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Dictionary Resources

The Protein Data Bank (PDB) uses macromolecular Crystallographic Information File (mmCIF) data dictionaries to describe the information content of PDB entries. The PDB Exchange data dictionary consolidates content from a variety of crystallographic dictionaries including: the IUCr Core, mmCIF, Image and symmetry dictionaries. The PDB Exchange Dictionary also includes extensions describing NMR, Cryo-EM, and protein production data. PDB data processing, data exchange, annotation, and database management operations all make heavy use of the data format and the content of the PDB Exchange Dictionary. Software tools are used to convert mmCIF data files to the older PDB format and to PDBML/XML.

• mmCIF/PDBx example files for PDB entries containing large structures
• Data files in mmCIF format can be downloaded from the RCSB PDB website or by ftp.
• Software tools are available for preparing and editing depositions.
• Software tools are available for converting mmCIF data files to PDB and PDBML formats
• A complete list of PDB software tools for managing PDB data in mmCIF format can be found here.

Dictionary Content and Representation

• Background and Introduction about mmCIF
• Chapter 3.6. Classification and use of macromolecular data. (PDF) in International Tables for Crystallography G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. 2005, Springer: Dordrecht, The Netherlands. p. 144-198.
• Appendix 3.6.2 The Protein Data Bank exchange dictionary (PDF) in International Tables for Crystallography G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. 2005, Springer: Dordrecht, The Netherlands. p. 195-198.
• Chapter 4.5. The Macromolecular dictionary (mmCIF) in International Tables for Crystallography, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. (2005) Springer: Dordrecht, The Netherlands. pp. 295-443.
• The Macromolecular Crystallographic Information File (mmCIF) Meth. Enzymol. (1997) 277, 571-590.
• STAR/mmCIF: An Extensive Ontology for Macromolecular Structure and Beyond (PDF) Bioinformatics (2000) 16(2), 159-168.
• mmCIF Software Developers Workshop 1997
• mmCIF Dictionary Templates
• mmCIF Examples
• References

Data Dictionaries

• PDB mmCIF Exchange Dictionary supporting PDB Data File Format V3.3 | (ASCII)| (compressed) | (HTML) | XML Schema |
  Data dictionary developed as a collaboration between PDBe, PDBj and RCSB and used by wwPDB members for data exchange.


• PDB mmCIF Exchange Dictionary supporting PDB Data File Format V3.2/3.15 | (ASCII)| (compressed) | (HTML) | XML Schema |
  PDB exchange data dictionary frozen at version 1.0697.


• PDB mmCIF Exchange Dictionary supporting PDB Data File Format V3.1 | (ASCII) | (compressed) | (HTML) | XML Schema |
  PDB exchange data dictionary frozen at version 1.0524.


• mmCIF Dictionary | (ASCII) | (compressed) | (HTML)
  IUCr Standard Dictionary
  Originial working group members: Paula M. Fitzgerald, Helen Berman, Phil Bourne, Brian McMahon, Keith Watenpaugh, and John Westbrook
  


• DDL2 Dictionary | (ASCII) | (compressed) | (HTML) |
  Syd Hall and John Westbrook


• 3D EM Extension Dictionary | (ASCII) | (compressed) | (HTML) |
  Community extension data dictionary describing 3D EM structure and experimental data to be deposited in the EMDB and PDB databases.


• 3D EM Exchange Dictionary | (ASCII) | (compressed) | (HTML) |
  Development version of the 3D EM data dictionary for program to program data exchange.


• NMRSTAR Dictionary | (ASCII) | (compressed) | (HTML) |
  NMRSTAR data dictionary developed by the BioMagResBank


• imgCIF/CBF Extension Dictionary | (ASCII) | (compressed) | (HTML)|
  Andy Hammersley, Herbert J. Bernstein, I. David Brown, and John Westbrook


• BIOSYNC Extension Dictionary | (ASCII) | (compressed) | (HTML) |
  Anne Kuller and John Westbrook


• MDB Modeling Extension Dictionary | (ASCII) | (compressed) | (HTML) |
  Alexei Adzhubei and Eugenia Migliavacca


• Provisional Symmetry Extension Dictionary | (ASCII) | (compressed) | (HTML) |
  I. David Brown, Editor


• CCP4 Harvest Extension Dictionary | (ASCII) | (compressed) | (HTML) |
  Data dictionary developed by CCP4 in collaboration with EBI for data harvesting.

Proposed Data Items for Structural Genomics Depositions

• Proposed data items for X-ray structure determinations
• Proposed data items for NMR structure determinations
• Proposed data items for protein production

Format Correspondences

• Recommended PDB->mmCIF data item correspondences V3.3
• Recommended PDB->mmCIF data item correspondences V3.2
• Recommended PDB->mmCIF data item correspondences V2.3

• Tutorials from the mmCIF Software Developers Workshop 1997

Related Sites

• RCSB mmCIF Software Tools site
• RCSB PDBML Resource site
• CIF page at the IUCr

 

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