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@warwick.ac.uk

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

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

________________________________ From: chimera-users-bounces@cgl.ucsf.edu chimera-users-bounces@cgl.ucsf.edu on behalf of chimera-users-request@cgl.ucsf.edu chimera-users-request@cgl.ucsf.edu Sent: 22 December 2016 20:00 To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 164, Issue 26

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Today's Topics:

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

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Message: 1 Date: Thu, 22 Dec 2016 16:11:00 +0000 From: "Muk, Sanychen" smuk@coh.org To: "chimera-users@cgl.ucsf.edu" chimera-users@cgl.ucsf.edu Subject: [Chimera-users] Saving Output From Match Align Message-ID: A69D81CB04F0734E96302AA9E36F9B233E521BEE@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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