Re: [modeller_usage] Retrieving full sequence from PDB file

Hello,

You can try the PDB module of the Biopython, it does it very
well.

http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf

How do I extract polypeptides from a Structure object?

Use PolypeptideBuilder. You can use the resulting
Polypeptide object to get the
sequence as a Seq object or to get a list of C  atoms as
well. Polypeptides can be built using a C-N or a C -C 
distance criterion.
Example:
# Using C-N
ppb=PPBuilder()
for pp in ppb.build_peptides(structure):
    print pp.get_sequence()

# Using CA-CA
ppb=CaPPBuilder()
for pp in ppb.build_peptides(structure):
    print pp.get_sequence()

Note that in the above case only model 0 of the structure is
considered by PolypeptideBuilder.
However, it is possible to use PolypeptideBuilder to build
Polypeptide objects from Model and Chain objects as well.
How do I get the sequence of a structure?
The first thing to do is to extract all polypeptides from
the structure (see previous entry). The sequence of each
polypeptide can then easily be obtained from the Polypeptide
objects. The sequence is represented as a Biopython Seq
object, and its alphabet is defined by a ProteinAlphabet
object.
Example:
> > > seq=polypeptide.get_sequence()
> > > print seq
Seq(?SNVVE...?, <class Bio.Alphabet.ProteinAlphabet>)



Best regards,
Romain 


----- Original Message -----
Expéditeur: sneha bairy <>
à: 
Sujet: [modeller_usage] Retrieving full sequence from PDB
file
Date: Mon, 7 Feb 2011 11:23:10 -0600

> Hello,
> For the project I am working on, I need all the sequence
> residues from the pdb file irrespective of whether the
> residues have atom information or not. I saw that there is
> a way to write out the residues with atom information from
> the pdb file. But is there a way to write out all the
> sequence residues mentioned at the top of the pdb file?
> 
> Thanks,
> Sneha
> 
> 
> _______________________________________________
> modeller_usage mailing list
> 
> https://salilab.org/mailman/listinfo/modeller_usage
> 

-----

Romain Studer
Dept of Structural and Molecular Biology
Darwin Building
University College London
Gower Street, WC1E 6BT London
Tel +44(0)20 7679 3890
Fax +44(0)20 7679 7193