CCL: Automated standardization of atom names in PDB?

[Nathan Baker <baker---biochem.wustl.edu>]

 Sent to CCL by: Nathan Baker [baker---biochem.wustl.edu]
You might try PDB2PQR:  http://agave.wustl.edu/pdb2pqr.  This will
 assign atom names, add missing atoms, etc.
 Good luck,
 Nathan
 CCL wrote:
>  Sent to CCL by: Dr Seth Olsen [s.olsen1*|*uq.edu.au]
>  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?
>  Cheers,
>  Seth
>  ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
>  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
>  email: s.olsen1---uq.edu.au
> Web: www.ccms.uq.edu.au
>  
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>  
>  
 --
 Nathan Baker, Assistant Professor
 Washington Univ., Dept. of Biochemistry and Molecular Biophysics
 <http://cholla.wustl.edu/>;