Subject: Re: Problem in reading PDB files

From: "Simon Kilvington" <[email-masked]>
Date: Fri, 8 Dec 1995 16:42:34 +0000 (GMT)

> 
> Have you ever used SYBYL? During the last few days, I was astonished to 
> find SYBYL does have problem in reading PDB files. Let me elaborate now.
> 
[troubles with aromatic atoms deleted]

	the problem is PDB files don't have any data explicitly stored
in them about bond orders and atom hybridisations.  As the PDB format
was initially designed to store protein structures it was assumed that
all the molecules would be composed of only atoms in the twenty common
amino acids.  Therefore the residue field ie (TRP, PRO, etc) is used to
look up a template which describes the connectivity [and bond type?].

	now people are using PDB as a general molecule format and this
causes problems. 

	there should be no reason to use PDB files for storing general
molecular structures because there are already *far* too many chemical
structure file formats and most of these allow you to store connectivity,
bond order, and hybridisation information.

	if I were you I would use a file format like MOL2 - this is text
based, free format, and capable of storing a wide variety of information. 

	even if you need to import your structure files into a program
that doesn't support MOL2 files you can use the invaluable program BABEL
to convert it. 

	I think a standard molecule file format is needed.  What
happened to the chemical MIME type? is this still being designed or is
it all agreed on yet?

--
Simon Kilvington, [email-masked]