CCL: Automated standardization of atom names in PDB?

 Sent to CCL by: Nathan Baker []
You might try PDB2PQR: This will assign atom names, add missing atoms, etc.
 Good luck,
 CCL wrote:
 Sent to CCL by: Dr Seth Olsen [s.olsen1*|*]
 Hi CCLers,
 Does software exist that will take a PDB format file with non-standard
 atom names and determine the standard atom labelling for the atoms in a
file (if the file contains a protein with regular amino acid residues)?
 I have a PDB file that was run through a chemistry utility, and in the
 process the usual PDB labelling (i.e. CA, CB, HB etc.) was changed to a
 much less informative format.  The program also modified the structure
 in such a way that pasting the old names in to the appropriate field is
 not feasible.  To check all atoms would be time-consuming, but since
 most amino acids in the protein are unmodified, the correct atom
 labelling should be clear from the bond topology.  Is there a program
 that will read the topology and determine the standard atom names?
 Dr Seth Olsen, PhD
 Postdoctoral Fellow, Biomolecular Modeling Group
 Centre for Computational Molecular Science
 Chemistry Building,
 The University of Queensland
 Qld 4072, Brisbane, Australia
 tel (617) 33653732
 fax (617) 33654623
Web: ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms>
 Nathan Baker, Assistant Professor
 Washington Univ., Dept. of Biochemistry and Molecular Biophysics