[Biopython] Module Polypeptide

[Peter]

On Mon, Jun 8, 2009 at 11:25 PM, stanam bharat<bharat.s007 at gmail.com> wrote:
> Hi all
>
> I am new to Python and Biopython.I am trying to extract sequence from PDB
> file. As you stated in previous posts, i took help of biopdb_faq.pdf and
> used polypeptide module.
>
> In some PDB files like "3FCS" which has only 4 chains, but the resulting
> sequence has 14 chain pieces.Why is it? Is this problem with PDB files? Can
> I overcome this?

In some PDB files the stated chain can have gaps in it. I would guess
(and without seeing your code this is just a guess) that you have told
Bio.PDB to automatically break up the stated chains using the atomic
distances.

Can you show us how your code is loading the 3FCS PDB file?

Peter