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, p. 144

Section 3.6.1. Introduction

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

3.6.1. Introduction

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As described in Chapter 1.1[link] , the macromolecular crystallographic information file (mmCIF) dictionary (Fitzgerald et al., 1996[link]; Bourne et al., 1997[link]) was initially commissioned as an extension to the core CIF dictionary (Hall et al., 1991[link]), with the intention of adding data names suitable for a full description of a macromolecular crystallographic experiment and its results. However, the need to specify relationships between the data items describing different components of a complex macromolecular structure led to the development of a richer dictionary definition language (DDL2). The data names were then defined according to the DDL2 formalism. For consistency, the existing core dictionary data items were also recast in the DDL2 formalism. Since no other DDL2 applications were envisaged at that time, the core items were then embedded in the mmCIF dictionary as a subset of the complete dictionary. The current release of the mmCIF dictionary described in this chapter includes all the data items in version 2.3.1 of the core dictionary. The mmCIF dictionary is not routinely updated to match additions to the core dictionary, but it is expected that when new versions of the mmCIF dictionary are released to meet the requirements of the macromolecular community, the most recent version of the core dictionary will be incorporated in the new mmCIF dictionary as part of the revision.

The resulting stand-alone dictionary is very large and is described in detail in this chapter. The philosophy behind the design of the dictionary is discussed in Section 3.6.2[link] and an example of its use is given and discussed in Section 3.2.3[link] . The contents of the dictionary are then described in the remainder of the chapter, starting at Section 3.6.4.[link] The discussion follows the sequence of Table 3.1.10.1[link] : experimental measurements, analysis, structure, publication and file metadata are considered in turn. The discussion of individual categories may be found by using the overview of the dictionary structure given in Appendix 3.6.1[link].

The data names in the mmCIF dictionary derived from the core CIF dictionary differ from their DDL1 counterparts in that a full stop (.) is used to designate explicitly the category to which the data name belongs, e.g. _cell.length_a is used in place of _cell_length_a. Sometimes the mmCIF counterpart of a core data name may have a different form, for example to enforce the rule in DDL2 that the category name is the initial part of any data name within that category. This convention is generally observed in DDL1, but is not mandatory. Formally, the corresponding DDL1 core data name is obtained from the _item_aliases.alias_name attribute of the definition. The provision of a formal alias for all data names derived from the core dictionary allows a DDL2-compliant parser to read and interpret a data file constructed according to the DDL1 dictionary described in Chapter 3.2[link] . Achieving this compatibility with CIFs built using DDL1 dictionaries was a very important goal in the design of DDL2 and the mmCIF dictionary.

In this chapter, categories and individual data names that correspond to matching entries in the core dictionary are not discussed in detail unless they are used in a different way in mmCIF. Chapter 3.2[link] should therefore be read first for a description of the categories common to both the core and mmCIF dictionaries. This chapter concentrates on the categories specific to mmCIF. Formal differences between mmCIF categories and core CIF categories are also summarized.

References

Bourne, P., Berman, H. M., McMahon, B., Watenpaugh, K. D., Westbrook, J. D. & Fitzgerald, P. M. D. (1997). Macromolecular Crystallographic Information File. Methods Enzymol. 277, 571–590.
Fitzgerald, P. M. D., Berman, H., Bourne, P., McMahon, B., Watenpaugh, K. & Westbrook, J. (1996). The mmCIF dictionary: community review and final approval. Acta Cryst. A52 (Suppl.), C575.
Hall, S. R., Allen, F. H. & Brown, I. D. (1991). The crystallographic information file (CIF): a new standard archive file for crystallography. Acta Cryst. A47, 655–685.








































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