International Tables for Crystallography
Volume G: Definition and exchange of crystallographic data

Second online edition (2026)   ISBN: 978-1-3944-4588-2   doi: 10.1107/97809553602060000119  

Edited by J. R. Hester and B. McMahon

Contents

• Setting the scene
  • 1.1. How to navigate this volume  (pp. 1-2) | html | pdf | chapter contents |
    James R. Hester and Brian McMahon
    • 1.1.1. Introduction  (p. 1) | html | pdf |
    • 1.1.2. The general reader  (p. 1) | html | pdf |
    • 1.1.3. The structural scientist  (p. 1) | html | pdf |
    • 1.1.4. The software developer  (p. 1) | html | pdf |
    • 1.1.5. The database manager  (p. 2) | html | pdf |
    • 1.1.6. The non-crystallographer  (p. 2) | html | pdf |
    • 1.1.7. The dictionary developer  (p. 2) | html | pdf |
    • References | html | pdf |
  • 1.2. Crystallographic data in the digital era| html | pdf | chapter contents |
    James R. Hester and Brian McMahon

• Specifications
  • 2.1. An overview of the Crystallographic Information Framework  (pp. 1-8) | html | pdf | chapter contents |
    James R. Hester and Brian McMahon
    • 2.1.1. Executive summary  (pp. 1-2) | html | pdf |
    • 2.1.2. Introduction  (p. 2) | html | pdf |
    • 2.1.3. The CIF format  (pp. 2-8) | html | pdf |
    • 2.1.4. Dictionary definitions  (pp. 4-6) | html | pdf |
    • 2.1.5. Administration of the standard  (pp. 6-7) | html | pdf |
    • 2.1.6. Software resources  (p. 7) | html | pdf |
    • References | html | pdf |
  • 2.2. Specification of the Crystallographic Information Framework format (CIF format)  (pp. 1-20) | html | pdf | chapter contents |
    John C. Bollinger and James R. Hester
    • 2.2.1. Introduction  (p. 1) | html | pdf |
    • 2.2.2. Data model and terminology  (pp. 1-2) | html | pdf |
    • 2.2.3. CIF syntax  (pp. 2-13) | html | pdf |
    • 2.2.4. CIF semantics  (pp. 14-19) | html | pdf |
    • 2.2.5. Considerations for CIF exchange and archiving  (pp. 19-20) | html | pdf |
    • References | html | pdf |
  • 2.3. Specification of the Crystallographic Binary Format  (pp. 1-12) | html | pdf | chapter contents |
    Herbert J. Bernstein and Andrew P. Hammersley
    • 2.3.1. Introduction  (p. 1) | html | pdf |
    • 2.3.2. CBF and imgCIF  (pp. 1-3) | html | pdf |
    • 2.3.3. Overview of the format  (pp. 3-7) | html | pdf |
    • 2.3.4. Compression schemes  (pp. 7-10) | html | pdf |
    • 2.3.5. A complex example  (pp. 10-11) | html | pdf |
    • 2.3.6. imgCIF encodings  (pp. 10-11) | html | pdf |
    • 2.3.7. Concluding remarks  (pp. 11-12) | html | pdf |
    • References | html | pdf |
  • 2.4. Data definition languages for CIF dictionaries  (pp. 1-30) | html | pdf | chapter contents |
    James R. Hester and Nick Spadaccini
    • 2.4.1. Introduction  (pp. 1-2) | html | pdf |
    • 2.4.2. DDLm  (pp. 2-17) | html | pdf |
    • 2.4.3. DDL2  (pp. 17-30) | html | pdf |
      John D. Westbrook, Helen M. Berman and Sydney R. Hall
    • References | html | pdf |
  • 2.5. dREL: an embedded dictionary algorithm language  (pp. 1-11) | html | pdf | chapter contents |
    James R. Hester and Nick Spadaccini
    • 2.5.1. Introduction  (pp. 1-2) | html | pdf |
    • 2.5.2. dREL concepts  (pp. 2-5) | html | pdf |
    • 2.5.3. dREL syntax and semantics  (pp. 5-10) | html | pdf |
    • 2.5.4. dREL for validation  (p. 10) | html | pdf |
    • 2.5.5. Historical notes  (p. 10) | html | pdf |
    • References | html | pdf |
  • 2.6. Alternative syntaxes  (pp. 1-11) | html | pdf | chapter contents |
    John C. Bollinger, James R. Hester and Brian McMahon
    • 2.6.1. Introduction  (p. 1) | html | pdf |
    • 2.6.2. Representing CIF data in JSON format  (pp. 1-5) | html | pdf |
    • 2.6.3. Data interchange in structural biology  (pp. 5-9) | html | pdf |
    • 2.6.4. Other database and interoperability implementations  (pp. 9-10) | html | pdf |
    • References | html | pdf |
  • 2.7. NeXus HDF5 format for crystallography  (pp. 1-17) | html | pdf | chapter contents |
    Aaron S. Brewster, Graeme Winter, Tobias S. Richter, Daniel W. Paley, Jonathan Sloan and Herbert J. Bernstein
    • 2.7.1. Introduction  (pp. 1-2) | html | pdf |
    • 2.7.2. NXmx overview  (pp. 2-6) | html | pdf |
    • 2.7.3. Available software  (pp. 6-7) | html | pdf |
    • 2.7.4. Concluding remarks  (p. 7) | html | pdf |
    • Appendix 2.7.1. Summary concordance of CIF data names and NeXus entries  (pp. 7-17) | html | pdf |
    • References | html | pdf |

• CIF data definitions
  • 3.1. Creating and expanding CIF dictionaries| html | pdf | chapter contents |
    James R. Hester and Brian McMahon
  • 3.2. Classification and use of core data| html | pdf | chapter contents |
    Sydney R. Hall, Paula M. D. Fitzgerald, Brian McMahon, I. David Brown, James R. Hester, Matthew R. Rowles, Antanas Vaitkus, Andrius Merkys, John C. Bollinger and Simon P. Westrip
  • 3.3. Definitions for multi-block data files| html | pdf | chapter contents |
    James R. Hester, Antanas Vaitkus and Matthew R. Rowles
  • 3.4. Classification and use of restraints and constraints| html | pdf | chapter contents |
    I. David Brown
  • 3.5. Classification and use of twinning data  (pp. 1-5) | html | pdf | chapter contents |
    Victor G. Young Jr
    • 3.5.1. Introduction  (p. 1) | html | pdf |
    • 3.5.2. TLS and TLQS twins  (pp. 1-3) | html | pdf |
    • 3.5.3. Twin dictionary design  (pp. 3-4) | html | pdf |
    • 3.5.4. Twin dictionary examples  (pp. 4-5) | html | pdf |
    • 3.5.5. Future developments  (p. 5) | html | pdf |
    • References | html | pdf |
  • 3.6. Classification and use of powder diffraction data| html | pdf | chapter contents |
    Brian H. Toby, Matthew R. Rowles, James R. Hester and Antanas Vaitkus
  • 3.7. Classification and use of modulated and composite structures data| html | pdf | chapter contents |
    Gotzon Madariaga
  • 3.8. Classification and use of electron density data| html | pdf | chapter contents |
    Paul R. Mallinson and I. David Brown
  • 3.9. Classification and use of magnetic data| html | pdf | chapter contents |
    Branton Campbell, J. Manuel Perez-Mato, Václav Petříček, Juan Rodriguez-Carvajal and James R. Hester
  • 3.10. Classification and use of topological data  (pp. 1-10) | html | pdf | chapter contents |
    Vladislav A. Blatov, Davide M. Proserpio and Robert M. Hanson
    • 3.10.1. Introduction  (p. 1) | html | pdf |
    • 3.10.2. Dictionary design considerations  (p. 1) | html | pdf |
    • 3.10.3. Classification of data definitions  (pp. 1-4) | html | pdf |
    • 3.10.4. Examples  (pp. 4-9) | html | pdf |
    • 3.10.5. Available reference implementations  (p. 9) | html | pdf |
    • References | html | pdf |
  • 3.11. Classification and use of macromolecular data  (pp. 1-) | html | pdf | chapter contents |
    Paula M. D. Fitzgerald, John D. Westbrook, Philip E. Bourne, Brian McMahon, Keith D. Watenpaugh, Helen M. Berman, Ezra Peisach, Kyle L. Morris, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar and Stephen K. Burley
    • 3.11.1. Introduction  (p. 1) | html | pdf |
    • 3.11.2. Considerations underlying the design of the dictionary  (pp. 1-2) | html | pdf |
    • 3.11.3. Overview of the mmCIF data model  (pp. 2-4) | html | pdf |
    • 3.11.4. Content of the macromolecular CIF dictionary  (pp. 4-5) | html | pdf |
    • 3.11.5. Experimental measurements  (pp. 5-9) | html | pdf |
    • 3.11.6. Analysis  (pp. 9-21) | html | pdf |
    • 3.11.7. Atomicity, chemistry and structure  (pp. 21-47) | html | pdf |
    • 3.11.8. Publication  (pp. 47-51) | html | pdf |
    • 3.11.9. File metadata  (pp. 51-52) | html | pdf |
    • Appendix 3.11.1. Category structure of the mmCIF dictionary  (p. 52) | html | pdf |
    • Appendix 3.11.2. The Protein Data Bank exchange data dictionary  (pp. 53-55) | html | pdf |
      John D. Westbrook, Ezra Peisach, Kyle L. Morris, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar and Stephen K. Burley
    • References | html | pdf |
  • 3.12. Classification and use of image data| html | pdf | chapter contents |
    Herbert J. Bernstein

• The CIF ontology
  • 4.1. Management and use of CIF dictionaries| html | pdf | chapter contents |
    James R. Hester and Brian McMahon
  • 4.2. Core dictionary (coreCIF)| html | pdf | chapter contents |
    Sydney R. Hall, Frank H. Allen, I. David Brown, James R. Hester, Antanas Vaitkus and Matthew R. Rowles
  • 4.3. Multi-block CIF dictionary| html | pdf | chapter contents |
    Matthew R. Rowles, James R. Hester and Antanas Vaitkus
  • 4.4. Restraints dictionary| html | pdf | chapter contents |
    I. David Brown
  • 4.5. Twinning dictionary (twinCIF)| html | pdf | chapter contents |
    Victor G. Young Jr, I. David Brown and James R. Hester
  • 4.6. Powder dictionary (pdCIF)| html | pdf | chapter contents |
    Brian H. Toby, James R. Hester and Matthew R. Rowles
  • 4.7. Modulated structures dictionary (msCIF)| html | pdf | chapter contents |
    Gotzon Madariaga
  • 4.8. Electron density dictionary (rhoCIF)| html | pdf | chapter contents |
    Paul R. Mallinson
  • 4.9. Magnetic dictionary (magCIF)| html | pdf | chapter contents |
    Branton Campbell, J. Manuel Perez-Mato, Václav Petříček, Juan Rodriguez-Carvajal and Wiesława Sikora
  • 4.10. Topology dictionary (topoCIF)| html | pdf | chapter contents |
    Vladislav A. Blatov, Davide M. Proserpio and Robert M. Hanson
  • 4.11. Macromolecular dictionary (mmCIF)| html | pdf | chapter contents |
    Paula M. D. Fitzgerald, John D. Westbrook, Philip E. Bourne, Brian McMahon, Keith D. Watenpaugh and Helen M. Berman
  • 4.12. Image dictionary (imgCIF)| html | pdf | chapter contents |
    Andrew P. Hammersley, Herbert J. Bernstein and John D. Westbrook
  • 4.13. DDLm dictionary| html | pdf | chapter contents |
    Sydney R. Hall, Nick Spadaccini and James R. Hester
  • 4.14. DDL2 dictionary| html | pdf | chapter contents |
    John D. Westbrook and Sydney R. Hall

• Software
  • 5.1. General considerations in programming CIF applications  (pp. 1-10) | html | pdf | chapter contents |
    Herbert J. Bernstein, John C. Bollinger and Antanas Vaitkus
    • 5.1.1. Introduction  (pp. 1-2) | html | pdf |
    • 5.1.2. Flavours of CIF  (p. 2) | html | pdf |
    • 5.1.3. Dictionary usage  (pp. 4-5) | html | pdf |
    • 5.1.4. Strategies and considerations in designing a CIF-aware application  (pp. 5-9) | html | pdf |
    • 5.1.5. Concluding remarks  (p. 9) | html | pdf |
    • References | html | pdf |
  • 5.2. CIF application programming interface and reference implementation| html | pdf | chapter contents |
    John C. Bollinger
  • 5.3. Other programming libraries and packages| html | pdf | chapter contents |
    Herbert J. Bernstein, Sydney R. Hall, Paul J. Ellis, Aaron S. Brewster, Daniel W. Paley, Andrius Merkys, Antanas Vaitkus, Saulius Gražulis, James R. Hester, Graeme Winter and Brian McMahon
  • 5.4. Syntactic utilities for CIF  (pp. 1-9) | html | pdf | chapter contents |
    Brian McMahon
    • 5.4.1. Introduction  (p. 1) | html | pdf |
    • 5.4.2. Syntax checkers  (pp. 1-3) | html | pdf |
    • 5.4.3. Syntax conversion  (pp. 3-4) | html | pdf |
    • 5.4.4. Data extractors  (pp. 4-6) | html | pdf |
    • 5.4.5. Syntax highlighting modes  (pp. 6-8) | html | pdf |
    • References | html | pdf |
  • 5.5. Semantic utilities for CIF and crystallographic packages| html | pdf | chapter contents |
    James R. Hester and Brian McMahon
  • 5.6. End-user applications  (pp. 1-8) | html | pdf | chapter contents |
    Simon P. Westrip, Ian J. Bruno, Andrew J. Peel, Seth B. Wiggin, Daniel Kratzert and Robert M. Hanson
    • 5.6.1. Introduction  (p. 1) | html | pdf |
    • 5.6.2. publCIF  (pp. 1-2) | html | pdf |
    • 5.6.3. enCIFer and Mercury  (pp. 2-4) | html | pdf |
    • 5.6.4. FinalCIF  (pp. 4-5) | html | pdf |
    • 5.6.5. Jmol and JSmol  (pp. 5-8) | html | pdf |
    • References | html | pdf |

• Publishing
  • 6.1. Small-molecule crystal structure publication using CIF  (pp. 1-10) | html | pdf | chapter contents |
    Peter R. Strickland, Michael A. Hoyland and Brian McMahon
    • 6.1.1. Introduction  (p. 1) | html | pdf |
    • 6.1.2. Direct publication from CIF: IUCrData as a case study  (pp. 1-3) | html | pdf |
    • 6.1.3. Desirable information in a reported structure  (pp. 3-7) | html | pdf |
    • 6.1.4. Automated validation of structures by checkCIF  (pp. 7-8) | html | pdf |
    • 6.1.5. Concluding remarks  (p. 8) | html | pdf |
    • Appendix 6.1.1. Data validation tests for single-crystal structures using checkCIF  (pp. 9-14) | html | pdf |
    • References | html | pdf |
  • 6.2. Publication of biological macromolecule structures using CIF| html | pdf | chapter contents |
    Brian McMahon
  • 6.3. Use of CIF in raw data publication workflows| html | pdf | chapter contents |
    Loes M. J. Kroon-Batenburg and James R. Hester

• Databases
  • 7.1. Chemical crystallography databases  (pp. 1-) | html | pdf | chapter contents |
    Ian J. Bruno, Clare A. Tovee, Suzanna C. Ward, Matthew P. Lightfoot, Saulius Gražulis, Stephan Rühl, Annett Steudel, Silke Rehme, Soorya N. Kabekkodu, Jon Gabirondo-López, Emre S. Tasci and Gotzon Madariaga
    • 7.1.1. Introduction  (pp. 1-2) | html | pdf |
    • 7.1.2. The Cambridge Structural Database  (pp. 2-7) | html | pdf |
    • 7.1.3. The Crystallography Open Database  (pp. 7-11) | html | pdf |
    • 7.1.4. The Inorganic Crystal Structure Database  (pp. 11-14) | html | pdf |
    • 7.1.5. The Powder Diffraction File  (pp. 14-17) | html | pdf |
    • 7.1.6. The Bilbao Modulated Structures Database  (pp. 17-21) | html | pdf |
    • References | html | pdf |
  • 7.2. Macromolecular databases  (pp. 1-6) | html | pdf | chapter contents |
    Ezra Peisach and Stephen K. Burley
    • 7.2.1. Introduction  (p. 1) | html | pdf |
    • 7.2.2. Representation of macromolecular structure data  (pp. 1-3) | html | pdf |
    • 7.2.3. PDB data-processing system overview  (pp. 3-4) | html | pdf |
    • 7.2.4. Access  (p. 5) | html | pdf |
    • 7.2.5. Interoperability with other resources  (p. 5) | html | pdf |
    • References | html | pdf |

• Historical material
  • 8.1. Genesis of the Crystallographic Information File  (pp. 1-10) | html | pdf | chapter contents |
    Sydney R. Hall and Brian McMahon
    • 8.1.1. Editorial note  (p. 1) | html | pdf |
    • 8.1.2. Prologue  (pp. 1-2) | html | pdf |
    • 8.1.3. Past approaches to data exchange  (p. 2) | html | pdf |
    • 8.1.4. Card-image formats  (p. 2) | html | pdf |
    • 8.1.5. The Standard Crystallographic File Structure (SCFS)  (pp. 2-3) | html | pdf |
    • 8.1.6. The impact of networking on crystallography  (pp. 3-4) | html | pdf |
    • 8.1.7. The Working Party on Crystallographic Information (WPCI)  (p. 4) | html | pdf |
    • 8.1.8. The Crystallographic Information File  (p. 4) | html | pdf |
    • 8.1.9. Diversification: the Molecular Information File and dictionary definition language  (pp. 4-6) | html | pdf |
    • 8.1.10. The macromolecular Crystallographic Information File  (pp. 6-7) | html | pdf |
    • 8.1.11. The Crystallographic Binary File  (p. 7) | html | pdf |
    • 8.1.12. Future-proofing: syntax and dictionary enhancements  (pp. 7-8) | html | pdf |
    • 8.1.13. Other extension dictionaries  (p. 8) | html | pdf |
    • Appendix 8.1.1. A timeline of crystallographic information  (pp. 8-9) | html | pdf |
    • References | html | pdf |
  • 8.2. Specification of the STAR File  (pp. 1-7) | html | pdf | chapter contents |
    Sydney R. Hall and Nick Spadaccini
    • 8.2.1. Editorial note  (p. 1) | html | pdf |
    • 8.2.2. Introduction  (p. 1) | html | pdf |
    • 8.2.3. Universal data language concepts  (pp. 1-2) | html | pdf |
    • 8.2.4. The syntax of the STAR File  (pp. 2-6) | html | pdf |
    • 8.2.5. Referencing data  (p. 6) | html | pdf |
    • References | html | pdf |
  • 8.3. Specification of the legacy core CIF dictionary definition language (DDL1)  (pp. 1-9) | html | pdf | chapter contents |
    Sydney R. Hall and Anthony P. F. Cook
    • 8.3.1. Editorial note  (p. 1) | html | pdf |
    • 8.3.2. Introduction  (p. 1) | html | pdf |
    • 8.3.3. The organization of a CIF dictionary  (p. 2) | html | pdf |
    • 8.3.4. Definition attributes  (p. 2) | html | pdf |
    • 8.3.5. The structure of DDL1 definitions  (pp. 2-5) | html | pdf |
    • 8.3.6. DDL1 attribute descriptions  (pp. 5-7) | html | pdf |
    • Appendix 8.3.1. DDL1 dictionary  (pp. 7-9) | html | pdf |
    • References | html | pdf |
  • 8.4. Historical software| html | pdf | chapter contents |
    Brian McMahon