "structures that is a sibling of wherever the file
resides? Is that how LOCALPATH works...? If I'm off base, let me know
(however if I'm on base, this is amazing and awesome).
Cheers, Mike
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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>
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>
>
--
Mike Evans
Organic Chemistry Graduate Student
Moore Group
University of Illinois, Urbana-Champaign
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