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

First online edition (2006)   ISBN: 978-1-4020-3138-0   doi: 10.1107/97809553602060000107  

Edited by S. R. Hall and B. McMahon

Contents

• Preface  (p. xi) | html | pdf |
  S. R. Hall and B. McMahon

• Historical introduction
  • 1.1. Genesis of the Crystallographic Information File  (pp. 2-10) | html | pdf | chapter contents |
    S. R. Hall and B. McMahon
    • 1.1.1. Prologue  (p. 2) | html | pdf |
    • 1.1.2. Past approaches to data exchange  (pp. 2-3) | html | pdf |
    • 1.1.3. Card-image formats  (p. 3) | html | pdf |
    • 1.1.4. The Standard Crystallographic File Structure (SCFS)  (p. 3) | html | pdf |
    • 1.1.5. The impact of networking on crystallography  (pp. 4-5) | html | pdf |
    • 1.1.6. The Working Party on Crystallographic Information (WPCI)  (p. 5) | html | pdf |
    • 1.1.7. The Crystallographic Information File  (pp. 6-7) | html | pdf |
    • 1.1.8. Diversification: the Molecular Information File and dictionary definition language  (p. 7) | html | pdf |
    • 1.1.9. The macromolecular Crystallographic Information File  (pp. 7-8) | html | pdf |
    • 1.1.10. The Crystallographic Binary File  (p. 8) | html | pdf |
    • 1.1.11. Other extension dictionaries  (pp. 8-9) | html | pdf |
    • 1.1.12. The broader context: CIF and XML  (p. 9) | html | pdf |
    • References | html | pdf |

• Concepts and specifications
  • 2.1. Specification of the STAR File  (pp. 13-19) | html | pdf | chapter contents |
    S. R. Hall and N. Spadaccini
    • 2.1.1. Introduction  (p. 13) | html | pdf |
    • 2.1.2. Universal data language concepts  (pp. 13-14) | html | pdf |
    • 2.1.3. The syntax of the STAR File  (pp. 14-16) | html | pdf |
    • Appendix 2.1.1. Backus–Naur form of the STAR syntax and grammar  (pp. 16-19) | html | pdf |
    • References | html | pdf |
  • 2.2. Specification of the Crystallographic Information File (CIF)  (pp. 20-36) | html | pdf | chapter contents |
    S. R. Hall, J. D. Westbrook, N. Spadaccini, I. D. Brown, H. J. Bernstein and B. McMahon
    • 2.2.1. Introduction  (p. 20) | html | pdf |
      S. R. Hall and J. D. Westbrook
    • 2.2.2. Terminology  (pp. 20-21) | html | pdf |
      S. R. Hall and J. D. Westbrook
    • 2.2.3. The syntax of a CIF  (pp. 21-22) | html | pdf |
      S. R. Hall and J. D. Westbrook
    • 2.2.4. Portability and archival issues  (pp. 22-23) | html | pdf |
      S. R. Hall and J. D. Westbrook
    • 2.2.5. Common semantic features  (pp. 23-24) | html | pdf |
      S. R. Hall and J. D. Westbrook
    • 2.2.6. CIF metadata and dictionary compliance  (p. 25) | html | pdf |
      S. R. Hall and J. D. Westbrook
    • 2.2.7. Formal specification of the Crystallographic Information File. Version 1.1 specification  (pp. 25-36) | html | pdf |
      S. R. Hall, N. Spadaccini, I. D. Brown, H. J. Bernstein, J. D. Westbrook and B. McMahon
    • References | html | pdf |
  • 2.3. Specification of the Crystallographic Binary File (CBF/imgCIF)  (pp. 37-43) | html | pdf | chapter contents |
    H. J. Bernstein and A. P. Hammersley
    • 2.3.1. Introduction  (p. 37) | html | pdf |
    • 2.3.2. CBF and imgCIF  (pp. 37-39) | html | pdf |
    • 2.3.3. Overview of the format  (pp. 39-41) | html | pdf |
    • 2.3.4. A complex example  (p. 42) | html | pdf |
    • 2.3.5. imgCIF encodings  (pp. 42-43) | html | pdf |
    • Appendix 2.3.1. Deprecated CBF conventions  (p. 43) | html | pdf |
    • References | html | pdf |
  • 2.4. Specification of the Molecular Information File (MIF)  (pp. 44-52) | html | pdf | chapter contents |
    F. H. Allen, J. M. Barnard, A. P. F. Cook and S. R. Hall
    • 2.4.1. Introduction  (p. 44) | html | pdf |
    • 2.4.2. Historical background  (pp. 44-45) | html | pdf |
    • 2.4.3. MIF objectives  (p. 45) | html | pdf |
    • 2.4.4. MIF concepts and syntax  (pp. 45-47) | html | pdf |
    • 2.4.5. Atoms, bonds and molecular representations  (pp. 47-48) | html | pdf |
    • 2.4.6. Bonding conventions  (p. 48) | html | pdf |
    • 2.4.7. Structural templates  (p. 48) | html | pdf |
    • 2.4.8. Stereochemistry and geometry at stereogenic centres  (pp. 48-50) | html | pdf |
    • 2.4.9. MIF query applications  (pp. 50-51) | html | pdf |
    • 2.4.10. Conclusion  (p. 51) | html | pdf |
    • References | html | pdf |
  • 2.5. Specification of the core CIF dictionary definition language (DDL1)  (pp. 53-60) | html | pdf | chapter contents |
    S. R. Hall and A. P. F. Cook
    • 2.5.1. Introduction  (p. 53) | html | pdf |
    • 2.5.2. The organization of a CIF dictionary  (pp. 53-54) | html | pdf |
    • 2.5.3. Definition attributes  (p. 54) | html | pdf |
    • 2.5.4. DDL versions  (pp. 54-55) | html | pdf |
    • 2.5.5. The structure of DDL1 definitions  (pp. 55-57) | html | pdf |
    • 2.5.6. DDL1 attribute descriptions  (pp. 57-60) | html | pdf |
    • References | html | pdf |
  • 2.6. Specification of a relational dictionary definition language (DDL2)  (pp. 61-70) | html | pdf | chapter contents |
    J. D. Westbrook, H. M. Berman and S. R. Hall
    • 2.6.1. Introduction  (p. 61) | html | pdf |
    • 2.6.2. The DDL2 presentation  (p. 61) | html | pdf |
    • 2.6.3. Overview of the elements of DDL2  (p. 62) | html | pdf |
    • 2.6.4. DDL2 organization  (p. 63) | html | pdf |
    • 2.6.5. DDL2 dictionary applications  (pp. 63-66) | html | pdf |
    • 2.6.6. Detailed DDL2 specifications  (pp. 65-70) | html | pdf |
    • References | html | pdf |

• CIF data definition and classification
  • 3.1. General considerations when defining a CIF data item  (pp. 73-91) | html | pdf | chapter contents |
    B. McMahon
    • 3.1.1. Introduction  (pp. 73-74) | html | pdf |
    • 3.1.2. Informal definition procedures  (p. 74) | html | pdf |
    • 3.1.3. Formal definition process  (pp. 74-75) | html | pdf |
    • 3.1.4. Choice of data model  (pp. 75-76) | html | pdf |
    • 3.1.5. Constructing a DDL1 dictionary  (pp. 76-79) | html | pdf |
    • 3.1.6. Constructing a DDL2 dictionary  (pp. 79-83) | html | pdf |
    • 3.1.7. Composing new data definitions  (pp. 83-85) | html | pdf |
    • 3.1.8. Management of multiple dictionaries  (pp. 85-88) | html | pdf |
    • 3.1.9. Composite dictionaries  (pp. 88-89) | html | pdf |
    • 3.1.10. Public CIF dictionaries  (pp. 89-91) | html | pdf |
    • References | html | pdf |
  • 3.2. Classification and use of core data  (pp. 92-116) | html | pdf | chapter contents |
    S. R. Hall, P. M. D. Fitzgerald and B. McMahon
    • 3.2.1. Introduction  (p. 92) | html | pdf |
    • 3.2.2. Experimental measurements  (pp. 92-98) | html | pdf |
    • 3.2.3. Analysis  (pp. 98-102) | html | pdf |
    • 3.2.4. Atomicity, chemistry and structure  (pp. 102-112) | html | pdf |
    • 3.2.5. Publication  (pp. 112-114) | html | pdf |
    • 3.2.6. File metadata  (pp. 114-116) | html | pdf |
    • Appendix 3.2.1. Category structure of the core CIF dictionary  (p. 116) | html | pdf |
    • References | html | pdf |
  • 3.3. Classification and use of powder diffraction data  (pp. 117-130) | html | pdf | chapter contents |
    B. H. Toby
    • 3.3.1. Introduction  (p. 117) | html | pdf |
    • 3.3.2. Dictionary design considerations  (p. 117) | html | pdf |
    • 3.3.3. pdCIF dictionary sections  (pp. 117-118) | html | pdf |
    • 3.3.4. Experimental measurements  (pp. 118-121) | html | pdf |
    • 3.3.5. Analysis  (pp. 121-123) | html | pdf |
    • 3.3.6. Atomicity, chemistry and structure  (p. 123) | html | pdf |
    • 3.3.7. File metadata  (pp. 123-126) | html | pdf |
    • 3.3.8. pdCIF for storing unprocessed measurements  (pp. 126-128) | html | pdf |
    • 3.3.9. Use of pdCIF for Rietveld refinement results  (pp. 128-129) | html | pdf |
    • 3.3.10. Other pdCIF applications  (pp. 129-130) | html | pdf |
    • Appendix 3.3.1. Category structure of the powder CIF dictionary  (p. 130) | html | pdf |
    • References | html | pdf |
  • 3.4. Classification and use of modulated and composite structures data  (pp. 131-140) | html | pdf | chapter contents |
    G. Madariaga
    • 3.4.1. Introduction  (p. 131) | html | pdf |
    • 3.4.2. Dictionary design considerations  (pp. 131-132) | html | pdf |
    • 3.4.3. Arrangement of the dictionary  (pp. 132-137) | html | pdf |
    • 3.4.4. Use of the msCIF dictionary  (pp. 137-139) | html | pdf |
    • Appendix 3.4.1. Category structure of the msCIF dictionary  (p. 139) | html | pdf |
    • References | html | pdf |
  • 3.5. Classification and use of electron density data  (pp. 141-143) | html | pdf | chapter contents |
    P. R. Mallinson and I. D. Brown
    • 3.5.1. Introduction  (p. 141) | html | pdf |
    • 3.5.2. Dictionary design considerations  (p. 141) | html | pdf |
    • 3.5.3. Classification of data definitions  (pp. 141-143) | html | pdf |
    • 3.5.4. Development of the dictionary and supporting software  (p. 143) | html | pdf |
    • References | html | pdf |
  • 3.6. Classification and use of macromolecular data  (pp. 144-198) | html | pdf | chapter contents |
    P. M. D. Fitzgerald, J. D. Westbrook, P. E. Bourne, B. McMahon, K. D. Watenpaugh and H. M. Berman
    • 3.6.1. Introduction  (p. 144) | html | pdf |
    • 3.6.2. Considerations underlying the design of the dictionary  (pp. 144-145) | html | pdf |
    • 3.6.3. Overview of the mmCIF data model  (pp. 145-147) | html | pdf |
    • 3.6.4. Content of the macromolecular CIF dictionary  (pp. 147-148) | html | pdf |
    • 3.6.5. Experimental measurements  (pp. 148-152) | html | pdf |
    • 3.6.6. Analysis  (pp. 152-164) | html | pdf |
    • 3.6.7. Atomicity, chemistry and structure  (pp. 164-190) | html | pdf |
    • 3.6.8. Publication  (pp. 190-194) | html | pdf |
    • 3.6.9. File metadata  (pp. 194-195) | html | pdf |
    • Appendix 3.6.1. Category structure of the mmCIF dictionary  (p. 195) | html | pdf |
    • Appendix 3.6.2. The Protein Data Bank exchange data dictionary  (pp. 195-197) | html | pdf |
      J. D. Westbrook, K. Henrick, E. L. Ulrich and H. M. Berman
    • References | html | pdf |
  • 3.7. Classification and use of image data  (pp. 199-205) | html | pdf | chapter contents |
    H. J. Bernstein
    • 3.7.1. Introduction  (p. 199) | html | pdf |
    • 3.7.2. Binary image data  (pp. 199-201) | html | pdf |
    • 3.7.3. Axes  (pp. 201-202) | html | pdf |
    • 3.7.4. The diffraction experiment  (pp. 202-205) | html | pdf |
    • Appendix 3.7.1. Category structure of the CBF/imgCIF dictionary  (p. 205) | html | pdf |
    • References | html | pdf |
  • 3.8. Classification and use of symmetry data  (pp. 206-208) | html | pdf | chapter contents |
    I. D. Brown
    • 3.8.1. Introduction  (p. 206) | html | pdf |
    • 3.8.2. Dictionary design considerations  (pp. 206-207) | html | pdf |
    • 3.8.3. Arrangement of the dictionary  (pp. 207-208) | html | pdf |
    • 3.8.4. Future developments  (p. 208) | html | pdf |
    • References | html | pdf |

• Data dictionaries
  • 4.1. Core dictionary (coreCIF)  (pp. 210-257) | html | pdf | chapter contents |
    S. R. Hall, F. H. Allen and I. D. Brown
  • 4.2. Powder dictionary (pdCIF)  (pp. 258-269) | html | pdf | chapter contents |
    B. H. Toby
  • 4.3. Modulated and composite structures dictionary (msCIF)  (pp. 270-289) | html | pdf | chapter contents |
    G. Madariaga
  • 4.4. Electron density dictionary (rhoCIF)  (pp. 290-294) | html | pdf | chapter contents |
    P. R. Mallinson
  • 4.5. Macromolecular dictionary (mmCIF)  (pp. 295-443) | html | pdf | chapter contents |
    P. M. D. Fitzgerald, J. D. Westbrook, P. E. Bourne, B. McMahon, K. D. Watenpaugh and H. M. Berman
  • 4.6. Image dictionary (imgCIF)  (pp. 444-458) | html | pdf | chapter contents |
    A. P. Hammersley, H. J. Bernstein and J. D. Westbrook
  • 4.7. Symmetry dictionary (symCIF)  (pp. 459-466) | html | pdf | chapter contents |
    I. D. Brown
  • 4.8. Molecular Information File dictionary (MIF)  (pp. 467-470) | html | pdf | chapter contents |
    F. H. Allen, J. M. Barnard, A. P. F. Cook and S. R. Hall
  • 4.9. DDL1 dictionary  (pp. 471-472) | html | pdf | chapter contents |
    S. R. Hall
  • 4.10. DDL2 dictionary  (pp. 473-478) | html | pdf | chapter contents |
    J. D. Westbrook and S. R. Hall

• Applications
  • 5.1. General considerations in programming CIF applications  (pp. 481-487) | html | pdf | chapter contents |
    H. J. Bernstein
    • 5.1.1. Introduction  (p. 481) | html | pdf |
    • 5.1.2. Background  (pp. 481-483) | html | pdf |
    • 5.1.3. Strategies in designing a CIF-aware application  (pp. 483-486) | html | pdf |
    • 5.1.4. Conclusion  (p. 486) | html | pdf |
    • References | html | pdf |
  • 5.2. STAR File utilities  (pp. 488-498) | html | pdf | chapter contents |
    N. Spadaccini, S. R. Hall and B. McMahon
    • 5.2.1. Introduction  (p. 488) | html | pdf |
    • 5.2.2. Data instances and context  (pp. 488-491) | html | pdf |
    • 5.2.3. Star_Base: a general-purpose data extractor for STAR Files  (pp. 491-494) | html | pdf |
    • 5.2.4. Editing STAR Files with Star.vim  (p. 494) | html | pdf |
    • 5.2.5. Browser-based viewing with StarMarkUp  (pp. 494-495) | html | pdf |
    • 5.2.6. Object-oriented STAR programming  (pp. 495-497) | html | pdf |
    • References | html | pdf |
  • 5.3. Syntactic utilities for CIF  (pp. 499-525) | html | pdf | chapter contents |
    B. McMahon
    • 5.3.1. Introduction  (p. 499) | html | pdf |
    • 5.3.2. Syntax checker  (pp. 499-501) | html | pdf |
    • 5.3.3. Editors with graphical user interfaces  (pp. 501-507) | html | pdf |
    • 5.3.4. Data-name validation  (pp. 507-509) | html | pdf |
    • 5.3.5. File transformation software  (pp. 509-515) | html | pdf |
    • 5.3.6. Libraries for scripting languages  (pp. 515-517) | html | pdf |
    • 5.3.7. Rapid development tools  (pp. 517-522) | html | pdf |
    • 5.3.8. Tools for mmCIF  (pp. 522-525) | html | pdf |
    • 5.3.9. Concluding remarks  (p. 525) | html | pdf |
    • References | html | pdf |
  • 5.4. CIFtbx: Fortran tools for manipulating CIFs  (pp. 526-538) | html | pdf | chapter contents |
    H. J. Bernstein and S. R. Hall
    • 5.4.1. Introduction  (p. 526) | html | pdf |
    • 5.4.2. An overview of the library  (p. 526) | html | pdf |
    • 5.4.3. Initialization commands  (pp. 526-527) | html | pdf |
    • 5.4.4. Read commands  (p. 527) | html | pdf |
    • 5.4.5. Write commands  (pp. 527-528) | html | pdf |
    • 5.4.6. Variables  (pp. 528-529) | html | pdf |
    • 5.4.7. Name aliases  (pp. 529-530) | html | pdf |
    • 5.4.8. Implementation of the tools  (p. 530) | html | pdf |
    • 5.4.9. How to read CIF data  (p. 530) | html | pdf |
    • 5.4.10. How to write a CIF  (pp. 530-531) | html | pdf |
    • 5.4.11. Error-message glossary  (pp. 531-535) | html | pdf |
    • 5.4.12. Internals and programming style  (pp. 535-538) | html | pdf |
    • 5.4.13. Distribution  (p. 538) | html | pdf |
    • References | html | pdf |
  • 5.5. The use of mmCIF architecture for PDB data management  (pp. 539-543) | html | pdf | chapter contents |
    J. D. Westbrook, H. Yang, Z. Feng and H. M. Berman
    • 5.5.1. Introduction  (p. 539) | html | pdf |
    • 5.5.2. Representing macromolecular structure data  (pp. 539-541) | html | pdf |
    • 5.5.3. Integrated data-processing system: overview  (pp. 541-543) | html | pdf |
    • 5.5.4. Access  (p. 543) | html | pdf |
    • References | html | pdf |
  • 5.6. CBFlib: an ANSI C library for manipulating image data  (pp. 544-556) | html | pdf | chapter contents |
    P. J. Ellis and H. J. Bernstein
    • 5.6.1. Introduction  (pp. 544-545) | html | pdf |
    • 5.6.2. CBFlib function descriptions  (pp. 545-552) | html | pdf |
    • 5.6.3. Compression schemes  (p. 552) | html | pdf |
    • 5.6.4. Sample templates  (pp. 552-554) | html | pdf |
    • 5.6.5. Example programs  (pp. 555-556) | html | pdf |
    • References | html | pdf |
  • 5.7. Small-molecule crystal structure publication using CIF  (pp. 557-569) | html | pdf | chapter contents |
    P. R. Strickland, M. A. Hoyland and B. McMahon
    • 5.7.1. Introduction  (p. 557) | html | pdf |
    • 5.7.2. Case study: the fully automated reporting of small-unit-cell crystal structures  (pp. 557-562) | html | pdf |
    • 5.7.3. CIF and other journals  (pp. 562-564) | html | pdf |
    • Appendix 5.7.1. Request list for Acta Crystallographica Section C  (pp. 564-566) | html | pdf |
    • Appendix 5.7.2. Data validation using checkcif  (pp. 566-568) | html | pdf |
    • References | html | pdf |