Hello all,

I am much obliged for the information, I will try it as soon as possible. The information seems to be just what I needed. The problem was that I was trying to work around the creation of a new file, but if it is the only way I will give it a try.

Thank you very much for the time,
All the best,
José

On Wed, Sep 14, 2016 at 9:05 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Jose,
All Elaine’s info is correct.  In case your question was about using Chimera functions from your own Python interpreter, see this recent chimera-users thread:

http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-September/012704.html

—Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Sep 14, 2016, at 11:02 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

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:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/startup.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/options.html>

Input file types including Chimera command files and Python scripts:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#command>

Basic primer on Python scripting for Chimera:
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

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
-----
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@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


_______________________________________________
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu
Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users