[BioPython] Drawing Ramanchandran plot

[Peter]

Lee, Byung-chul wrote:
> Hi all,
> 
> During calculating the torsion angles of some atoms in PDB files, I want
> to draw the Ramanchandran plot of those.
> However, I cannot find any modules or methods of doing that in Bio.PDB,
> so if anyone knows where it is os how to make it, please inform me.
> 
> Thanks,
> Byung-chul.
> 

A work in progress:

http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/ramachandran/

Short summary about calculating the angles:
* MMTK is great, providing it can load the PDB file.
   Very very easy to get the angles
* BioPython's Bio.PDB will load most/al PDB files, but
   you have to work out the backbone and angles yourself.
* Python Macromolecular Library (mmLib) might also be worth looking at.

Once you have the angles, you will want to draw the plots - the link 
above suggests a package like Excel, R, or Peter Robinson's Java Program:

http://www.charite.de/ch/medgen/compgen/ramachandran/

Peter