On Apr 27, 2010, at 3:14 PM, Scott Classen wrote:

Hi all, I have a number of PDB files that I would like to open, run a buriedArea calculation, save the results to a file, and exit

I can put a bunch of commands in a file and launch it from a terminal shell

chimera --nogui --nostatus --script calculate_buriedArea.com > results.txt

the calculate_buriedArea.com file looks like this:

open my.pdb measure buriedArea #0:.A #0:B

This works, but is a bit cumbersome. I would like to make a python script so I can call my calculation with the name of the PDB file on the command line like this:

chimera --nogui --nostatus --script calculate_buriedArea.py -- my.pdb

.... so can someone please get me started here?

import chimera myfile = chemera.somefunctiontoopenaPDBfile($1)

Hi Scott, For the relatively simple scripting you're describing I don't think you really need the --script argument. You can basically run Chimera like this: chimera --nogui --nostatus my.pdb calculate_buriedArea.py Chimera will open the PDB file normally and then run your script. You only really need to use --script when you need to pass arguments to the script that Chimera shouldn't process. So, with above command line the PDB file will be open when your script runs. In fact, it doesn't seem like you actually need a Python script. You could just use your .com script (minus the "open" command): chimera --nogui --nostatus my.pdb calculate_buriedArea.com > results.txt or some such. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu