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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, which 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. This chapter is also available as HTML from the International Tables Online site hosted by the IUCr. [ABSTRACT FROM AUTHOR]

The dictionary definition language version 2 (DDL2) extends the version 1 DDL used by the IUCr for the description of data items common to all crystallographic studies (i.e. core items). The DDL2 extensions were introduced primarily to address two issues arising during the development of a CIF dictionary for the terminology of macromolecular crystallography: the need to accurately describe the hierarchical nature of macromolecular structure and associated structural features, and the desire to encode dictionary definitions in a manner that would permit more detailed software-driven validation. This chapter presents the attribute sets described by the DDL2 language and illustrates their relational character. DDL2 attributes are classified in categories with unique key items; these categories play the roles of tables in a relational database structure. The relationships between categories are illustrated graphically and are described in detail in the chapter. The organization of DDL2 reflects the organization of the data model the attributes of which it describes (i.e. in the mmCIF and related data dictionaries). Consequently, the dictionary of DDL2 attributes is itself constructed in the DDL2 formalism. The use of a self-referential data description scheme allows the consistency and relational integrity of the data model to be independently verified. This chapter is also available as HTML from the International Tables Online site hosted by the IUCr. [ABSTRACT FROM AUTHOR]

The macromolecular CIF (mmCIF) dictionary is a major extension of the core CIF dictionary designed to provide data names to be used in a machine-readable description of a macromolecular structure determination experiment and the derived structural model. To allow a complete and self-consistent account of a macromolecular structure at various levels of detail, the dictionary has been implemented in the relational dictionary definition language DDL2. It includes the data items defined in the core CIF dictionary. mmCIF supersedes an older file format of the Protein Data Bank (PDB), and therefore includes a representation of all the information historically archived at the PDB. In addition, it provides data items suitable for use in: a journal `materials and methods' article; descriptions of biologically active molecules and any important subcomponents; descriptions of crystallographic and noncrystallographic symmetry; information about the chemistry and geometry of monomer components of macromolecules, and of any ligands or small-molecule complexes; and descriptions of functional and structural aspects of macromolecules. This chapter is also available as HTML from the International Tables Online site hosted by the IUCr. [ABSTRACT FROM AUTHOR]

This is version 2.0.09 of the macromolecular CIF dictionary (mmCIF). The history and philosophy of this dictionary are described in Chapter 1.1 and a commentary on its use may be found in Chapter 3.6. The data names defined here include a modified representation of those in the core CIF dictionary (Chapter 4.1). This chapter is also available as HTML from the International Tables Online site hosted by the IUCr. [ABSTRACT FROM AUTHOR]

This is version 1.3.2 of the image CIF dictionary (imgCIF) and crystallographic binary file (CBF) dictionary. Use of this dictionary is described in Chapter 3.7. The CBF format is described in Chapter 2.3 and Chapter 5.6 describes a software library for manipulating image data. The data names defined here extend the macromolecular CIF dictionary (Chapter 4.5). This chapter is also available as HTML from the International Tables Online site hosted by the IUCr. [ABSTRACT FROM AUTHOR]

This is version 2.1.3 of the dictionary definition language (DDL2). It provides a machine-readable description of the attributes of data items in the mmCIF and related dictionaries. This version of DDL is described in Chapter 2.6. This chapter is also available as HTML from the International Tables Online site hosted by the IUCr. [ABSTRACT FROM AUTHOR]

The Protein Data Bank (PDB) has grown from an archive of seven entries in 1973 to a large and rapidly growing collection of more than 30 000 structures as of May 2005. The PDB now provides a key information resource for the structural biology community. A software framework has been developed that supports automation and scalability, and that can adapt to changes in data content and delivery technology, to permit future development. The mmCIF data dictionary and an accompanying extended dictionary of local data items provide the core ontology which is the basis for software development. The associated software tools exchange and validate data, create and load databases, translate data formats, and serve application program interfaces. They are made available to the scientific community through an open-source licence. This chapter is also available as HTML from the International Tables Online site hosted by the IUCr. [ABSTRACT FROM AUTHOR]