Chapter

Chapter 3.6 Classification and use of macromolecular data

Definition and exchange of crystallographic data

First Online Edition (2006)

Part 3. CIF data definition and classification

  1. P. M. D. Fitzgerald1,
  2. J. D. Westbrook2,
  3. P. E. Bourne3,
  4. B. McMahon4,
  5. K. D. Watenpaugh5,
  6. H. M. Berman6

Published Online: 1 JAN 2006

DOI: 10.1107/97809553602060000738

International Tables for Crystallography

International Tables for Crystallography

How to Cite

Fitzgerald, P. M. D., Westbrook, J. D., Bourne, P. E., McMahon, B., Watenpaugh, K. D. and Berman, H. M. 2006. Classification and use of macromolecular data. International Tables for Crystallography. G:3:3.6:144–198.

Author Information

  1. 1

    Merck Research Laboratories, Rahway, New Jersey, USA

  2. 2

    Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA

  3. 3

    Research Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA

  4. 4

    International Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England

  5. 5

    retired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA

  6. 6

    Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA

Publication History

  1. Published Online: 1 JAN 2006

Abstract

The macromolecular CIF (mmCIF) dictionary is a major extension of the core CIF dictionary designed to provide data names to be used in a machine-readable description of a macromolecular structure determination experiment and the derived structural model. To allow a complete and self-consistent account of a macromolecular structure at various levels of detail, the dictionary has been implemented in the relational dictionary definition language DDL2. It includes the data items defined in the core CIF dictionary. mmCIF supersedes an older file format of the Protein Data Bank (PDB), and therefore includes a representation of all the information historically archived at the PDB. In addition, it provides data items suitable for use in: a journal ‘materials and methods’ article; descriptions of biologically active molecules and any important subcomponents; descriptions of crystallographic and noncrystallographic symmetry; information about the chemistry and geometry of monomer components of macromolecules, and of any ligands or small-molecule complexes; and descriptions of functional and structural aspects of macromolecules.

Keywords:

  • atom sites;
  • atom properties;
  • bond angles;
  • bond distances;
  • bond types;
  • category groups;
  • chemical components;
  • chemistry;
  • connectivity;
  • macromolecular Crystallographic Information File;
  • mmCIF dictionary;
  • data collection;
  • disorder;
  • experimental measurements;
  • geometry;
  • hydrogen bonds;
  • instrumentation;
  • intensity measurements;
  • reflection measurements;
  • interatomic contacts;
  • macromolecular structure;
  • molecular geometry;
  • noncrystallographic symmetry;
  • secondary structure;
  • macromolecular sequence;
  • phasing;
  • Protein Data Bank;
  • R factors;
  • bond valence;
  • databases;
  • software;
  • computer programs;
  • citations;
  • metadata;
  • publishing;
  • refinement;
  • space-group information;
  • structural models;
  • structure analysis;
  • symmetry;
  • torsion angles