2.2. Specification of the Crystallographic Information File (CIF)
S. R. Hall and J. D. Westbrook, with Section 2.2.7 by S. R. Hall, N. Spadaccini, I. D. Brown, H. J. Bernstein, J. D. Westbrook and B. McMahon
Abstract
The Crystallographic Information File (CIF) is an electronic file containing specific data items relevant to crystallographic structure determinations and descriptions in the form of numbers and text. These data items are represented as ASCII character strings. The structure and format of a CIF are based on a restricted subset of the syntax of a Self-defining Text Archive and Retrieval (STAR) File. The CIF is intended as a general, flexible and extensible free-format file suitable for the transmission, storage and publication of crystallographic data. Since 1990 it has been recommended by the International Union of Crystallography as the preferred data structure for the exchange of data.
This chapter provides a detailed description of the syntax features of a CIF and its conventions for associating meaning or semantic content to included data. Particular care is taken to describe how the file format handles issues of portability and archival integrity.
The chapter includes the complete official specification, and a formal grammar in extended Backus-Naur form.
Links
Dictionaries
The following dictionaries are referenced in this chapter:
Specifications
Complete formal specification
- Summary Backus-Naur form of the CIF syntax and grammar (HTML format)
- Summary Backus-Naur form of the CIF syntax and grammar (plain text file with Unix-style line endings)
Software
The following software is relevant to this chapter:
- vcif (syntax checker)
- syntax test suite
References
Bernstein, H. J. (2002). Some comments on parsing for computer programming languages. http://www.bernstein-plus-sons.com/TMM/Parsing.
Fielding, R., Gettys, J., Mogul, J., Frystyk, H., Masinter, L., Leach, P. & Berners-Lee, T. (1999). Hypertext Transfer Protocol - HTTP/1.1. RFC 2616. Network Working Group. http://www.w3.org/Protocols/rfc2616/rfc2616.html.
Freed, N. & Borenstein, N. (1996). Multipurpose Internet Mail Extensions (MIME) Part two: media types. RFC 2046. Network Working Group. http://www.ietf.org/rfc/rfc2046.txt.
Hall, S. R. (1991). The STAR file: a new
format for electronic data transfer and archiving.
J. Chem. Inf. Comput. Sci. 31, 326-333.
Hall, S. R., Allen, F. H. &
Brown, I. D. (1991). The Crystallographic Information File
(CIF): a new standard archive file for crystallography.
Acta Cryst. A47, 655-685.
See also
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HTML version
(http://www.iucr.org/iucr-top/cif/standard/cifstd1.html).
Hall, S. R. & Cook, A. P. F.
(1995). STAR dictionary definition language: initial
specification. J. Chem. Inf. Comput. Sci. 35,
819-825.
Hall, S. R. & Spadaccini, N. (1994).
The STAR File: detailed specifications. J. Chem. Inf. Comput.
Sci. 34, 505-508.
McMahon, B., Westbrook, J. D. & Bernstein, H. J. (2000). Report of the COMCIFS Working Group on Dictionary Maintenance. http://www.iucr.org/iucr-top/cif/spec/dictionaries/maintenance.html.
Ulrich, E. L. et al. (1998). XVIIth Intl Conf. Magn. Res. Biol. Systems. Tokyo, Japan.
Westbrook, J. D. & Hall, S. R. (1995). A dictionary description language for macromolecular structure. http://ndbserver.rutgers.edu/mmcif/ddl.