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. 1.1, pp. 7-8

Section 1.1.9. The macromolecular Crystallographic Information File

S. R. Halla* and B. McMahonb

aSchool of Biomedical and Chemical Sciences, University of Western Australia, Crawley, Perth, WA 6009, Australia, and bInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England
Correspondence e-mail:  syd@crystal.uwa.edu.au

1.1.9. The macromolecular Crystallographic Information File

| top | pdf |

The original goal of CIF was the creation of an archive format for the description and results of experiments in small-molecule and inorganic crystallography. The data names and their definitions were embodied in the core dictionary, so called because most of the terms in it were considered common to any crystallographic application. In 1990, the IUCr formed a working group, chaired by Paula Fitzgerald, to expand this dictionary to meet the additional requirements of macromolecular crystallography. The resulting expanded dictionary was to be known as the macromolecular CIF (mmCIF) dictionary.

The group's original short-term goal was to fulfil the IUCr mandate of defining data names for an adequate description of a macromolecular crystallographic experiment and its results. Longer-term goals were also determined: to provide sufficient data names so that the experimental section of a structure paper could be written automatically and to facilitate the development of tools so that computer programs could easily interface with CIF data files. A number of informal and formal meetings were held to describe the progress of this project and to solicit community feedback.

An important meeting took place at the University of York in April 1993. The attendees included the mmCIF working group, structural biologists and computer scientists. Vigorous discussion arose on whether the formal structure of the dictionary implemented in the then-current dictionary definition language (DDL1) could deal with the complexity of macromolecular data sets. There were criticisms that the data typing was not strong enough and that there were no formal links expressing relationships between data items. A working group was formed to address these issues, resulting in a second workshop in Tarrytown, New York, in October 1993. The discussions at this second meeting focused on the development of software tools and the requirements of an enhanced DDL. Such a DDL was proposed during a third workshop at the Free University of Brussels in October 1994. This new DDL (DDL2; Chapter 2.6[link] ) was designed by John Westbrook and sought to address the various problems identified at the preceding workshops, while retaining compatibility with existing CIF data files.

The macromolecular dictionary was built using DDL2 and was presented as a draft to the community at the American Crystallographic Association meeting in Montreal in July 1995. The draft was subsequently posted on a website and community comment solicited via an e-mail discussion list. This provoked lively discussions, leading to continuous correction and updating of the dictionary over an extended period of time. Software for parsing the dictionary and managing mmCIF data sets was developed and was also presented on the website.

In January 1997, the mmCIF dictionary was completed and submitted to COMCIFS for review. In June 1997, version 1.0 was approved by COMCIFS and released (Bourne et al., 1997[link]; Fitzgerald et al., 1996[link]). A workshop was held at Rutgers University in October 1997, at which tutorials were presented to demonstrate the use of the various tools that had been developed.

More than 100 new definitions have been incorporated in version 2 of the mmCIF dictionary, presented in Chapter 4.5[link] .

References

Bourne, P., Berman, H. M., McMahon, B., Watenpaugh, K. D., Westbrook, J. D. & Fitzgerald, P. M. D. (1997). Macromolecular Crystallographic Information File. Methods Enzymol. 277, 571–590.
Fitzgerald, P. M. D., Berman, H., Bourne, P., McMahon, B., Watenpaugh, K. & Westbrook, J. (1996). The mmCIF dictionary: community review and final approval. Acta Cryst. A52 (Suppl.), C575.








































to end of page
to top of page