[Chimera-users] how to run the command line chimera without actually opening the GUI

[Elaine Meng]

Hi Nurul,
I think you can just use Chimera in nogui mode with a Chimera command file as input.  No programming is needed if there are commands to do what you want.  In this case, it sounds like the commands "open" (to open the input PDB files), "match" (or maybe instead "matchmaker"?) and "write" will do what you need.

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html>
 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>

First figure out the exact commands you would need, then put them in a plain text file, which is the Chimera command file.  If you just tried the commands by typing them in Chimera the regular way, you can save them to a text file from the Command History.

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/history.html>

>From terminal, you would run Chimera with the --nogui startup option and specify the command file as input.   Details on that:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/startup.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 20, 2011, at 2:05 AM, nurul wrote:

> Hello,
> I have two structures to superimpose using the match command in chimera. Once the structures are matched, I save the two models in one pdb file. I can then just view this pdb file whenever I want. My question is: can I somehow just do this using the terminal? Meaning the graphic of chimera doesn't launch, but I get the pdb file that has the correct rotation matrix of the two superimposed structures. I don't have much programming experience, and I have no knowledge of calculating rmsd. Would appreciate if someone would pinpoint me where to start. Thanks.
>