[BioPython] bio.PDB module

[quantrum75]

Hi Peter,
  Thanks for your reply. I did go through the links which you made a mention of to me including the structural bioinformatics FAQ.  However, I feel the documentation pertaining to bio.PDB module is seriously short on any practical examples for a person like me who likes to learn from examples.
  I would love to be able to write a "getting started with bio.PDB" wiki or document with examples. However, I need to get the basic ideas on how to use the module which I am unable to from the current documentation which is why I made the request for a script which can compute the phi and psi angle of a pdb file.
  I ll see what I can do and if you could direct to any resources, that would be great.
  Thanks
  Rama

Peter <biopython at maubp.freeserve.co.uk> wrote:
  On Jan 11, 2008 12:16 AM, quantrum75 wrote:
> Hi
> I am a biopython newbie. I was wondering if someone could show me or send me
> ( I would be thankful) where I could find a script which can read a pdb file and out
> the phi and psi angles of the protein structure.

I see Byung chul has already suggested reading this page:
http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/ramachandran/calculate/

Do you think we should incorporate some that into the main Biopython
documentation?

> I have read through the bio.PDB module and structural module documentation,
> but still do not have an idea on how to proceed to tackle the problem. I wish the
> bio.PDB documentation was a bit more detailed and included some examples to
> work with.

Have you read the Biopython Structural Bioinformatics FAQ,
http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf
This is linked to from our documentation webpage, but doesn't seem to
me mentioned in the main Biopython Tutorial and Cookbook...

> I really would like to contribute to the project and maybe if I got an
> initial idea on how to work with the same, I can contribute in some small way.

Maybe you could start a "Getting started with Bio.PDB" page on the Wiki?

Peter


       
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