[BioPython] filtering PDB files by resolution

Peter biopython at maubp.freeserve.co.uk
Tue Jul 10 12:03:15 UTC 2007


FFFFF AAAAA wrote:
> Hi,
> How to choose pdb files from Richardson Top500H pdbs with aresolution =< 1.00 Angstroms using python scripts.
> Thanks
> Fawzia

I've never had to look at the resolution itself, but the REMARK 2 lines 
in the header looks relevant. You may find it easiest to do this your 
self rather than using the Biopython module Bio.PDB as that focuses on 
the atomistic structure rather than the metadata.

Alternatively maybe you could take the list of PDB identifiers and your 
1.00 Angstroms, and put these into the www.pdb.org web query interface.

Peter

P.S.

There might be something useful here:
http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/ramachandran/top500/

Incidentally, are you working with original PDB files from www.pdb.org 
or the modified versions from the Richardson group which had hydrogens 
added with reduce?





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