[Chimera-users] Chimera input from command line

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 14 11:02:08 PDT 2016

Hi Jose,
You can create an input test file that is a script with a series of instructions in either Chimera commands or Python, and then from the command line, start Chimera in nogui mode and specify that input file.

Startup from system command line, see also  - -nogui startup option:

Input file types including Chimera command files and Python scripts:

Basic primer on Python scripting for Chimera:

Some possible reasons to use Python instead of Chimera command scripts are if you need looping, or some function that is not available as a Chimera command.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 10, 2016, at 6:45 PM, José Almeida <jose.gcp.almeida at gmail.com> wrote:

> Hello,
> I am a beggining Chimera user and was wondering if it was possible to run, all in the same command, something that enabled me to use a function (e.g. hbonds) without utilizing the console or the gui. I am trying to include this into a program so that I can calculate H-Bond data on several proteins in order to automatize the procedure, but I haven't been able to do so.
> Already thanking any attention given to this problem,
> Best regards,
> José Guilherme de Almeida

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