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

[Eric Pettersen]

Hi Michał,
	Redirecting output from a program into a file is pretty easy in any Unix/Linux shell.  This would redirect Chimera's non-error output into a file named "chimera-output.txt":

	chimera chimera-arguments-you-normally-use > chimera-output.txt

You can also redirect the error output, but the syntax for that depends on the shell you are using.  You should be able to easily Google it if you need to do that.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On May 19, 2015, at 1:16 AM, Michał Kadlof <ramidas at gmail.com> wrote:

> 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
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> Chimera-users at cgl.ucsf.edu
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