Section 3.1.10. Public CIF dictionaries

The only formal unit of classification common to all CIF dictionaries is the category. For example, in the core CIF dictionary information about the chemical and physical properties of the different atomic species in a crystal cell is collected in a few data names such as _atom_type_oxidation_number which belong to the same category, in this case the ATOM_TYPE category. As described in Section 3.1.5.3, it is conventional (although not mandatory) that CIF data names begin with components corresponding to the name of the category to which they belong.

The term category as used in CIF dictionaries has a technical meaning which constrains its normal use in grouping items that are understood to have a `natural' relationship. In a CIF, only items belonging to the same category may appear together in the same looped list. This means, for example, that data items describing collective properties of the atom sites in the lattice (such as the number of atoms of each atomic species in the unit cell) must be assigned to a different category from the data items that describe the properties of the individual sites. Hence the properties of individual sites (such as the positional coordinates defined by _atom_site_fract_x etc.) belong to the ATOM_SITE category, while the transformation matrix between Cartesian and fractional components (expressed by a collection of data names such as _atom_sites_fract_tran_matrix_11) belong to the ATOM_SITES category. Clearly, the category names have been chosen to be similar to reflect their close relationship, while the EXPTL category containing data names such as _exptl_crystal_colour is named quite differently. It is natural to wish to describe related categories in a common higher level of classification, and indeed category groups exist as formal components of DDL2-structured dictionaries. We shall, however, refer informally to `category groups' in discussions of DDL1 dictionaries as collections of categories with a close relationship that is usually implicit in their names.

Table 3.1.10.1 provides an informal classification at a high level of the category groups represented in each of the CIF dictionaries in this volume. Related category groups are clustered within the table in families sharing a common function. The five families (a) to (e) in Table 3.1.10.1 refer to: the crystallographic experiment itself; the processing and analysis of data from the experiment; the derived structural model; the reporting and publication of the results; and general auditing of the file itself, its purpose, authorship, history and links to other data sets, i.e. the file metadata. Detailed discussions of the individual categories (and formal category groups for DDL2 dictionaries) will be found in the relevant chapters in the rest of this part of the volume.

Table 3.1.10.1 shows the different characters of the seven dictionaries. The macromolecular dictionary (mmcif_std.dic; Chapter 4.5 ) contains an embedded version of the core dictionary (cif_core.dic; Chapter 4.1 ) in DDL2 format and so includes all the categories defined in the core. However, it extends the description of the structural model extensively by introducing families of categories for the description of chemical components of a macromolecular structure (ENTITY) and for the detailed description of the structure itself (STRUCT). New categories are also introduced to describe the phasing of the structure and the SOFTWARE category allows the inclusion of more details of computational techniques than the core COMPUTING category does.

The other dictionaries are purely extensions which either introduce new data names (and occasionally new categories) into existing category groups or, where necessary, introduce completely new groups of categories.

The powder dictionary (cif_pd.dic; Chapter 4.2 ) contains several new category groups reflecting the need for substantially different methods of describing the experiment and analysing the data, as well as a need for the structural model to be able to handle multiple crystalline phases. The modulated structures dictionary (cif_ms.dic; Chapter 4.3 ) introduces no new category groups, but does introduce several new data names and categories within the existing framework. The electron density dictionary (cif_rho.dic; Chapter 4.4 ) introduces two new categories within an existing category group. The image CIF dictionary (cif_img.dic; Chapter 4.6 ) has several new categories that characterize arrays of data from two-dimensional X-ray detectors and the consequent detailed descriptions of the relevant axes within the experimental setup. The symmetry dictionary (cif_sym.dic; Chapter 4.7 ) was commissioned specifically to replace the symmetry categories in the core dictionary with a more detailed treatment.