On Mar 5, 2009, at 12:21 PM, Drew Bryant wrote:

Currently I'm using a non-gui daily build of Chimera for 64-bit Linux
and calling the chimera binary via the shell (which works), but I need
to be able to pass parameters to the script being run at the command
line.

I'm hoping others will chime in with regard to the errors you got when trying to import chimera modules into a standalone Python, but specifically in regard to the above you can pass arguments to your script if you tell Chimera it's a script (rather than a session file, say) by using the --script flag. Here's the pertinent info from the Chimera documentation:

--script script.py
Put all unprocessed arguments into sys.argv for the script to handle. The end of arguments for Chimera can be indicated with --. For example,
chimera --nogui --nostatus --script myscript.py -- -p 1jhg -r 1.8
would pass the arguments -p 1jhg -r 1.8 to the script. See the Programmer's FAQ for more details. See also the commandrunscript.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

http://www.cgl.ucsf.edu