[Biopython] Bio.PDB and Bio.SeqIO.PdbIO

[Peter Cock]

On Fri, Feb 20, 2015 at 2:28 PM, Tiago Antao <tra at popgen.net> wrote:
> Hi,
>
> I am trying to get around the relationship between Bio.PDB and
> Bio.SeqIO.PdbIO, lets see if I got this right:
>
> 1. Bio.PDB is quite limited in terms of what records it can parse. For
> example I cannot get to SEQRES or anything related to secondary
> structure (SHEET, HELIX)?

Bio.PDB ought to give you everything on the coordinate data,
although the PDB header lines are on the tricky side (which if
memory serves is where the SHEET and HELIX lines lie?).

> 2. PdbIO allows to extract the protein sequences from SEQRES

The "pdb" support via Bio.SeqIO is very limited and focusses
just on the protein sequences.

Peter