[Chimera-users] Computing 'basic' structure characteristics

Healey, Joe J.R.J.Healey at warwick.ac.uk
Tue Oct 11 02:29:00 PDT 2016


That looks spot on thanks Eric.


Does chimera specify anything other than "isHelix"/"isSheet"/"isTurn"?


I can see these in chimera's object model (stole your image below!). Is disordered sequence treated differently or just as Turn in Chimera?


I'll run this through the commandline with Jaime's pychimera (a real game changer for me!) so creating output files I'll probably just handle with piping STDOUT.


[cid:bae07725-f281-4ce3-a9f2-72666f911e0b]

Thanks,


Joe



Joe Healey


M.Sc. B.Sc. (Hons)
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Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk

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________________________________
From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: 10 October 2016 18:54:08
To: Healey, Joe
Cc: chimera List
Subject: Re: [Chimera-users] Computing 'basic' structure characteristics

On Oct 9, 2016, at 9:53 AM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

If you just want to look at predominance of secondary structures, you would not use those integers which mean first strand, second strand, first helix, etc.  Instead you could just see how many residues are already assigned as strand, helix, and coil.  There aren't commands to do this directly, only some very cumbersome approaches that I imagine are vastly inferior to using Python (like "select strand" and then writing a list of all those residues with "writesel" etc.).

I can't help with the Python side, this is just the perspective from the commands side. All the commands I mentioned are documented,
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>

To supplement this part of the answer, you can loop through a bunch of PDB files in Python as outlined here:

http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html

You can determine the fraction of residues in helix and sheet with code like this:

from chimera import openModels, Molecule

#... inside the loop...
for mol in openModels.list(modelTypes=[Molecule]):
sheet_fract = len([r for r in mol.residues if r.isSheet]) / len(mol.residues)
helix_fract = len([r for r in mol.residues if r.isHelix]) / len(mol.residues)
# write them to a file with "print>>f" or to the reply log with just "print"

The above assumes you have a little bit of familiarity with Python.  I can provide more explanation if you need it.

-Eric

Eric Pettersen
UCSF Computer Graphics Lab




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