[BioPython] SASA calculation

[Peter]

On Fri, Feb 27, 2009 at 3:16 PM, Bala subramanian
<bala.biophysics at gmail.com> wrote:
> Friends,
>
> I want to open a pdb file, calculate the solvent accessible surface area for
> each atom and write a new pdb with SASA as the last column of the pdb. Your
> inputs would be highly helpful for me.

Hi Bala,

Have a look at the example script hsexpo to see if there is anything
useful to you (e.g. writing out a PDB file containing extra data).
This is the source code archive but there was a bug fixed since we
released Biopython 1.49.  You can just download the latest version
from here:
http://biopython.org/SRC/biopython/Scripts/Structure/hsexpo
or:
http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Scripts/Structure/hsexpo?cvsroot=biopython

I would also look at the Bio.PDB.NACCESS module in Biopython - this
acts as a wrapper for the command line tool NACCESS,
http://www.bioinf.manchester.ac.uk/naccess/

Peter