[Chimera-users] Clustering docking results using "headless" Chimera
Hurt, Darrell (NIH/NIAID) [E]
darrellh at niaid.nih.gov
Wed Jun 27 13:59:17 PDT 2012
This is fantastic. I'll give it a try and let you know how things go.
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
http://bioinformatics.niaid.nih.gov (Within NIH)
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On 6/27/12 2:03 PM, "Conrad Huang" <conrad at cgl.ucsf.edu> wrote:
>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
>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
>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:
>> Is this still the preferred method for doing what I'm hoping?
>> Also, is it possible to do a MatchMaker alignment before the
>> Thanks, Darrell
>> -- Darrell Hurt, Ph.D. Section Head, Computational Biology
>> Bioinformatics and Computational Biosciences Branch (BCBB)
>> 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office
>> 301-402-0095 Mobile 301-758-3559
>> (Within NIH) http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/>
>> Disclaimer: The information in this e-mail and any of its attachments
>> is confidential and may contain sensitive information. It should not
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>> Institute of Allergy and Infectious Diseases shall not accept
>> liability for any statements made that are sender's own and not
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