From herrmann@hermes.informatik.uni-stuttgart.de Thu Oct 24 11:11 EDT 1996
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Date: Thu, 24 Oct 1996 17:08:49 +0200
Message-Id: <199610241508.RAA13871@odysseus.informatik.uni-stuttgart.de>
From: Frank Herrmann 
To: jkl@ccl.net
Subject: script for conversion from car to pdb
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Status: RO


Dear Jan,

I wrote a script to convert Insight car/mdf files to pdb files. I
think it may be useful for other people. Maybe you can install them in
your software archive or repost it to the list. Find attached the
installation instructions, the motivation for writing the scripts and
the scripts.

with best regards,

-- 
--------------------------------------------------------------
       Frank Herrmann, Computer Scientist, PhD Student
Institute of Parallel and Distributed High-Performance Systems
             (IPVR) University of Stuttgart
                Breitwiesenstrasse 20-22
              D-70565 Stuttgart  (Germany)
       Tel: (49) 711-7816-358, FAX: (49) 711-7816-250
    email: Herrmann@odysseus.informatik.uni-stuttgart.de

INSTALLATION

1) copy the files

	- car2pdb.csh
	- car2pdbatom.awk
	- mdf2connect.awk
	- name2number.awk

to a directory in your path.
e.g. create ~/bin and add it to your path in ~/.cshrc
add execute permission: chmod +x car2pdb.csh ...

2) Change the path of nawk in the first line "!#..." of the awk scripts.

3) Uncomment the line 
	set var = #"-v"
in car2pdb.csh if your nawk needs to precede command line variables by -v

LIMITATIONS

Only H N C O S L (lone pair) atomic species are recognized

Atom names in car files of non protein structures often do not conform
to the IUPAC rules or do not indicate the atomic species in the first
two characters of the four character atom name field as required by
the pdb format. The atoms (H N C O S L) are therefore renamed if
necessary.

MOTIVATION

I wanted to create 2-dimensional structure plots with atoms labeled
with numbers using csed from the cactvs system. It can read pdb
files. I also wanted to view the structures using xmol and
rasmol. Both Insight and babel generated pdb files that didn't
work. Insight changed the atom numbering and didn't generate CONECT
records. babel do not use a mdf file and therefore calculates distance
based connectivity that in my case was wrong.