From owner-chemistry \\at// ccl.net Thu Mar  5 06:59:00 2009
From: "Peter Schmidtke pschmidtke^mmb.pcb.ub.es" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: PDB file format : List of atom name / element type correspondance
Message-Id: <-38755-090305065521-6383-ccJjf5hqMvIjVPZk7weT9Q(_)server.ccl.net>
X-Original-From: "Peter  Schmidtke" <pschmidtke]|[mmb.pcb.ub.es>
Date: Thu, 5 Mar 2009 06:55:18 -0500


Sent to CCL by: "Peter  Schmidtke" [pschmidtke**mmb.pcb.ub.es]
Dear CCL subscribers,

I am looking for a list of atom names that occur in PDB files and their corresponding elements. Normally the PDB file convention says that the element has to be given explicitely in the column 77-78. Unfortunately, this is currently not systematically the case within the PDB and for PDB files saved with software packages (some commercial software I won't mention here and other packages).

Last, Softwares often change atom names before output, in order to encode program internal atom types. 

Is there any way to guess the element from the atom name or is there any translation list out there?

Thanks in advance.

Peter Schmidtke

----------------------
PhD Student at the Molecular Modeling and Bioinformatics Group
Dep. Physical Chemistry
Faculty of Pharmacy
University of Barcelona