[Chimera-users] Chimera input from command line

Eric Pettersen pett at cgl.ucsf.edu
Wed Sep 14 13:05:14 PDT 2016

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:



	Eric Pettersen
	UCSF Computer Graphics Lab

> On Sep 14, 2016, at 11:02 AM, Elaine Meng <meng at 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 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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