[Chimera-users] Computing 'basic' structure characteristics

[Eric Pettersen]

Hi Joe,
	Back in the day, when that diagram was created, the PDB had TURN records which defined the location of various specific turn types (hairpin, etc.).  That’s what “isTurn” indicated, not just all non-helix/sheet.  Eventually the PDB dropped support for TURN records, and the isTurn attribute went the way of the dodo — we removed it.

—Eric

> On Oct 11, 2016, at 2:29 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk> wrote:
> 
> 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.
> 
> <pastedImage.png>
> Thanks,
> 
> Joe
> 
> 
> Joe Healey
> 
>                                         
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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 <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 <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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