[Chimera-users] Measuring dihedral angles using chimera
Aswani Kumar Kancherla
ashwin2952 at gmail.com
Thu Aug 28 22:13:59 PDT 2014
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
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.
So that should solve one issue. I can save the reply log and parse it
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.
*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
*for pdbfilename in paths:*
* filename = pdbfilename.split("/")*
* 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*
Molecular Biophysics Unit
Indian Institute of Science
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