[Biopython-dev] [Bug 3166] Bio.PDB.DSSP fails to work on PDBs with HETATM

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Jan 5 18:08:24 UTC 2011


------- Comment #3 from macrozhu+biopy at gmail.com  2011-01-05 13:08 EST -------
Created an attachment (id=1557)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1557&action=view)
handle DSSP results on PDBs with HETATM, parse PHI and PSI angles

Hi, Peter,

The current version of DSSP can not handle some PDB files with HETATM in it.
e.g. 3jui. This can be illustrated by the following example:

> python DSSP.py 3jui.pdb
KeyError: (' ', 547, ' ')

Here is a patch file DSSP.py for addressing this problem.

In addition, PHI and PSI angles calculated by DSSP are useful in many cases.
Therefore, in this patch I also revised the code so that PHI and PSI angles in
DSSP output files are parsed and assigned to residue feature xtra.

hongbo zhu

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