Protein Data Bank format

Codename: pdb

Contents

• PDB format
• Reference

PDB format

• Title section:
  • HEADER contains the following fields: classification="PROTEIN" (or imported value), date, idCode="NONE" (or imported value).
  • TITLE, SOURCE, KEYWDS, EXPDTA: The imported value is exported. Default: "NULL".
  • COMPND: The imported value is exported. Default: "MOLECULE: name", where "name" is the molecule name.
  • AUTHOR: The imported value is exported. Default: "Marvin".
  • REVDAT: The following line plus the imported value.
    REVDAT   N   DD-MMM-YY         3
    (N is the modification number, DD-MMM-YY is the date of the modification.)
• Coordinate section:
  • ATOM and HETATM: The atom name includes the remoteness indicator and the branch designator character in case of amino acids. For non-standard residues, the atom name and the element symbol field contain the same value. The occupancy and the temperature factor are zero. The residue field contains one of the standard residue symbols.
• Connectivity section:
  • CONECT: Only the first five fields are used. If the number of bonds is greater than four, a second CONECT line with the same atom serial number (first field) will be used.
  • TER: Indicates the end of a chain. Imported but not exported in the current version.
• Bookkeeping section:
  • MASTER

Export options can be specified in the format string. The format descriptor and the options are separated by a colon.

...	Basic options for H atom adding/removal.
-c	Do not write connections in output. Example: "pdb:-c"

• Bond orders are not stored. Marvin guesses unknown bonds from valence rules.
• Query properties cannot be stored in PDB files.

• The exporter writes the atoms in the molecule object's internal atom order which may be different from the order of residues in a chain. Thus export is still not reliable for macromolecules with residues.
• Import can be very slow (time ~ n²) for large molecules if the file does not have CONECT records. It will be improved in a future version.

Reference:

• Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description