pdbpars parses PDB files and writes cleaned-up protein coordinate files.
Here is a sample session with pdbparse:
% pdbparse
Location of PDB files (PDB format input).
Extension of PDB files (PDB format input).
The group will not appear in either the CO or SQ records of the clean coordinate file.
The amino acid will not appear in the CO record, but will still be present in the SQ record of the clean coordinate file.
The amino acid will appear not appear in the CO record but will still be present in the SQ record of the clean coordinate file.
Location of coordinate files (EMBL format output).
Extension of coordinate files (EMBL format output).
Name of log file for the build.
Minimum number of residues in a chain for it to be parsed.
Use pdbid code to name files.
Maximum number of permissible mismatches between the ATOM and SEQRES sequences.