[BioPython] Extracting residue list from PDB

[thamelry at binf.ku.dk]

> SEQRES and ATOM records have different semantics: the SEQRES is what
> the crystallographer puts into the experiment, the ATOM records is
> what she sees. Presumably you have covalent chain-breaks between
> residues, or parts of the polypeptide chain were not traceable in
> electron density and were omitted.
>
> So even though they numbers are inconsistent, they are both right.

That's correct. The discussed code locates all the connected peptide
fragments in the structure and returns their sequences. Connectivity
is evaluated by looking for proper peptide bonds between consecutive
residues.

If you want to get the sequence of the whole protein you can
take a look at the SEQRES record or use some kind of database
info.

Cheers,

-Thomas