Hi Chris, And if you feel you still need to use Python (for looping perhaps) then you should look at the Chimera Programmer's Guide, particularly the examples and the FAQ. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 7, 2009, at 12:18 PM, Elaine Meng wrote:

Dear Chris, I can't answer about Python, but you may be able to do what you want using Chimera command scripts. There is a rich set of commands, and the same commands you would enter at the command line can be placed in a text file. Simply opening that command file in Chimera will execute all the commands.

Chimera command documentation for the current daily build: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>

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

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

On Apr 7, 2009, at 11:11 AM, christopher lau wrote:

...

Dear Madam/Sir

I am new to Chimera and this forum so I apologize in advance if I my question is inappropriate. I want to start writing python scripts such that I can run the script and the color code, orientation, etc of the molecule opened can be automated. Do you know of any good tutorials that teach what commands are available to use in python for chimera and how to run some basic python scripts in chimera? I have figured out enough to open the Python Shell in Chimera, but that is all. An example python script would be helpful.

Thanks everyone,

Chris Lau _

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