[Biopython] polypeptide residue ids

[João Rodrigues]

The Peptide Builder serves for much more than generating sequenes. However,
having the SMCRA representation of the model is much handier (IMO) to get
this kind of information.

I'm not really sure if I answered your question though..

João [...] Rodrigues
http://doeidoei.wordpress.com



On Fri, Nov 19, 2010 at 9:31 PM, km <srikrishnamohan at gmail.com> wrote:

> Thanks. that works well.
> but why have polypeptide builder for generating the sequence ?
> ppb.get_sequence() ?
> when we can do the same by reading the residues under chain of the
> structure hierarchy as u suggested?
>
>
> On Sat, Nov 20, 2010 at 12:24 AM, João Rodrigues <anaryin at gmail.com>
> wrote:
> > Hello KM,
> >
> > You can iterate over the chains as described in the manual and then for
> each
> > residue call get_id().
> >
> > for residue in structure.get_residues():
> >    print residue.get_id()[1]
> >
> > Best
> >
> > João [...] Rodrigues
> > http://doeidoei.wordpress.com
> >
> >
> >
> > On Fri, Nov 19, 2010 at 7:43 PM, km <srikrishnamohan at gmail.com> wrote:
> >>
> >> Hi all,
> >> I would like to derive amino acid ids (number) corresponding to the
> >> residues in polypeptide chains extracted from PDB file using biopython
> >> PDB module.
> >> Is it possible to obtain this information with PDB module of biopython ?
> >>
> >> regards,
> >> KM
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> >> http://lists.open-bio.org/mailman/listinfo/biopython
> >
> >
>