[Chimera-users] Measuring dihedral angles using chimera

[Elaine Meng]

Hi Aswani,
I can answer only part of the question.

For writing scripts to loop through multiple PDBs please see:
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

The script that you included gives specific residue numbers for the four atoms.  You would need to know the residue numbers for the CB-SG-SG-CB in each structure.  I’m not sure how you would get that or pass it in.  (also: the script has four different residue numbers, which doesn’t really make sense to me; if it’s really a disulfide dihedral you would just have two residue numbers, one cysteine CB,SG and the other cysteine SG,CB).

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 28, 2014, at 10:13 PM, Aswani Kumar Kancherla <ashwin2952 at gmail.com> wrote:

> ​Hello Chimera Users,
> ​
> ​I have recently installed chimera ​version 1.9 in Linux OpenSuSe 11.4 and am trying to get acquainted with its features.
> 
> I am trying to measure dihedral angles (specifically the angle chiSS defined by Cb-Sg-Sg'-Cb' about disulfide bonds) for a list of pdb files containing NMR structure ensembles. ​I was trying to ​do this using a script (kindly given by a friend and pasted below) to which I can pass the coordinates of the four atoms and get the measured values for the "reply log" information. 
> 
> ​I need to put the files in a directory called pdb_files, open ​chimera and call the script and retrieve information from the "reply log". However, there is a problem:
> 
> Since the coordinates of (Cb,Sg, etc ) will be different for each of the ensemble (since each ensemble is structure of a different molecule), I need to pass the coordinates dynamically for each pdbid. 
> 
> ​I have found from Chimera User group  archives that reply log can be saved using a function.
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003184.html
>  So that should solve one issue. I can save the reply log and parse it later.
> 
> ​What is the best way to ​m​easure specific dihedral angles from multiple pdb files? Is it possible to invoke ​ ​chimera in tty mode and make it execute functions? In that case, I could probably write a shell script​ to invoke chimera once for each pdb and ask it to execute python script having appropriate atom coordinates. 
> 
> I apologize for slightly long an e-mail. Any hints or directions to enable me figure out how to get this done efficiently in chimera will be of great help to me.
> 
> ​with regards,
> Aswani
> 
> ​script:
> ================================================================​
> 
> import os
> import Matrix
> from chimera import openModels, selection, runCommand
> 
> #angle #0:resno at CB :resno at SG :resno at SG :resno at CB  34.6289
> 
> 
> # Directory containing PDB files
> directory = 'pdb_files'
> 
> # Get paths to all files in the specfied directory 
> paths = [os.path.join(directory,f) for f in os.listdir(directory) if f.endswith('.pdb')]
> 
> for pdbfilename in paths:
>     filename = pdbfilename.split("/")[1]
>     openModels.open(pdbfilename, baseId = 0)  # Open as model #2
>     runCommand('angle #0:863 at CB :980 at SG :1130 at SG :1235 at CB')                  # calculate torsion angle
> 
>     runCommand('close #0')                  # close molecule and map
> ​=================================================================​
> 
> 
> 
> 
> -- 
> K.Aswani Kumar
> ​Graduate Student
> Molecular Biophysics Unit
> Indian Institute of Science
> Bangalore-560012
> Karnataka, India.
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