On Thu, Nov 4, 2010 at 12:24 PM, Dr. Christoph Gille <
christoph.gi...@charite.de> wrote:
> >select 1.1
> >save coordinates 1
>
> Thanks Bob,
> superposition works fine now.
>
>
> Two questions:
> 1. How to specify pdb insertion codes in selections
>
%x
so, for example,
select %A // just the "A" set
select % or %A // "unmarked" or "A" set -- a "configuration"
select *.ca%A
Mostly these are useful in the sense of whole-model "configurations".
"configuration 1" is the model using first insertion code for a given
residue, whatever that might be for a given residue; "configuration 2" is
the second, etc. If you want to load just one configuration, you can use:
load xxxx.pdb FILTER "conf 1"
for example. This is a "safe" load for any PDB file, even if it contains no
insertion code information. It means you will have no atoms present except
those.
You can also use:
load xxxx.pdb FILTER "%A"
This will load only the configuration involving alternative location A (and,
of course, the unmarked atoms as well), regardless the order of "A" among
the alternative locations for a given residue.
The issue is that %A may apply to some residues, while %B may apply to
others, and in certain rare cases whole residues are "A" or "B".
I learned this while verifying the DSSP implementation in Jmol recently.
(And doing that also found a minor bug in the CMBI DSSP program!)
> 2. Can I obtain the JMenuBar?
>
>
OK, so you have an application that has Jmol embedded in it, right? Or are
you using the Jmol application itself? The JMenuBar is not part of the
viewer itself. Are you referring to the popup menu? That you have complete
control over.
Bob
> Three bugs:
>
> 1. Why zoom with wheel and not ctrl-wheel? Bug or by intention?
>
I guess no one has suggested it. Why would you want ctrl-wheel? Same as just
wheeling? or different?
> 2. Tilde (i.e. $HOME) not working in file paths
>
Tilde is ~. This must be a UNIX implementation? Maybe there's a switch that
Java can use to recognize that; I don't know. Jmol has the CD command, and
CD ""
gets you to the directory containing the JAR file.
There is also
set defaultDirectory "whereever"
that would allow you to set a general default directory when you start the
program.
> 3. Tab-File-path-completion not working.
>
Perhaps you can track that down. Are you compiling Jmol yourself? Can you
run the debugger within Eclipse?
Also, if you are on a UNIX system, could you check out file dropping? I've
had a report of problems with that with LINUX. Since I don't have UNIX to
work on, I'll need help getting that. Can you do some experimentation and
see what the problem is and suggest a solution? The code point would be
Viewer.openFileAsynchronously(String fileName). Just
>
> Otherwise I am happy with jmol.
>
>
> And here an Exception.
> I think I did not wait for Jmol to be completely loaded
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> at org.jmol.modelset.ModelCollection.isTrajectory(Unknown Source)
> at org.jmol.shapebio.BioShapeCollection.setVisibilityFlags(Unknown
> Source)
> at org.jmol.viewer.ShapeManager.setModelVisibility(Unknown Source)
> at org.jmol.viewer.Viewer.setModelVisibility(Unknown Source)
> at org.jmol.viewer.Viewer.renderScreenImage(Unknown Source)
> at org.jmol.viewer.Viewer.renderScreenImage(Unknown Source)
> at charite.christo.protein.ChJmol.paintHook(ChJmol.java:237)
> at charite.christo.ChUtils.paintHooks(ChUtils.java:8299)
> at charite.christo.ChPanel.paintComponent(ChPanel.java:38)
> at javax.swing.JComponent.paint(JComponent.java:1029)
> at charite.christo.ChPanel.paint(ChPanel.java:58)
> at javax.swing.JComponent.paintToOffscreen(JComponent.java:5124)
> at
> javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1479)
>
>
>
>
>
> ------------------------------------------------------------------------------
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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
------------------------------------------------------------------------------
The Next 800 Companies to Lead America's Growth: New Video Whitepaper
David G. Thomson, author of the best-selling book "Blueprint to a
Billion" shares his insights and actions to help propel your
business during the next growth cycle. Listen Now!
http://p.sf.net/sfu/SAP-dev2dev
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