CIF Applications. VIII. pdb2cif: Translating PDB entries into mmCIF format

Abstract

pdb2cif is a new version of an awk script originally written by P. E. Bourne in 1993 to translate from the 1992 Protein Data Bank (PDB) format to the then-emerging macromolecular Crystallographic Information File (mmCIF) definition. This new version of pdb2cif translates from all current PDB formats, including the 1992 PDB format and the 1996 PDB Atomic Coordinate Entry Format. Version 2.0, to the 1997 mmCIF format as defined in the mmCIF dictionary 1.0.00. The program is provided as an m4 script from which both perl and awk versions can be produced. The program identifies mmCIF entities implicitly by sequence homology among PDB SEQRES records. With minor additions to the dictionary, the resultant mmCIF data-sets are substantially compliant with the mmCIF 1.0.00 dictionary.