[Chimera-users] Chimera input from command line

José Almeida jose.gcp.almeida at gmail.com
Thu Sep 15 07:10:53 PDT 2016

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,

On Wed, Sep 14, 2016 at 9:05 PM, Eric Pettersen <pett at 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 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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