[BioPython] SASA calculation
Peter
biopython at maubp.freeserve.co.uk
Fri Feb 27 15:30:12 UTC 2009
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
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