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.