[Chimera-users] How can I calculate RMSD with chimera script

Michał Kadlof ramidas at gmail.com
Tue May 19 01:16:39 PDT 2015


I have a need of calculating about 1000 of RMSDs between two particular
regions of reference model and testing model. I would like to do this with
chimera script. I'm using chimera-1.10.1-Headless Linux 64-bit and have no
access to any GUI.

Currently my script looks like this:

import sys, os, re
from chimera import runCommand as rc

<< not important stuff >>

rc("open %s" % (native))
for i in models:
    rc("open " + i)
    rc("rmsd #0:{0}-{1} #1:{0}-{1}".format(s,k))
    rc("close #1")

rc("close all")
rc("stop now")

This allow me to see output on the screen, but I don't know how to capture
it for further processing. I found somewhere something like this:

from chimera.tkgui import saveReplyLog
<< do something >>

But it seem to work only in versions with GUI.

Please help.

best whishes
Michał Kadlof

University of Warsaw
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