[Bioperl-l] Parsing PDB entries in BioPerl

[Sri Krishna S.]

> I also looked very quickly at some software packages (X-PLOR, dyana, swiss-pdb
> viewer) and PDB seems the only/preferred format.

That is generally true. You would also note that these software packages
either tend to eliminate that part of the PDB that dont confirm to
standards or worse dump core!
 > 
> So I guess it not a question about which format is best, but which
> format is used most.
Then you should be looking at a module that can readin pdbfiles and check
for errors and correct them if possible (make non-standard standard). 
My programmer started off writing one such module for me sometime
ago which I thought was decent for a start. However we didnt have much
time to pursue it. 
I can mail you the module/s or better still ask him to release it under
GNU if somebody tells me the best way it can be done.

I see lots of work going on with seqs but none really with PDB's. So I
guess the time has come...

krishna

> 
> Kris,
> -- 
> Kris Boulez 				Tel: +32-9-241.11.00
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*******************************************
Sri Krishna S.
Postdoctoral Researcher / Department of Biochemistry
U.T. Southwestern Medical Center at Dallas
5323 Harry Hines Blvd., Dallas, TX 75390-9038
Tel:(214)648-7119 (Office)     (214)772-9439 (Home) 
Fax:(214)648-9099
krishna@chop.swmed.edu
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