Yes, a script is still probably the easiest way to do what you want. However, there is a call in the old script that no longer exists in the new one. I'm attaching a new script that will do a couple things differently than before: - Instead of opening files in the script, it will now use models that have already been opened. - It will call matchmaker to align all models to the model with the lowest model/submodel number (usually the first model opened). To run it, save the script as "cluster.py" and run the command: chimera --nogui --silent your_model_files cluster.py where cluster.py is the name of the script. The first model opened will be the reference structure to which everything else is aligned. In the script, Matchmaker is invoked by the line: chimera.runCommand("mm %s %s" % (ref.oslIdent(), m.oslIdent())) If you want to use more options (see http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html for details), just add it after the second "%s" on the line. Please let me if this does what you need, or if you'd like it to do more stuff. Conrad On 6/26/2012 7:57 PM, Hurt, Darrell (NIH/NIAID) [E] wrote:
Hi there,
I want to use Chimera on a server (or in an automated fashion by command line; "-nogui") to read in a bunch (1000s) of PDB structures (each having an identical number of atoms) and then do clustering using the NMRCLUST code that you've so conveniently adapted.
I found this old thread: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003193.html
Is this still the preferred method for doing what I'm hoping?
Also, is it possible to do a MatchMaker alignment before the clustering?
Thanks, Darrell
-- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH
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