Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases

pdbpars parses PDB files and writes cleaned-up protein coordinate files.

Here is a sample session with pdbparse:

% pdbparse

Mandatory qualifiers:

[-pdb] (string)

Location of PDB files (PDB format input).

[-pdbextn] (string)

Extension of PDB files (PDB format input).

-nocamask (boolean)

The group will not appear in either the CO or SQ records of the clean coordinate file.

-nocamaska (boolean)

The amino acid will not appear in the CO record, but will still be present in the SQ record of the clean coordinate file.

-atommask (boolean)

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.

[-cpdb] (string)

Location of coordinate files (EMBL format output).

[-cpdbextn] (string)

Extension of coordinate files (EMBL format output).

-errf (outfile)

Name of log file for the build.

Optional qualifiers:

-chnsiz (integer)

Minimum number of residues in a chain for it to be parsed.

Advanced qualifiers:

-[no]cpdbnaming (boolean)

Use pdbid code to name files.

-maxmis (integer)

Maximum number of permissible mismatches between the ATOM and SEQRES sequences.