[BioRuby] bio.pdb + biographics

[K. Shameer]

Dear Alex,

>> Infact I am specifically interested in
>> something that has not taktions to start wen up by any of the Bio-toolkit
>> libraries :).
>> Can we (Alex, Jan, all other bioruby pros and Shameer) work on to
>> develop a module that integrated both Bio.Pdb and Bio-Graphics module to
>> generate odular topology diagrams ? Please let me know your comments,
we >> can discuss and work on this :) !!!
> The parser reads the SHEET / HELIX / TURN records from the PDB file.
> I've never really played with them, but they look easily readable.

It is always better to get the structure information from DSSP/SSTRUC sort
of accessory files than the orginal PDB files. The secondory structure
information will be in detail in these accessory files. If it works well
with PDB, we can parse the  SHEET / HELIX / TURN as well.

>
> Going from there to an overall topology diagram (are you thinking of
> something like this:
> http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/1tca/domA01.gif)
>   is more complicated.
Yep, some thing similar and elaboraded. If it is available as a  module
the interactivity will be high. In PDBSum only domain based topology
diagrams are available. They are getting domain information from CATH. In
our module there should be many possibilities : user can define the
canvas, color the sec str, print residue no, residue details etc. The
module should also be able to plot different chains of a given protein as
well... (i think am all excited, am getting unlimited ideas ... :) )

> I guess the first step would be analysing the
> structure to see how the secondary structure elements interact and
> then applying some kind of layout algorithm (putting sheets side by
> side, etc...) Once you have the layout, using Bio-graphics, Cairo or
> something else to do the drawing is pretty straight forward (I assume!).

There you go - You are right. I think we can easily trace out the
structure layout from DSSP/SSTRUC file. I will talk to my Boss and get
back to you with details.
>
> I know Roman Laskowski, who runs PDBSum. So I could ask him how his
> topology generation script works - if that's the kind of thing you are
> thinking of.

That will be great !! I asked Roman Laskowski about the availability of
that program, thats not available for the public at the moment.

Thanks,
Shameer