CIF developers' frequently-asked questions

• What is the Crystallographic Information File?

  The Crystallographic Information File (CIF) is the standard file format for the exchange of crystallographic information published by the International Union of Crystallography (IUCr) in 1991.

  A CIF is an ASCII file conforming to the STAR File syntax with some additional restrictions. It contains tags identifying many quantities or elements of information, and the associated values. The meanings of the tags are specified in standard library files known as CIF dictionaries, although files may also contain pieces of information defined implicitly or in non-standard dictionaries.

  The specification of the CIF standard can be found on the web pages at http://www.iucr.org/iucr-top/cif.

• What are coreCIF, pdCIF, msCIF, mmCIF, imgCIF...?

  Several standard dictionaries of data names are maintained for use in different branches of crystallography or related structural sciences. The various dictionaries and the project teams responsible for their specification and maintenance are identified by acronyms such as

  coreCIF

  Data names relating to the core of crystallography and to single-crystal small-molecule or ionic structural studies.

  pdCIF

  Data names used in powder diffraction.

  msCIF

  Data names used in the description of modulated aperiodic structures.

  mmCIF

  The dictionary used in macromolecular crystallography. It includes the data items defined in the core dictionary, but with a slightly different formalism.

  imgCIF

  A dictionary of terms used in the representation of images and higher-dimensional data sets.

  Information on these and other specialised dictionaries may be found on the CIF home page.

  Reference:
  Hall, S. R., Allen, F. H. and Brown, I. D. (1991). Acta Cryst. A47, 655-685.

• Why use CIF? What is wrong with SHELX/PDB/RasMol format, XML/SGML, ASN.1, JPEG/TIFF/PNG, Word/TeX/WordPerfect?

  Nothing is necessarily "wrong" with any of these file formats listed; but typically they serve the purpose of a specific program; in some cases are undocumented or not stable over time; and are unstructured. CIF, however, is specifically designed for data exchange between software packages of many different types. It is publicly documented and intended to be very stable; and it also describes in detail the data model appropriate for the data it conveys.

  But most importantly, it provides a framework for all data of crystallographic interest: raw intensity sets, reduced data sets, images, graphical representations, tables of derived data, experimental logs, or literature submissions. It has a very rich vocabulary of recognised data names drawn up by experts in crystallography. While it may be useful to transform some or all of the contents of a CIF to some or all of the above formats, the CIF remains the single most comprehensive repository of information suitable for archiving or data interchange.

• What is a STAR File?

  STAR is an acronym for Self-defining Text Archive and Retrieval. It refers to a file format published in 1990, to satisfy the following design goals: the data structure is completely self-defined; the data items are completely self-defined; the data syntax rules are few and simple; the data may be of any type and in any order; the file is easy to read visually, or by machine.

  References:
  Hall, S. R. (1991). J. Chem. Inf. Comput. Sci. 31, 326-333.
  Hall, S. R. and Spadaccini, N. (1994). J. Chem. Inf. Comput. Sci. 34, 505-508.

• What is the difference between a STAR File and a CIF?

  A CIF is a STAR File with additional syntax rules, conventions on data typing, and using data names with crystallographic relevance defined in external library files, known as data dictionaries.

  STAR Files (with or without the syntax restrictions of CIF) are used in other disciplines. Examples are the NMR-STAR datasets of the BioMagResBank, the World Database of Crystallographers source files, and the Molecular Information File (MIF). Clearly, the less another STAR application departs from the restricted CIF syntax, the easier it will be to handle overlap between CIF and non-CIF applications.

• Is there a BNF for STAR?

  Yes. A formal Backus-Naur specification of the STAR syntax was published in J. Chem. Inf. Comput. Sci. (1994), 34, p. 507.

• What is DDL?

  DDL is the Dictionary Definition Language, a formal mechanism for defining data types and data dependencies in CIF or in certain other STAR File applications.

  Here is a simple example. In the CIF Core dictionary, the data tag _chemical_melting_point that identifies the melting point of a chemical compound is defined in the following way:

  data_chemical_melting_point
      _name                      '_chemical_melting_point'
      _category                    chemical
      _type                        numb
      _enumeration_range           0.0:
      _units                       K
      _units_detail              'kelvins'
      _definition
  ;              The temperature in kelvins at which a crystalline solid changes
                 to a liquid.
  ;  
  

  The dictionary is itself a STAR File; the identifiers _name, _type etc. comprise the DDL. From this example, it can be seen that the purpose of many of the terms in DDL can be readily deduced; however, the formalism permits machine parsing of dictionaries and consequent automatic validation of CIFs (or other STAR Files applications) containing the data names defined in the dictionaries.

  Reference:
  McMahon, B. (1995). A Brief History of the DDL. http://www.iucr.org/iucr-top/cif/ddlhist.html.

• What is DDL0?

  DDL0 is the name sometimes given to the set of properties associated with CIF data names in the original CIF dictionary published in 1991. These have been superseded by more refined formalisms, and it is not in general considered necessary that DDL parsers should recognise these properties.

• What is DDL1?

  DDL version 1 is the set of properties associated with CIF data names in the coreCIF dictionary and in other CIF extension dictionaries, largely concerned with small-molecule crystallography.

  References:
  Hall, S. R. and Cook, A. P. F. (1995). J. Chem. Inf. Comput. Sci.. 35, 819-825.
  DDL Version 1.4 Dictionary (1995). ftp://ftp.iucr.org/pub/ddldic.c95.

• What is DDL2?

  DDL version 2 is the set of properties associated with CIF data names in the mmCIF dictionary for macromolecular structures, and in related projects such as the imgCIF work on images. It embraces a data model that is very close to that of a relational database. CIF data names described by DDL2 include a period character `.' to indicate the category (or, equivalently, relational table) to which they have been assigned.

  Reference:
  DDL Version 2.1.1 Dictionary (1995). ftp://ftp.iucr.org/pub/ddl2.c96.

• What is DDL3?

  DDL version 3 is the name given to some work in progress by Syd Hall and his colleagues at the University of Western Australia. It is intended to build on the greater consistency and data typing abilities of DDL2 without tying the data model too closely to that of a relational database. A particular goal of DDL3 is to introduce methods into data dictionaries through a formal language known as dREL (Dictionary Regular Expression Language).

• What is CBF?

  CBF is the Crystallographic Binary File. It is an outgrowth from the imgCIF project to describe area-detector and image-plate images in CIF terms. While the imgCIF dictionary allows a fully compliant CIF archive file to be created of an image, it was felt that the ASCII representation of huge data sets was unnecessarily verbose, and a packed binary representation was designed to be of more use in everyday working. The information content of a CBF is identical to that of its associated imgCIF ASCII representation: only the internal data storage (and file size) differ.

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