Electronic resources

This CD-ROM contains STAR and CIF specifications, dictionaries, software libraries and applications. Where appropriate, links are provided to web addresses from which the current versions of an item should be available. The material on this CD-ROM may be useful for educational purposes, for access to unsupported and legacy software, and as a convenient resource if access to the web or to individual web sites is unavailable.

Throughout these pages indicates resources on the CD-ROM, indicates resources on the Web.

The navigation bar on each page will take the user back to this page ("Contents") or to the main points of entry to the major components of this collection: supplementary material for each chapter ("Resources"), CIF specifications ("Specifications"), CIF and related dictionaries ("Dictionaries") or software collections ("Software").

For information on copyright and terms and conditions of use, please see the pages listed under the heading Legal in the contents list below.

Contents

Dictionaries

• Core dictionary (coreCIF) [ASCII | HTML | PDF | More information ]
• DDL1 dictionary [ASCII | HTML | PDF | More information ]
• DDL2 dictionary [ASCII | HTML | PDF | More information ]
• Dictionary of data items describing registered dictionaries [ASCII]
• Electron density dictionary (rhoCIF) [ASCII | HTML | PDF | More information ]
• Image dictionary (imgCIF) [ASCII | HTML | PDF | More information ]
• Macromolecular dictionary (mmCIF) [ASCII | HTML | PDF | More information ]
• Modulated and composite structures dictionary (msCIF) [ASCII | HTML | PDF | More information ]
• Molecular Information File dictionary (MIF) [ASCII | HTML | PDF | More information ]
• Powder dictionary (pdCIF) [ASCII | HTML | PDF | More information ]
• Protein Data Bank exchange dictionary (pdbx) [ASCII | HTML | More information ]
• Symmetry dictionary (symCIF) [ASCII | HTML | PDF | More information ]

Documentation

• CIFtbx Primer and Reference Manual
• Data-validation tests applied by checkcif and PLATON

Examples

• (coreCIF) Request list of CIF data items for Acta Crytallographica Section C
• (coreCIF) Template for the submission of single-crystal diffraction studies to an IUCr journal
• (coreCIF) Template for use with SHELX97
• (coreCIF) Example single-crystal diffraction study submitted to Acta Crystallographica Section C
• (coreCIF) Example single-crystal diffraction study submitted to Acta Crystallographica Section E
• (imgCIF/CBF) Example image file in MAR format and different CBF and imgCIF representations
• (imgCIF/CBF) Template for use with ADSC Quantum 4 detector
• (imgCIF/CBF) Template for use with MAR 345 detector
• (msCIF) Example one-dimensional incommensurately modulated structure (K₂SeO₄)
• (msCIF) Example modulated structure of inorganic misfit layer compound [(LaS)_1.14NbS₂]
• (msCIF) Alternative example of inorganic misfit layer compound [(LaS)_1.14NbS₂]
• (msCIF) Example modulated incommensurate composite crystal [(PbS)_1.12VS₂]
• (pdCIF) Template form for Rietveld refinement results submitted to a journal
• (pdCIF) Example Rietveld submission to a journal
• (pdCIF) Template form for the submission of powder diffraction data to a journal
• (pdCIF) Example powder data set submitted to a journal
• (pdCIF) Example powder CIF for a multiple phase/multiple data set refinement

Figures

Some figures from the volume are reproduced in colour or at a larger size on this CD-ROM. They may be found in the additional resources for the following chapters:

• 1.1 Genesis of the Crystallographic Information File
• 3.6 Classification and use of macromolecular data
• 3.7 Classification and use of image data
• 5.2 STAR File utilities
• 5.3 Syntactic utilities for CIF
• 5.5 The use of mmCIF architecture for PDB data management

Historical materials

• CBF draft specification of A. P. Hammersley, ESRF, 1997
• CBF draft specification reworked by H. J. Bernstein 1998-2001
• CIF document #1, version 22 October 1989
• CIF document #2, version 22 October 1989
• CIF document #3, version 22 October 1989
• CIF document #4, version 22 October 1989
• CIF document #5, version 22 October 1989
• 'DDL0': unpublished dictionary definition language used for first release of core CIF dictionary
• Guide to CIF for Authors. Booklet produced by Acta Crystallographica in 1995 to help authors to produce articles with CIF.
• Preliminary CIF description, version 15 July 1988
• Preliminary CIF description, version 3 August 1988
• Preliminary CIF description, version 25 September 1989
• Standard Crystallographic File Structure-87 Specification of IUCr exchange standard predating CIF (Brown, 1988)

Legal

• Copyright notice (see also individual entry pages for each software package)
• IUCr policy for the Protection and the Promotion of the STAR File and CIF Standards for Exchanging and Archiving Electronic Data
• Software terms and conditions of use (see also licenses described on individual entry pages for each software package)

Software

• CBFlib C library for accessing crystallographic binary files (CBF) and image-supporting CIF (imgCIF) files
• cif2cif copies some or all CIF data from one file to another, with various transformations
• cif2pdb converts mmCIF data sets to PDB format
• cif2sx converts CIF files to SHELXL instruction files
• cif2xml copies a CIF on standard input to equivalent XML on standard output
• CIFEDIT allows viewing and editing of CIFs
• CIFFOLD application for folding and unfolding long lines in CIF
• CIFIO CIF input/output module of Xtal
• CIFLIB class library and C API for CIF
• CIFOBJ class library of mmCIF access tools
• CIFPARSE C-language function library of mmCIF access tools
• CIFPARSE-OBJ object-oriented application interface to information in mmCIF format
• CifSieve uses a modified CIF dictionary as a template for inputting data structures
• CIFtbx Fortran toolbox version 1
• CIFtbx Fortran toolbox version2
• CIFtbx Fortran toolbox version3
• ciftex filter for translating CIF to TeX
• CYCLOPS CIF data name checker version 1
• CYCLOPS CIF data name checker version 2
• DIFRAC converts diffractometer output files to CIF format
• ISTable (CIFTable) collection of classes for managing table objects
• makedict.pl and makedicthtml.pl produce TeX and HTML formatted versions of CIF dictionaries
• mmCIF Loader loads CIF data into a variety of relational database engines
• mmLib Python library for mmCIF and other bioinformatics applications
• OOSTAR Object C libraries and applications for DDL1 and DDL2 compliant CIFs
• OpenMMS toolkit for representing macromolecular structure data in several common formats
• pdb2cif converts PDB data to mmCIF format
• PDB_EXTRACT conversion of output from macromolecular structure packages to mmCIF
• pdCIFplot allows inspection of Rietveld fits from pdCIF
• PREPUB CIF validation module of Xtal
• printCIF for Word for visualizing and preparing for publication structure reports in Word format
• PyCifRW provides basic support for reading and writing CIF using Python
• QUASAR CIF syntax checking and file manipulation tool
• RasMol molecular visualizer for CIF, mmCIF and other formats
• Star_Base STAR File validator and general-purpose access tool
• STAR::Parser and related Perl modules for parsing STAR compliant data files and dictionaries
• syntax test suite: test files conforming (or not) to STAR/CIF syntax rules, to assist parser development
• vcif CIF syntax checker
• Xtal system of crystallographic software
• ZINC interface to CIF for standard Unix tools

Specifications

• CIF formal specification Version 1.1: Overview
• CIF formal specification Version 1.1: File syntax
• CIF formal specification Version 1.1: Common semantic features
• CIF syntax and grammar in Backus-Naur form (HTML format)
• CIF syntax and grammar in Backus-Naur form (text format)
• Format of date/time strings
• Format of telephone/fax numbers
• Format of proper names
• Placeholders for unknown and inapplicable values
• Recommended abbreviations within data names
• Register of public CIF dictionaries
• Report of the COMCIFS Working Group on Dictionary Maintenance
• Reserved prefixes for local dictionary extensions
• STAR syntax and grammar in Backus-Naur form (HTML format)
• STAR syntax and grammar in Backus-Naur form (text format)

Supplementary materials

Colour or larger versions of figures, web links, references, historical documents and other supplementary materials are provided for each chapter.

• 1.1. Genesis of the Crystallographic Information File
• 2.1. Specification of the STAR File
• 2.2. Specification of the Crystallographic Information File (CIF)
• 2.3. Specification of the Crystallographic Binary File (CBF/imgCIF)
• 2.4. Specification of the Molecular Information File (MIF)
• 2.5. Specification of the core CIF dictionary definition language (DDL1)
• 2.6. Specification of a relational dictionary definition language (DDL2)
• 3.1. General considerations when defining a CIF data item
• 3.2. Classification and use of core data
• 3.3. Classification and use of powder diffraction data
• 3.4. Classification and use of modulated and composite structures data
• 3.5. Classification and use of electron density data
• 3.6. Classification and use of macromolecular data
• 3.7. Classification and use of image data
• 3.8. Classification and use of symmetry data
• 4.1. Core dictionary (coreCIF)
• 4.2. Powder dictionary (pdCIF)
• 4.3. Modulated and composite structures dictionary (msCIF)
• 4.4. Electron density dictionary (rhoCIF)
• 4.5. Macromolecular dictionary (mmCIF)
• 4.6. Image dictionary (imgCIF)
• 4.7. Symmetry dictionary (symCIF)
• 4.8. Molecular Information File dictionary (MIF)
• 4.9. DDL1 dictionary
• 4.10. DDL2 dictionary
• 5.1. General considerations in programming CIF applications
• 5.2. STAR File utilities
• 5.3. Syntactic utilities for CIF
• 5.4. CIFtbx: Fortran tools for manipulating CIFs
• 5.5. The use of mmCIF architecture for PDB data management
• 5.6. CBFlib: an ANSI C library for manipulating image data
• 5.7. Small-molecule crystal structure publication using CIF