[Chimera-users] Chimera-users Digest, Vol 164, Issue 26

Healey, Joe J.R.J.Healey at warwick.ac.uk
Fri Dec 23 09:14:25 PST 2016


I might be able to offer a bit of help here, the Chimera team and Jaime helped me with basically this exact problem.


I have a script here https://github.com/jrjhealey/bioinfo-tools/blob/master/strucfit.py that you could take from. You'll probably want to look specifically at lines 216-240. (Note - you'll also need to look at the relevant module imports for match and pychimera etc.


The script will need Jaime's implementation of pychimera too (he's super helpful!)

https://github.com/insilichem/pychimera


The script gives output as below, as the script automatically finds the best matching PDB file (that's what the first 150 lines or so is looking for), there is additional information there.

Best        Model I'm
Hit           Comparing                             RMSD                     Assorted homology metrics
2k4r PAK_01796_model5.pdb 2.81843275676 37.5 13 0.00035 21.5
2k4r PAK_01796_model4.pdb 12.6869844869 37.5 13 0.00035 21.5
2k4r PAK_01796_model3.pdb 14.4133021316 37.5 13 0.00035 21.5
2k4r PAK_01796_model1.pdb 0.459177533295 37.5 13 0.00035 21.5
2k4r PAK_01796_model2.pdb 15.1861411912 37.5 13 0.00035 21.5



Hope that's useful! Happy to offer more help (though I'm sure the chimera team have it covered!)



Joe


M.Sc. B.Sc. (Hons) MSRB
PhD Student
MOAC CDT, Senate House
University of Warwick
Coventry
CV47AL
Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk

Jointly working in:
Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)

Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738


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Subject: Chimera-users Digest, Vol 164, Issue 26

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Today's Topics:

   1. Saving Output From Match Align (Muk, Sanychen)


----------------------------------------------------------------------

Message: 1
Date: Thu, 22 Dec 2016 16:11:00 +0000
From: "Muk, Sanychen" <smuk at coh.org>
To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] Saving Output From Match Align
Message-ID:
        <A69D81CB04F0734E96302AA9E36F9B233E521BEE at ppwexch2kx03.coh.org>
Content-Type: text/plain; charset="iso-8859-1"

Hello,

I'm working on a script to superimpose pdb structures onto one another and then run the match -> align tool to align them to get the RMSD between residues of the pdb structures. I know that from the multialign interviewer window, I can then go to structure acess match and then save the attributes as a text file that will contain the residue number and RMSD. Is there a command that I can use to output this attributes file automatically? Thank you, and happy holidays.

Best,
Sanychen Muk


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