Hello,

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 >>

saveReplyLog('replyLog.txt')

But it seem to work only in versions with GUI.

Please help.

best whishes

Michał Kadlof

University of Warsaw