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

measure 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@CB :resno@SG :resno@SG :resno@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@CB :980@SG :1130@SG :1235@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.