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. 5.3, p. 499

Section 5.3.1. Introduction

B. McMahona*

aInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England
Correspondence e-mail: bm@iucr.org

5.3.1. Introduction

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Since the introduction of the Crystallographic Information File (CIF), the crystallographic community has produced a wide vari­ety of tools and applications to handle CIFs. Many changes have been made to existing programs to input and output CIF data sets, and occasionally changes may have been made to internal crystallographic calculations to provide a better fit to the view of the data expressed by the standard CIF dictionaries. However, for most crystallographers with an involvement in programming, there is an understandable tendency to invest the minimum amount of effort needed to accommodate the new format. Their primary interest is in the understanding and discovery of the underlying physical model of a crystal structure.

This chapter reviews several general-purpose tools that have been developed for CIF to check, edit, extract or manipulate arbitrary data items, with little in the way of crystallographic computation. They are of interest to the end user who wishes to visualize a structure in three dimensions or submit an article to a journal but who does not want to be concerned about the details of CIF. They also include several utilities that are helpful for manipulating the contents of CIFs without the need to write a large and complex program. The programmer with an interest in writing complete and robust CIF applications should look at the comprehensive libraries described in Chapters 5.4[link] to 5.6[link] .

Many of the programs described in this chapter operate purely at the syntactic level; they require no knowledge of the scientific meaning of the data items being manipulated. Others have some bearing on the semantics of the file contents, either explicitly through information about data types and interrelationships carried in external CIF dictionaries, or implicitly through the user's choice and deliberate manipulation of items based on an understanding of what they signify. Nevertheless, most utilities described here are characterized by an ability to handle CIFs of any content and provenance. The best example of a program able to handle arbitrary CIFs at a purely syntactic level is Star_Base (Spadaccini & Hall, 1994[link]), described in Chapter 5.2[link] .

It should be noted that not all the programs described here are fully compliant with the specification of Chapter 2.2[link] , and others have implementation restrictions or known bugs. Many, especially the older programs, are no longer actively supported and need to be handled with care. However, they are included here for the record, and because they may provide useful ideas and suggestions to future developers in an area that can still accommodate a wider range of tools for different uses.

References

Spadaccini, N. & Hall, S. R. (1994). Star_Base: accessing STAR File data. J. Chem. Inf. Comput. Sci. 34, 509–516.








































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