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. 147-148

Section 3.6.4. Content of the macromolecular CIF 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

3.6.4. Content of the macromolecular CIF dictionary

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Because it is derived from the core CIF dictionary, the mmCIF dictionary shares the same general structure as outlined in Chapter 3.2[link] . However, DDL2 permits the formal assignment of categories to category groups. Table 3.6.4.1[link] lists the major category groups in the mmCIF dictionary (a full list is given in Appendix 3.6.1[link] and at the beginning of Chapter 4.5[link] ).

Table 3.6.4.1| top | pdf |
Major category groups defined in the mmCIF dictionary

The groups are listed in the order in which they are described in this chapter. There is also an INCLUSIVE category group, which serves as a formal higher-order container group to which all other category groups belong.

SectionCategory groupSubject covered
(a) Experimental measurements
3.6.5.1[link] CELL Unit cell
3.6.5.2[link] DIFFRN Diffraction experiment
3.6.5.3[link] EXPTL Experimental conditions
     
(b) Analysis
3.6.6.1[link] PHASING Phasing techniques
3.6.6.2[link] REFINE Refinement procedures
3.6.6.3[link] REFLN Reflection measurements
     
(c) Atomicity, chemistry and structure
3.6.7.1[link] ATOM Atom sites
3.6.7.2[link] CHEMICAL Chemical properties and nomenclature
3.6.7.3[link] ENTITY Chemical entities
3.6.7.4[link] GEOM Geometry of atom sites
3.6.7.5[link] STRUCT Crystallographic structure
3.6.7.6[link] SYMMETRY Symmetry information
3.6.7.7[link] VALENCE Bond-valence information
     
(d) Publication
3.6.8.1[link] CITATION Bibliographic references
3.6.8.2[link] COMPUTING Computational details of the experiment
3.6.8.3[link] DATABASE Database information
3.6.8.4[link] IUCR Journal housekeeping and the contents of a published article
     
(e) File metadata
3.6.9.1[link] AUDIT Dictionary maintenance and identification
3.6.9.2[link] ENTRY Links between data blocks
3.6.9.3[link] COMPLIANCE Compliance with previous dictionaries

Small capitals are used for the names of category groups and individual categories in this volume, but the identifiers in the dictionary are actually lower-case strings.

The ordering of category groups in the remainder of this chapter follows the thematic scheme of Table 3.1.10.1[link] . The discussion proceeds under the headings Experimental measurements (Section 3.6.5[link]), Analysis (Section 3.6.6[link]), Atomicity, chemistry and structure (Section 3.6.7[link]), Publication (Section 3.6.8[link]) and File metadata (Section 3.6.9[link]).

Certain conventions of style and layout have been followed to summarize the large amount of information in the mmCIF dictionary and to help the reader navigate their way through this chapter. Appendix 3.6.1[link] is an overview of the mmCIF dictionary structure by category and lists all the categories with the number of the section in which they are discussed. This acts as an index between the alphabetical ordering within the dictionary and the thematic ordering of this chapter. Each thematic section lists the categories discussed in that section. Within each subsection, the data names within the relevant categories are listed. Category keys, pointers to parent data items and aliases to data items in the core CIF dictionary are indicated. For each category, the data item (or set of data items that must be considered together) that forms the category key is marked by a bullet ([\bullet]) and listed first; the other data names follow in alphabetical order.

For measured or derived numerical quantities that should be specified with a standard uncertainty (in older terminology, an estimated standard deviation), the core dictionary uses the DDL1 attribute _type_conditions_esd and allows the standard uncertainty of the value to be placed in parentheses after the numerical value, as in [Scheme scheme9]

This is also permitted in mmCIF, but it is preferable to use a separate data item to record the standard uncertainty, as in [Scheme scheme10]

There are many of these kinds of data names in the mmCIF dictionary. The name of each is derived by adding _esd to the data name for the value. They are indicated by a + symbol in the category summaries in this chapter.








































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