CCL: PDB file format : List of atom name / element type correspond

 Sent to CCL by: "Konrad  Hinsen" [hinsen^^cnrs-orleans.fr]
 On 05.03.2009, at 12:55, Peter Schmidtke pschmidtke^mmb.pcb.ub.es wrote:
 > I am looking for a list of atom names that occur in PDB files and their
 corresponding elements.
 For files that fully respect the PDB conventions, you can find all the
 information you need in the
 PDB format definition:
 	http://www.wwpdb.org/docs.html
 As you noted, recent versions of the PDB format conventions state that the
 element should be
 given explicitly in columns 77-78. For files conforming to older versions of the
 PDB format, you
 can obtain the element as the first two letters of the atom name. If the first
 letter is a digit, then
 you should use only the second letter (which must then be H).
 However, the real problem is that the vast majority of programs write PDB files
 that do not fully
 respect the PDB file format conventions. The summary of my ten-year experience
 in dealing with
 PDB files of various origins is that you can't rely on anything concerning atom
 and residue names.
 There is no way to avoid special treatments for files produced by specific
 programs.
 My advice is:
 1) If you only need to handle PDB files from a specific source, write code
 specifically for that variety
 of the PDB format and get on with your science.
 2) If you want to write a general tool that can handle a large variety of PDB
 files, use existing PDB
 parser and support libraries that do at least part of the nasty work.
 In the category of existing libraries, I'll mention my own which are written in
 Python:
 - Module Scientific.IO.PDB in Scientific Python:
 	http://dirac.cnrs-orleans.fr/ScientificPython/
 - Modules MMTK.PDB and MMTK.PDBMoleculeFactory in the Molecular Modelling
 Toolkit:
 	http://dirac.cnrs-orleans.fr/MMTK/
 --
 ---------------------------------------------------------------------
 Konrad Hinsen
 Centre de Biophysique Molculaire, CNRS Orlans
 Synchrotron Soleil - Division Expriences
 Saint Aubin - BP 48
 91192 Gif sur Yvette Cedex, France
 Tel. +33-1 69 35 97 15
 E-Mail: hinsen|cnrs-orleans.fr
 ---------------------------------------------------------------------