International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 3.6, pp. 144-145

Section 3.6.2. Considerations underlying the design of the dictionary

P. M. D. Fitzgerald,a* J. D. Westbrook,b P. E. Bourne,c B. McMahon,d K. D. Watenpaughe and H. M. Bermanf

aMerck Research Laboratories, Rahway, New Jersey, USA,bProtein 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,cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and fProtein 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
Correspondence e-mail:  paula_fitzgerald@merck.com

3.6.2. Considerations underlying the design of the dictionary

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From the outset, mmCIF was envisaged as a providing a more detailed description of macromolecular structures than the existing Protein Data Bank (PDB) format (Chapter 1.1[link] ). A number of considerations guided the development of version 1 of the mmCIF dictionary. These included:

(i) Every field of every PDB record type should be represented by an mmCIF data item if the PDB field is important for describing the structure, the experiment that was conducted in determining the structure or the revision history of the entry. It is important to note that it is straightforward to convert an mmCIF data file to a PDB file without loss of information, since all the information is parsable. It is not possible, however, to automate completely the conversion of a PDB file to an mmCIF, since many mmCIF data items are either not present in the PDB file or are present in PDB REMARK records that in some cases cannot be parsed. The contents of PDB REMARK records are maintained as separate data items within mmCIF so as to preserve all the information, even if the information is not parsable.

(ii) Data items should be defined so that all the information given in the materials and methods section of an article describing the structure can be referenced. This includes major features of the crystal, the diffraction experiment, the phasing calculations and the refinement.

(iii) Data items should be provided for describing the biologically active molecule and any important structural subcomponents.

(iv) It should be possible to represent atom positions using either orthogonal ångström or fractional coordinates.

(v) Data items should be provided for describing the initial experimental reflection data, including all the data sets used in the phasing of the structure, and the final processed data.

(vi) Crystallographic and noncrystallographic symmetry should be described.

(vii) Data items should be present for describing the characteristics and geometry of canonical and non-canonical amino acids, nucleotides, sugars and ligand groups.

(viii) Data items should be provided that permit a detailed description of the chemistry of the component parts of the macromolecule to be given.

(ix) Data items should be present that provide specific pointers from elements of the structure (e.g. the sequence, bound inhibitors) to appropriate entries in publicly available databases.

(x) Data items should be present that provide meaningful three-dimensional views of the structure so as to highlight functional and structural aspects of the macromolecule.

(xi) Data items specific to an NMR experiment or modelling study would not in general be included in version 1. However, data items that summarize the features of an ensemble of structures and permit a description of each member of the ensemble to be given should be available.

(xii) A comprehensive set of data items for providing a higher-order structure description (for example, to cover super­secondary structure and functional classification) was considered to be beyond the scope of version 1.

Based on the above, the first version of the mmCIF dictionary with approximately 1700 data items (including those data items taken from the core CIF dictionary) was developed and officially approved in October 1997. Subsequent revisions have increased the number of data items to over 2000. It is not expected that all the data items will be present in every mmCIF data file. Instead, the goal was to provide a wide range of data items from which users can select those that best suit the structure they wish to describe.








































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