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. 3.2, p. 92

Section 3.2.1. Introduction

S. R. Hall,a* P. M. D. Fitzgeraldb and B. McMahonc

aSchool of Biomedical and Chemical Sciences, University of Western Australia, Crawley, 6009, Australia,bMerck Research Laboratories, Rahway, New Jersey, USA, and cInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England
Correspondence e-mail:  syd@crystal.uwa.edu.au

3.2.1. Introduction

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This chapter is concerned with the classification and organization of data items defined in the core CIF dictionary (Chapter 4.1[link] ). The core dictionary, as its name suggests, is central to the definition of data items found in most CIFs. It defines the measured and derived items common to most crystallographic experiments, analyses and publications, and, in particular, those items characterizing a classical single-crystal X-ray diffraction determination of a small-molecule or inorganic structure. As the nature of crystallographic studies evolves, so do the data items needed to describe them. New data names are introduced as needed to describe new techniques or technologies or simply to provide more details of subjects already covered. In addition, the developers of specialist dictionaries may find that some of the items they define have a wider application and propose that these items be added to the core dictionary instead.

Core data items are defined with two formalisms. The core dictionary, as presented in Chapter 4.1[link] , defines core data items exclusively using the data definition language DDL1 (described in Chapter 2.5[link] ). However, core data items are also embedded within the macromolecular CIF dictionary presented in Chapter 4.5[link] using the data definition language DDL2 (described in Chapter 2.6[link] ). Because the revision cycles of the core and mmCIF dictionaries are not synchronized, at any one time the mmCIF dictionary may not include the complete set of data items in the current core dictionary. The mmCIF dictionary described in this volume includes the full content of core CIF dictionary version 2.3.1, also described in this volume.

The discussion in this chapter will concentrate on the current DDL1 version of the core dictionary (version 2.3, released on 4 October 2003 and reissued with minor amendments as version 2.3.1 in this volume). There will be some discussion of the more formal approach to the classification of data items that DDL2 permits.

In accordance with the scheme given in Table 3.1.10.1[link] , groups of categories of data items in the core dictionary will be classified under the headings Experimental measurements (Section 3.2.2[link]), Analysis (Section 3.2.3[link]), Atomicity, chemistry and structure (Section 3.2.4[link]), Publication (Section 3.2.5[link]) and File metadata (Section 3.2.6[link]). To help the reader relate the thematic order of the discussion of these categories to the alphabetic layout of the dictionary, the category structure of the core dictionary is summarized in Table 3.2.1.1[link] and is listed in full in Appendix 3.2.1[link]. The appendix also lists for each category the section of this chapter in which the category is described.

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Category groups defined in the core CIF dictionary

The groups are listed in the order in which they are described in this chapter.

SectionCategory groupSubject covered
(a) Experimental measurements
3.2.2.1[link] CELL Unit cell
3.2.2.2[link] DIFFRN Diffraction experiment
3.2.2.3[link] EXPTL Experimental conditions
     
(b) Analysis
3.2.3.1[link] REFINE Refinement procedures
3.2.3.2[link] REFLN Reflection measurements
     
(c) Atomicity, chemistry and structure
3.2.4.1[link] ATOM Atom sites
3.2.4.2[link] CHEMICAL Chemical properties and nomenclature
3.2.4.3[link] GEOM Geometry of atom sites
3.2.4.4[link] SYMMETRY Symmetry information
3.2.4.5[link] VALENCE Bond-valence information
     
(d) Publication
3.2.5.1[link] CITATION Bibliographic references
3.2.5.2[link] COMPUTING Computational details of the experiment
3.2.5.3[link] DATABASE Database information
3.2.5.4[link] JOURNAL Journal housekeeping
3.2.5.5[link] PUBL Contents of a published article
     
(e) File metadata
3.2.6[link] AUDIT Dictionary maintenance and identification

The data items contained within each category are listed in the detailed commentary below. Where relevant, the data item or items that represent a unique identifier for a looped list (`category keys') are listed first and are marked by a bullet ([\bullet]). Note that category keys are defined more formally in the mmCIF dictionary (see Chapter 2.6[link] and the discussion of categories in Section 3.1.6.4[link] ). The remaining data items in each category are listed alphabetically.








































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