Section 5.7.2.1. Assembling the complete article

For many authors the generation of a CIF suitable for publication is quite straightforward, since diffractometer software and structure solution and refinement packages have all been capable of writing or reading the CIF format for some time. In some highly integrated systems, the entire experimental, analysis and report-generating pathway may be controlled through a common user interface.

In other cases, different components must be collected from different sources and merged together, either by software utilities or, in the worst case, by hand-editing. It is a useful feature of the text-based CIF format that it can be modified by text editors or in certain word-processing modes; indeed, this was the only way in which the earliest CIF-based papers could be constructed. However, significant expertise and understanding of the technical details of the file format are needed to produce hand-edited files that are totally free from error. Authors are now encouraged to use software designed to help them create complete and error-free files (e.g. the enCIFer and CIFEDIT editors described in Chapter 5.3 ).

A complete structure communication comprises the following components.

(a) Material common to the article as a whole:

(b) Material relevant to each structure:

(c) Graphical illustrations:

Different journals will have different requirements for the arrangement of these items. For example, at the time of publication (2005), Acta Crystallographica requires that diffraction data (structure factors or Rietveld refinement profiles) are provided as supplementary information in separate files from that containing the body of the paper. This policy originated in the early days of network file transfer where relatively large files of experimental data could be transferred only with difficulty. This is less of a practical constraint now, and a case could be made for including the experimental results as an integral part of a single submission file, especially since there is still no formal mechanism in the core CIF dictionary to enforce an unambiguous connection between separate data blocks containing related data.

There is also not at present a standard way to include graphics within a CIF. The mechanisms of the imgCIF dictionary (Chapter 3.7 ) offer a possible approach to this problem. It is also possible to envisage the automated generation of views of the structure directly from the numerical data in the CIF. Three-dimensional ellipsoid plots are routinely generated from CIFs submitted to Acta Crystallographica for use in the review process and incomplete categories of data names exist in the core dictionary for the representation of two-dimensional diagrams of chemical connectivity. At present, however, neither of these is sufficiently well developed to generate publication-quality graphics in different orientations and styles as preferred by an author.

A journal may provide a request list of the data items that it considers recommended or mandatory. The request list for Acta Cryst. C and E is given in Appendix 5.7.1. An author can test a file intended for publication against a request list with a general-purpose CIF parsing tool such as cif2cif (Bernstein, 1998) or QUASAR (Hall & Sievers, 1993) (Chapter 5.3 ). Different request lists may be provided for different kinds of experiments, such as for powder diffraction experiments or for single-crystal studies using area detectors.

Note that an author always has the freedom to include additional data items in a CIF; the journal will exercise its own policy for the handling of data items not specified in its public request lists. The PUBL_MANUSCRIPT_INCL category available in the CIF core dictionary provides a mechanism for requesting the publication of data items that are not normally published by the journal (see Sections 5.7.2.3 and 3.2.5.5 ).