[Biopython] polypeptide residue ids

[Rodrigo Faccioli]

Hi,

I'm not sure if my answer will be correct. Anyway, I'll try to write it.

I believe the Peptide Builder works with atoms section to build the
sequences. Therefore, if your atoms section has not all atoms of all
residues they will not appear correctly.

I have been worked with seqres section on pdb. More specific I have studied
the biopython pdb module and I tried to add it in SMCRA representation.
However, this moment I don't have time to talk with Biopython project
because I have to work with my Ph.D project. Anyway, if you want to test
this project, please see [1]. In this project, there is a script  to split
pdb in chains.

[1] https://github.com/rodrigofaccioli/ContributeToBioPython

I hope you enjoy it.

Best regards,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5


--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5


On Fri, Nov 19, 2010 at 6:35 PM, João Rodrigues <anaryin at gmail.com> wrote:

> 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
> > >> _______________________________________________
> > >> Biopython mailing list  -  Biopython at lists.open-bio.org
> > >> http://lists.open-bio.org/mailman/listinfo/biopython
> > >
> > >
> >
>
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