[Chimera-users] help with simple python script

Scott Classen sclassen at lbl.gov
Tue Apr 27 15:14:14 PDT 2010

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)


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