UPDB

Malcolm Gillies gillies@cmcind.far.ruu.nl
Fri, 28 Aug 1998 12:19:49 +0200


> I've been working on what I hope to be my last PDB parser.
> (I've been told by several people that I'm ambitious :)

I'm very curious to see how this pans out. I wouldn't like to
think too hard about how much time I've spent fiddling around
with PDB files.

What did you have in mind with regard to support of the various
mutations of the PDB format which are read and written by various
modelling programs? Most of the misery I've had to deal with has
been a result of the quirks of the PDB handling in programs such
as Insight, Sybyl, DelPhi, GRASP etc.

Unfortunately this would seem to be a never-ending battle, given
subtle differences in standard atom naming, use of occupancy and
B factor fields, number of significant characters in the atom and
residue names, formats for chain capping, etc.

Still, a configurable parser generator is a step in the
right direction. I'm looking forward to further developments.

cheers,

Malcolm
--
Malcolm Gillies <M.B.Gillies@pharm.uu.nl>
PhD student, computational medicinal chemistry
Dept Medicinal Chemistry, Faculty of Pharmacy
Utrecht University, The Netherlands