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 |
    • Figures
      • Fig. 1.1.3.1. An abbreviated example of a PDB format file  (p. 3) | html | pdf |
      • Fig. 1.1.3.2. An example of a CSD BCCAB format file  (p. 4) | html | pdf |
      • Fig. 1.1.4.1. An abbreviated example of a Standard Crystallographic File Structure (SCFS) format file  (p. 4) | html | pdf |
      • Fig. 1.1.6.1. Example 1 of a CIF  (p. 5) | html | pdf |
      • Fig. 1.1.6.2. Example 2 of a CIF  (p. 6) | html | pdf |
      • Fig. 1.1.7.1. Initial set of data items considered to be essential in a structure report submitted to Acta Crystallographica Section C  (p. 6) | html | pdf |
      • Fig. 1.1.8.1. Informal DDL used in the initial version of the core CIF dictionary (now superseded by DDL1.4).  (p. 7) | 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 |
      • 2.1.2.1. Data models  (pp. 13-14) | html | pdf |
    • 2.1.3. The syntax of the STAR File  (pp. 14-16) | html | pdf |
      • 2.1.3.1. Text string  (p. 14) | html | pdf |
      • 2.1.3.2. Data name  (p. 15) | html | pdf |
      • 2.1.3.3. Data value  (p. 15) | html | pdf |
      • 2.1.3.4. Data item  (p. 15) | html | pdf |
      • 2.1.3.5. Data loop list  (p. 15) | html | pdf |
      • 2.1.3.6. Save frame  (p. 15) | html | pdf |
      • 2.1.3.7. Data block  (pp. 15-16) | html | pdf |
      • 2.1.3.8. Global block  (p. 16) | html | pdf |
      • 2.1.3.9. Data sets and scopes  (p. 16) | html | pdf |
      • 2.1.3.10. Privileged constructs  (p. 16) | html | pdf |
      • 2.1.3.11. Using stop_ in looped lists  (p. 16) | html | pdf |
    • Appendix 2.1.1. Backus–Naur form of the STAR syntax and grammar  (pp. 16-19) | html | pdf |
      • A2.1.1.1. Lexical tokens  (p. 17) | html | pdf |
      • A2.1.1.2. STAR grammar  (pp. 17-19) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 2.1.3.1. Nested scopes of STAR data sets  (p. 16) | 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
      • 2.2.4.1. Character set  (p. 22) | html | pdf |
      • 2.2.4.2. Line terminators  (p. 22) | html | pdf |
      • 2.2.4.3. Line lengths  (p. 23) | html | pdf |
      • 2.2.4.4. Lengths of data names and block codes  (p. 23) | html | pdf |
      • 2.2.4.5. Case sensitivity  (p. 23) | html | pdf |
    • 2.2.5. Common semantic features  (pp. 23-24) | html | pdf |
      S. R. Hall and J. D. Westbrook
      • 2.2.5.1. Data-name semantics  (p. 23) | html | pdf |
      • 2.2.5.2. Data typing  (pp. 23-24) | html | pdf |
      • 2.2.5.3. Extended data typing: content type and encoding  (p. 24) | html | pdf |
    • 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
      • 2.2.7.1. Syntax  (pp. 25-29) | html | pdf |
        • 2.2.7.1.1. Introduction  (p. 25) | html | pdf |
        • 2.2.7.1.2. Definition of terms  (p. 25) | html | pdf |
        • 2.2.7.1.3. File syntax  (p. 25) | html | pdf |
        • 2.2.7.1.4. General features  (pp. 25-27) | html | pdf |
        • 2.2.7.1.5. Character set  (p. 27) | html | pdf |
        • 2.2.7.1.6. White space  (p. 27) | html | pdf |
        • 2.2.7.1.7. End-of-line conventions  (p. 27) | html | pdf |
        • 2.2.7.1.8. Case sensitivity  (p. 27) | html | pdf |
        • 2.2.7.1.9. Implementation restrictions  (p. 27) | html | pdf |
          • 2.2.7.1.9.1. Maximum line length and character set  (p. 27) | html | pdf |
          • 2.2.7.1.9.2. Maximum data-name, block-code and frame-code lengths  (p. 27) | html | pdf |
          • 2.2.7.1.9.3. Single-level loop constructs  (p. 27) | html | pdf |
          • 2.2.7.1.9.4. Non-expansion of save-frame references  (p. 27) | html | pdf |
          • 2.2.7.1.9.5. Exclusion of global_ blocks  (p. 27) | html | pdf |
        • 2.2.7.1.10. Version identification  (p. 29) | html | pdf |
      • 2.2.7.2. A formal grammar for CIF  (pp. 29-30) | html | pdf |
        • 2.2.7.2.1. Summary  (p. 29) | html | pdf |
        • 2.2.7.2.2. Explanation of the formal syntax  (pp. 29-30) | html | pdf |
      • 2.2.7.3. Lexical tokens  (pp. 30-32) | html | pdf |
        • 2.2.7.3.1. CIF grammar  (p. 32) | html | pdf |
      • 2.2.7.4. Common semantic features  (pp. 32-36) | html | pdf |
        • 2.2.7.4.1. Introduction  (p. 32) | html | pdf |
        • 2.2.7.4.2. Definition of terms  (p. 32) | html | pdf |
        • 2.2.7.4.3. Semantics of data items  (p. 32) | html | pdf |
        • 2.2.7.4.4. Data-name semantics  (pp. 32-33) | html | pdf |
        • 2.2.7.4.5. Name space  (p. 33) | html | pdf |
        • 2.2.7.4.6. Note on handling of units  (p. 33) | html | pdf |
        • 2.2.7.4.7. Data-value semantics  (pp. 33-34) | html | pdf |
          • 2.2.7.4.7.1. Data typing  (pp. 33-34) | html | pdf |
          • 2.2.7.4.7.2. Subtyping  (p. 34) | html | pdf |
        • 2.2.7.4.8. Special generic values  (p. 34) | html | pdf |
        • 2.2.7.4.9. Embedded data semantics  (p. 34) | html | pdf |
        • 2.2.7.4.10. CIF conventions for special characters in text  (p. 34) | html | pdf |
        • 2.2.7.4.11. Handling of long lines  (pp. 34-35) | html | pdf |
        • 2.2.7.4.12. Dictionary compliance  (p. 35) | html | pdf |
        • 2.2.7.4.13. CIF markup conventions  (p. 35) | html | pdf |
        • 2.2.7.4.14. Greek letters  (p. 36) | html | pdf |
        • 2.2.7.4.15. Accented letters  (p. 36) | html | pdf |
        • 2.2.7.4.16. Other characters  (p. 36) | html | pdf |
        • 2.2.7.4.17. Typographic style codes  (p. 36) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 2.2.3.1. Typical small-molecule CIF  (p. 21) | html | pdf |
    • Tables
      • Table 2.2.7.1. A formal grammar for CIF  (pp. 28-29) | 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 |
      • 2.3.2.1. A simple example  (pp. 37-39) | html | pdf |
    • 2.3.3. Overview of the format  (pp. 39-41) | html | pdf |
      • 2.3.3.1. Details of the magic number  (p. 40) | html | pdf |
      • 2.3.3.2. Details of the header section  (p. 40) | html | pdf |
      • 2.3.3.3. Details of binary sections  (p. 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 |
      • 2.4.4.1. Data identification  (p. 45) | html | pdf |
      • 2.4.4.2. Looped lists  (pp. 45-46) | html | pdf |
      • 2.4.4.3. Save frames  (p. 46) | html | pdf |
      • 2.4.4.4. Data blocks  (p. 46) | html | pdf |
      • 2.4.4.5. Global blocks  (p. 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 |
    • Figures
      • Fig. 2.4.4.1. MIF coding of atom and bond properties for thiabutyrolactone  (p. 46) | html | pdf |
      • Fig. 2.4.4.2. MIF coding of atom properties (including 3D coordinates), bond properties and display information for (+)-3-bromocamphor  (p. 46) | html | pdf |
      • Fig. 2.4.4.3. Atom and bond properties for cyclohexane, together with 3D coordinate representations of three alternative conformations: chair, boat and twisted boat  (p. 47) | html | pdf |
      • Fig. 2.4.6.1. Three alternative bonding conventions for toluene stored in the same MIF data block  (p. 48) | html | pdf |
      • Fig. 2.4.7.1. MIF representation of (2-methylcyclohexyl)(3-methylcyclohexyl)(4-methylcyclohexyl)phosphine  (p. 49) | html | pdf |
      • Fig. 2.4.7.2. MIF representation of the dipeptide alanylserine constructed using alanyl and seryl templates encapsulated in global save frames.  (p. 49) | html | pdf |
      • Fig. 2.4.8.1. CIP stereochemical descriptors for (+)-3-bromocamphor  (p. 50) | html | pdf |
      • Fig. 2.4.8.2. Archetypal coordination geometries used in stereochemical definition of the MIF data item _stereo_geometry.  (p. 50) | html | pdf |
      • Fig. 2.4.8.3. Stereochemical data for menthyl-p-toluenesulfinate.  (p. 51) | html | pdf |
      • Fig. 2.4.9.1. Query substructure for conjugated ketones or thioketones  (p. 51) | html | pdf |
    • Tables
      • Table 2.4.4.1. Brief overview of the MIF syntax  (p. 45) | 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 |
      • 2.5.1.1. The concept of a dictionary definition language (DDL)  (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 |
      • 2.5.3.1. Example 1: attributes of temperature  (p. 54) | html | pdf |
      • 2.5.3.2. Example 2: attributes of Miller indices  (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 |
      • 2.5.5.1. Definition example 1: formula units per cell (Z)  (p. 55) | html | pdf |
      • 2.5.5.2. Definition example 2: dictionary audit information  (pp. 55-56) | html | pdf |
      • 2.5.5.3. Definition example 3: irreducible data items  (p. 56) | html | pdf |
      • 2.5.5.4. Definition example 4: list data  (p. 56) | html | pdf |
      • 2.5.5.5. Definition example 5: category information  (p. 56) | html | pdf |
      • 2.5.5.6. Definition example 6: mandatory and linked items  (p. 56) | html | pdf |
      • 2.5.5.7. Definition example 7: joinable lists  (p. 56) | html | pdf |
      • 2.5.5.8. Definition example 8: equivalent items  (p. 56) | html | pdf |
      • 2.5.5.9. Definition example 9: enumeration states  (p. 57) | html | pdf |
    • 2.5.6. DDL1 attribute descriptions  (pp. 57-60) | html | pdf |
      • 2.5.6.1. Identification attributes  (p. 58) | html | pdf |
      • 2.5.6.2. Descriptive attributes  (p. 58) | html | pdf |
      • 2.5.6.3. Typing attributes  (pp. 58-59) | html | pdf |
      • 2.5.6.4. Relational attributes  (pp. 59-60) | html | pdf |
      • 2.5.6.5. Dictionary registration attributes  (p. 60) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 2.5.4.1. Comparison of DDL versions: (a) DDL1, (b) DDL2  (p. 55) | html | pdf |
      • Fig. 2.5.5.1. DDL1 definition with a few attributes  (p. 55) | html | pdf |
      • Fig. 2.5.5.2. DDL1 definition showing basic dictionary organization  (p. 55) | html | pdf |
      • Fig. 2.5.5.3. DDL1 definition of irreducible data items  (p. 56) | html | pdf |
      • Fig. 2.5.5.4. DDL1 definition of a `list' data item  (p. 56) | html | pdf |
      • Fig. 2.5.5.5. DDL1 overview of a category of items  (p. 57) | html | pdf |
      • Fig. 2.5.5.6. DDL1 definition of a `mandatory' data item  (p. 57) | html | pdf |
      • Fig. 2.5.5.7. DDL1 definition of a `parent' data item  (p. 57) | html | pdf |
      • Fig. 2.5.5.8. DDL1 definition showing `related' data items  (p. 57) | html | pdf |
      • Fig. 2.5.5.9. DDL1 definition showing enumeration states  (p. 58) | html | pdf |
      • Fig. 2.5.6.1. (a) Hypothetical example and (b) the typical definition of nested items  (p. 59) | html | pdf |
      • Fig. 2.5.6.2. Definition example: type constructions  (p. 59) | html | pdf |
    • Tables
      • Table 2.5.4.1. Comparison of DDL1 and DDL2 variants  (p. 54) | 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 |
      • 2.6.6.1. DDL2 definitions describing data items  (pp. 65-68) | html | pdf |
        • 2.6.6.1.1. ITEM  (pp. 65-66) | html | pdf |
        • 2.6.6.1.2. ITEM_ALIASES  (p. 66) | html | pdf |
        • 2.6.6.1.3. ITEM_DEFAULT  (p. 66) | html | pdf |
        • 2.6.6.1.4. ITEM_DEPENDENT  (p. 66) | html | pdf |
        • 2.6.6.1.5. ITEM_DESCRIPTION  (p. 66) | html | pdf |
        • 2.6.6.1.6. ITEM_ENUMERATION  (p. 67) | html | pdf |
        • 2.6.6.1.7. ITEM_EXAMPLES  (p. 67) | html | pdf |
        • 2.6.6.1.8. ITEM_LINKED  (p. 67) | html | pdf |
        • 2.6.6.1.9. ITEM_METHODS  (p. 67) | html | pdf |
        • 2.6.6.1.10. ITEM_RANGE  (p. 67) | html | pdf |
        • 2.6.6.1.11. ITEM_RELATED  (p. 67) | html | pdf |
        • 2.6.6.1.12. ITEM_STRUCTURE  (p. 67) | html | pdf |
        • 2.6.6.1.13. ITEM_STRUCTURE_LIST  (p. 67) | html | pdf |
        • 2.6.6.1.14. ITEM_SUB_CATEGORY  (p. 67) | html | pdf |
        • 2.6.6.1.15. ITEM_TYPE  (pp. 67-68) | html | pdf |
        • 2.6.6.1.16. ITEM_TYPE_CONDITIONS  (p. 68) | html | pdf |
        • 2.6.6.1.17. ITEM_TYPE_LIST  (p. 68) | html | pdf |
        • 2.6.6.1.18. ITEM_UNITS  (p. 68) | html | pdf |
        • 2.6.6.1.19. ITEM_UNITS_CONVERSION  (p. 68) | html | pdf |
        • 2.6.6.1.20. ITEM_UNITS_LIST  (p. 68) | html | pdf |
      • 2.6.6.2. DDL2 definitions describing categories  (pp. 68-70) | html | pdf |
        • 2.6.6.2.1. CATEGORY  (pp. 68-69) | html | pdf |
        • 2.6.6.2.2. CATEGORY_EXAMPLES  (p. 69) | html | pdf |
        • 2.6.6.2.3. CATEGORY_GROUP  (p. 69) | html | pdf |
        • 2.6.6.2.4. CATEGORY_GROUP_LIST  (p. 69) | html | pdf |
        • 2.6.6.2.5. CATEGORY_KEY  (p. 69) | html | pdf |
        • 2.6.6.2.6. CATEGORY_METHODS  (p. 69) | html | pdf |
        • 2.6.6.2.7. SUB_CATEGORY  (p. 70) | html | pdf |
        • 2.6.6.2.8. SUB_CATEGORY_EXAMPLES  (p. 70) | html | pdf |
        • 2.6.6.2.9. SUB_CATEGORY_METHODS  (p. 70) | html | pdf |
      • 2.6.6.3. DDL2 definitions describing methods  (p. 70) | html | pdf |
        • 2.6.6.3.1. METHOD_LIST  (p. 70) | html | pdf |
      • 2.6.6.4. DDL2 definitions describing dictionaries and data blocks  (p. 70) | html | pdf |
        • 2.6.6.4.1. DATABLOCK  (p. 70) | html | pdf |
        • 2.6.6.4.2. DATABLOCK_METHODS  (p. 70) | html | pdf |
        • 2.6.6.4.3. DICTIONARY  (p. 70) | html | pdf |
        • 2.6.6.4.4. DICTIONARY_HISTORY  (p. 70) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 2.6.4.1. DDL2 attributes used to specify item information  (p. 62) | html | pdf |
      • Fig. 2.6.4.2. DDL2 attributes used to specify category, subcategory and category group information  (p. 63) | html | pdf |
      • Fig. 2.6.4.3. DDL2 attributes used to specify dictionary and data-block information  (p. 63) | html | pdf |
    • Tables
      • Table 2.6.5.1. Relationships defined by _item_related.function_code  (p. 65) | 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 |
      • 3.1.1.1. Authorship of data dictionaries  (p. 73) | html | pdf |
      • 3.1.1.2. Certification for community use  (p. 73) | html | pdf |
      • 3.1.1.3. DDL versions  (pp. 73-74) | html | pdf |
    • 3.1.2. Informal definition procedures  (p. 74) | html | pdf |
      • 3.1.2.1. The _[local]_ prefix  (p. 74) | html | pdf |
      • 3.1.2.2. Reserved prefixes  (p. 74) | html | pdf |
      • 3.1.2.3. Name spaces  (p. 74) | html | pdf |
    • 3.1.3. Formal definition process  (pp. 74-75) | html | pdf |
      • 3.1.3.1. Dictionary maintenance groups  (p. 75) | html | pdf |
      • 3.1.3.2. mmCIF review cycle  (p. 75) | html | pdf |
      • 3.1.3.3. New dictionaries  (p. 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 |
      • 3.1.5.1. The dictionary identification block  (p. 77) | html | pdf |
      • 3.1.5.2. Irreducible sets of data items  (p. 77) | html | pdf |
      • 3.1.5.3. Category descriptions  (p. 77) | html | pdf |
      • 3.1.5.4. Data-item definitions  (pp. 77-79) | html | pdf |
        • 3.1.5.4.1. Definitions of single quantities  (pp. 77-78) | html | pdf |
        • 3.1.5.4.2. Looped data  (p. 78) | html | pdf |
        • 3.1.5.4.3. Units  (pp. 78-79) | html | pdf |
    • 3.1.6. Constructing a DDL2 dictionary  (pp. 79-83) | html | pdf |
      • 3.1.6.1. Dictionary identification  (p. 79) | html | pdf |
      • 3.1.6.2. Subcategory definitions  (pp. 79-80) | html | pdf |
      • 3.1.6.3. Category groupings  (p. 80) | html | pdf |
      • 3.1.6.4. Category definitions  (pp. 80-81) | html | pdf |
      • 3.1.6.5. Data-item definitions  (pp. 81-83) | html | pdf |
        • 3.1.6.5.1. Inheritance of identifiers  (p. 82) | html | pdf |
        • 3.1.6.5.2. Definitions of single quantities  (p. 83) | html | pdf |
      • 3.1.6.6. Units  (p. 83) | html | pdf |
    • 3.1.7. Composing new data definitions  (pp. 83-85) | html | pdf |
      • 3.1.7.1. Granularity  (pp. 83-84) | html | pdf |
      • 3.1.7.2. Category `special details' fields  (p. 84) | html | pdf |
      • 3.1.7.3. Construction of data names  (p. 84) | html | pdf |
      • 3.1.7.4. Parsable data values versus separate data names  (pp. 84-85) | html | pdf |
      • 3.1.7.5. Consistency of abbreviations  (p. 85) | html | pdf |
    • 3.1.8. Management of multiple dictionaries  (pp. 85-88) | html | pdf |
      • 3.1.8.1. Identification of dictionaries relevant to a data file  (pp. 85-86) | html | pdf |
      • 3.1.8.2. The dictionary register  (pp. 86-87) | html | pdf |
      • 3.1.8.3. Locating a dictionary for validation  (pp. 87-88) | html | pdf |
    • 3.1.9. Composite dictionaries  (pp. 88-89) | html | pdf |
      • 3.1.9.1. A dictionary merging protocol  (pp. 88-89) | html | pdf |
      • 3.1.9.2. Protocol implementation  (p. 89) | html | pdf |
    • 3.1.10. Public CIF dictionaries  (pp. 89-91) | html | pdf |
      • 3.1.10.1. Categories and category groups  (p. 90) | html | pdf |
      • 3.1.10.2. Overview of category classification  (pp. 90-91) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 3.1.5.1. Schematic structure of core CIF dictionary  (p. 76) | html | pdf |
      • Fig. 3.1.6.1. Schematic structure of the macromolecular CIF dictionary  (p. 80) | html | pdf |
      • Fig. 3.1.7.1. Alternative quantities described (a) by data-name extension (core dictionary) or (b) by paired data names (mmCIF dictionary)  (p. 84) | html | pdf |
    • Tables
      • Table 3.1.2.1. Reserved prefixes for private CIF data names  (p. 74) | html | pdf |
      • Table 3.1.5.1. Units codes and their interpretation in DDL1-based dictionaries  (p. 79) | html | pdf |
      • Table 3.1.7.1. Abbreviations in CIF data names  (p. 86) | html | pdf |
      • Table 3.1.8.1. CIF dictionary register (maintained as a STAR File)  (p. 87) | html | pdf |
      • Table 3.1.10.1. High-level grouping of categories by dictionary  (p. 90) | 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 |
      • 3.2.2.1. Crystal cell parameters and measurement conditions  (p. 93) | html | pdf |
      • 3.2.2.2. Data collection  (pp. 93-97) | html | pdf |
        • 3.2.2.2.1. General description  (pp. 93-94) | html | pdf |
        • 3.2.2.2.2. Apparatus and instrumentation before the crystal  (pp. 94-95) | html | pdf |
        • 3.2.2.2.3. Apparatus and instrumentation at the crystal  (p. 95) | html | pdf |
        • 3.2.2.2.4. Apparatus and instrumentation after the crystal  (p. 95) | html | pdf |
        • 3.2.2.2.5. Intensity measurements  (pp. 95-97) | html | pdf |
      • 3.2.2.3. Experimental measurements on the crystal  (pp. 97-98) | html | pdf |
    • 3.2.3. Analysis  (pp. 98-102) | html | pdf |
      • 3.2.3.1. Structure refinement  (pp. 98-100) | html | pdf |
      • 3.2.3.2. Reflection measurements  (pp. 100-102) | html | pdf |
        • 3.2.3.2.1. Individual reflections  (pp. 100-101) | html | pdf |
        • 3.2.3.2.2. Groups of reflections  (pp. 101-102) | html | pdf |
    • 3.2.4. Atomicity, chemistry and structure  (pp. 102-112) | html | pdf |
      • 3.2.4.1. Atom sites  (pp. 102-106) | html | pdf |
        • 3.2.4.1.1. Individual atom sites  (pp. 102-105) | html | pdf |
        • 3.2.4.1.2. Collections of atom sites  (pp. 105-106) | html | pdf |
        • 3.2.4.1.3. Atom types  (p. 106) | html | pdf |
      • 3.2.4.2. Chemical identification and connectivity information  (pp. 106-108) | html | pdf |
        • 3.2.4.2.1. Chemical identification  (pp. 106-107) | html | pdf |
        • 3.2.4.2.2. Chemical connectivity  (pp. 107-108) | html | pdf |
      • 3.2.4.3. Molecular or packing geometry  (pp. 108-110) | html | pdf |
        • 3.2.4.3.1. Contents of the geometry-related categories  (pp. 108-110) | html | pdf |
      • 3.2.4.4. Symmetry and space-group information  (pp. 110-111) | html | pdf |
        • 3.2.4.4.1. Data items in SYMMETRY and related categories  (pp. 110-111) | html | pdf |
        • 3.2.4.4.2. Data items in SPACE_GROUP and related categories  (p. 111) | html | pdf |
      • 3.2.4.5. Bond-valence information  (pp. 111-112) | html | pdf |
    • 3.2.5. Publication  (pp. 112-114) | html | pdf |
      • 3.2.5.1. Literature citations  (p. 112) | html | pdf |
      • 3.2.5.2. Citation of software packages  (p. 113) | html | pdf |
      • 3.2.5.3. Citation of related database entries  (p. 113) | html | pdf |
      • 3.2.5.4. Journal housekeeping, citation and indexing entries  (pp. 113-114) | html | pdf |
      • 3.2.5.5. Contents of a publication  (p. 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 |
    • Figures
      • Fig. 3.2.2.1. Scheme of a diffraction experiment  (p. 93) | html | pdf |
    • Tables
      • Table 3.2.1.1. Category groups defined in the core CIF dictionary  (p. 92) | html | pdf |
      • Table A3.2.1.1. Categories in the core CIF dictionary  (p. 116) | 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 |
      • 3.3.4.1. Characterization and preparation of the sample  (p. 118) | html | pdf |
      • 3.3.4.2. Description of the specimen used in the experiment  (p. 119) | html | pdf |
      • 3.3.4.3. Instrument calibration and description  (pp. 119-120) | html | pdf |
      • 3.3.4.4. Observations and measurement conditions  (pp. 120-121) | html | pdf |
    • 3.3.5. Analysis  (pp. 121-123) | html | pdf |
      • 3.3.5.1. Processed intensities, their positions and processing information  (pp. 121-122) | html | pdf |
      • 3.3.5.2. Simulated data  (p. 122) | html | pdf |
      • 3.3.5.3. Diffraction peak table  (p. 122) | html | pdf |
      • 3.3.5.4. Reflection assignments and intensities  (pp. 122-123) | html | pdf |
    • 3.3.6. Atomicity, chemistry and structure  (p. 123) | html | pdf |
      • 3.3.6.1. Table of phases  (p. 123) | html | pdf |
    • 3.3.7. File metadata  (pp. 123-126) | html | pdf |
      • 3.3.7.1. Use of block pointers  (pp. 124-126) | html | pdf |
    • 3.3.8. pdCIF for storing unprocessed measurements  (pp. 126-128) | html | pdf |
      • 3.3.8.1. Single pulse-counting detectors  (p. 126) | html | pdf |
      • 3.3.8.2. Detectors that do not count pulses  (p. 126) | html | pdf |
      • 3.3.8.3. Multiple detectors  (pp. 126-127) | html | pdf |
      • 3.3.8.4. Energy-dispersive X-ray detection  (p. 127) | html | pdf |
      • 3.3.8.5. Neutron time-of-flight detection  (p. 127) | html | pdf |
      • 3.3.8.6. Digitized film and image plates  (p. 127) | html | pdf |
      • 3.3.8.7. Direct background measurements  (p. 127) | html | pdf |
      • 3.3.8.8. Noting sample orientation  (pp. 127-128) | html | pdf |
      • 3.3.8.9. Use of an incident-intensity monitor  (p. 128) | html | pdf |
      • 3.3.8.10. Recording detector livetime  (p. 128) | html | pdf |
    • 3.3.9. Use of pdCIF for Rietveld refinement results  (pp. 128-129) | html | pdf |
      • 3.3.9.1. A single phase  (p. 128) | html | pdf |
      • 3.3.9.2. Multiple phases  (pp. 128-129) | html | pdf |
      • 3.3.9.3. One phase, multiple sets of measurements  (p. 129) | html | pdf |
      • 3.3.9.4. Multiple sets of measurements and phases  (p. 129) | html | pdf |
    • 3.3.10. Other pdCIF applications  (pp. 129-130) | html | pdf |
      • 3.3.10.1. Simulated intensities  (p. 129) | html | pdf |
      • 3.3.10.2. Phase identification and indexing  (pp. 129-130) | html | pdf |
    • Appendix 3.3.1. Category structure of the powder CIF dictionary  (p. 130) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 3.3.4.1. The axial and equatorial directions in a powder-diffraction experiment  (p. 120) | html | pdf |
    • Tables
      • Table 3.3.3.1. Category groups defined in the powder CIF dictionary  (p. 118) | html | pdf |
      • Table A3.3.1.1. Categories in the powder CIF dictionary  (p. 130) | 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 |
      • 3.4.3.1. Experimental measurements  (pp. 133-134) | html | pdf |
        • 3.4.3.1.1. Cell and modulation wave vectors  (p. 133) | html | pdf |
        • 3.4.3.1.2. Data collection  (p. 133) | html | pdf |
        • 3.4.3.1.3. Experimental measurements on the crystal  (pp. 133-134) | html | pdf |
      • 3.4.3.2. Analysis  (p. 134) | html | pdf |
        • 3.4.3.2.1. Refinement techniques and results  (p. 134) | html | pdf |
        • 3.4.3.2.2. The reflections used in the refinement  (p. 134) | html | pdf |
      • 3.4.3.3. Atomicity, chemistry and structure  (pp. 134-136) | html | pdf |
        • 3.4.3.3.1. Atom sites  (p. 135) | html | pdf |
        • 3.4.3.3.2. Modulation functions as Fourier series  (pp. 135-136) | html | pdf |
        • 3.4.3.3.3. Special modulation functions  (p. 136) | html | pdf |
        • 3.4.3.3.4. Molecular or packing geometry  (p. 136) | html | pdf |
        • 3.4.3.3.5. Symmetry information  (p. 136) | html | pdf |
      • 3.4.3.4. File metadata  (pp. 136-137) | html | pdf |
    • 3.4.4. Use of the msCIF dictionary  (pp. 137-139) | html | pdf |
      • 3.4.4.1. Description of reciprocal space  (p. 137) | html | pdf |
      • 3.4.4.2. Description of symmetry  (pp. 137-138) | html | pdf |
      • 3.4.4.3. Description of the structure  (pp. 138-139) | html | pdf |
      • 3.4.4.4. Block pointers  (p. 139) | html | pdf |
      • 3.4.4.5. Other information  (p. 139) | html | pdf |
    • Appendix 3.4.1. Category structure of the msCIF dictionary  (p. 139) | html | pdf |
    • References | html | pdf |
    • Tables
      • Table 3.4.2.1. Category groups defined in the msCIF dictionary  (p. 132) | html | pdf |
      • Table A3.4.1.1. Categories in the modulated structures CIF dictionary  (p. 139) | 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 |
      • 3.5.3.1. Specification of local axes at each atom  (pp. 141-142) | html | pdf |
      • 3.5.3.2. Atom-centred multipole expansion functions  (pp. 142-143) | 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 |
      • 3.6.5.1. Crystal cell parameters and measurement conditions  (pp. 148-149) | html | pdf |
      • 3.6.5.2. Data collection  (pp. 149-151) | html | pdf |
      • 3.6.5.3. Growth, description and analysis of the crystal  (pp. 151-152) | html | pdf |
        • 3.6.5.3.1. Crystal properties  (pp. 151-152) | html | pdf |
        • 3.6.5.3.2. Crystal growth  (p. 152) | html | pdf |
    • 3.6.6. Analysis  (pp. 152-164) | html | pdf |
      • 3.6.6.1. Phasing  (pp. 152-158) | html | pdf |
        • 3.6.6.1.1. Overall description of phasing  (p. 153) | html | pdf |
        • 3.6.6.1.2. Phasing via molecular averaging  (p. 153) | html | pdf |
        • 3.6.6.1.3. Phasing via isomorphous replacement  (pp. 153-154) | html | pdf |
        • 3.6.6.1.4. Phasing via multiple-wavelength anomalous dispersion  (pp. 154-155) | html | pdf |
        • 3.6.6.1.5. Phasing via multiple isomorphous replacement  (pp. 155-157) | html | pdf |
        • 3.6.6.1.6. Phasing data sets  (pp. 157-158) | html | pdf |
      • 3.6.6.2. Refinement  (pp. 158-162) | html | pdf |
        • 3.6.6.2.1. Overall description of the refinement  (pp. 158-159) | html | pdf |
        • 3.6.6.2.2. Analysis of the refined structure  (pp. 159-160) | html | pdf |
        • 3.6.6.2.3. Restraints and refinement by shells of resolution  (pp. 160-161) | html | pdf |
        • 3.6.6.2.4. Equivalent atoms in the refinement  (pp. 161-162) | html | pdf |
        • 3.6.6.2.5. History of the refinement  (p. 162) | html | pdf |
      • 3.6.6.3. Reflection measurements  (pp. 162-164) | html | pdf |
        • 3.6.6.3.1. Individual reflections  (pp. 162-163) | html | pdf |
        • 3.6.6.3.2. Groups of reflections  (pp. 163-164) | html | pdf |
    • 3.6.7. Atomicity, chemistry and structure  (pp. 164-190) | html | pdf |
      • 3.6.7.1. Atom sites  (pp. 164-169) | html | pdf |
        • 3.6.7.1.1. Individual atom sites  (pp. 164-166) | html | pdf |
        • 3.6.7.1.2. Collections of atom sites  (p. 167) | html | pdf |
        • 3.6.7.1.3. Atom types  (p. 167) | html | pdf |
        • 3.6.7.1.4. Alternative conformations  (pp. 168-169) | html | pdf |
      • 3.6.7.2. Molecular chemistry  (pp. 169-174) | html | pdf |
        • 3.6.7.2.1. Molecular chemistry in the core CIF dictionary  (p. 169) | html | pdf |
        • 3.6.7.2.2. Chemical components  (pp. 169-172) | html | pdf |
        • 3.6.7.2.3. Chemical links  (pp. 172-174) | html | pdf |
      • 3.6.7.3. Distinct chemical species  (pp. 174-176) | html | pdf |
        • 3.6.7.3.1. Description of entities  (pp. 174-175) | html | pdf |
        • 3.6.7.3.2. Polymer entities  (pp. 175-176) | html | pdf |
      • 3.6.7.4. Molecular or packing geometry  (pp. 176-178) | html | pdf |
      • 3.6.7.5. Molecular structure  (pp. 178-189) | html | pdf |
        • 3.6.7.5.1. Higher-level macromolecular structure  (pp. 179-181) | html | pdf |
        • 3.6.7.5.2. Secondary structure  (pp. 181-182) | html | pdf |
        • 3.6.7.5.3. Structural interactions  (pp. 182-183) | html | pdf |
        • 3.6.7.5.4. Structural features of monomers  (pp. 183-184) | html | pdf |
        • 3.6.7.5.5. Noncrystallographic symmetry  (pp. 184-186) | html | pdf |
        • 3.6.7.5.6. External databases  (pp. 186-187) | html | pdf |
        • 3.6.7.5.7. β-sheets  (pp. 187-188) | html | pdf |
        • 3.6.7.5.8. Molecular sites  (pp. 188-189) | html | pdf |
      • 3.6.7.6. Crystal symmetry  (p. 190) | html | pdf |
      • 3.6.7.7. Bond-valence information  (p. 190) | html | pdf |
    • 3.6.8. Publication  (pp. 190-194) | html | pdf |
      • 3.6.8.1. Literature citations  (pp. 190-191) | html | pdf |
      • 3.6.8.2. Citation of software packages  (p. 191) | html | pdf |
      • 3.6.8.3. Citation of related database entries  (pp. 191-193) | html | pdf |
        • 3.6.8.3.1. Related database entries  (p. 192) | html | pdf |
        • 3.6.8.3.2. Compatibility with PDB format files  (pp. 192-193) | html | pdf |
      • 3.6.8.4. Article publication  (pp. 193-194) | html | pdf |
        • 3.6.8.4.1. Journal housekeeping and citation entries  (pp. 193-194) | html | pdf |
        • 3.6.8.4.2. Contents of a publication  (p. 194) | html | pdf |
    • 3.6.9. File metadata  (pp. 194-195) | html | pdf |
      • 3.6.9.1. History of a data block  (p. 194) | html | pdf |
      • 3.6.9.2. Links between data blocks  (pp. 194-195) | html | pdf |
      • 3.6.9.3. Other category classifications  (p. 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
      • A3.6.2.1. Data exchange and format translation   (pp. 195-196) | html | pdf |
      • A3.6.2.2. Extensions for structural genomics  (p. 197) | html | pdf |
      • A3.6.2.3. Noncrystallographic methods  (p. 197) | html | pdf |
        • A3.6.2.3.1. NMR  (p. 197) | html | pdf |
        • A3.6.2.3.2. Cryo-electron microscopy  (p. 197) | html | pdf |
        • A3.6.2.3.3. Protein production  (p. 197) | html | pdf |
      • A3.6.2.4. Supporting software  (p. 197) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 3.6.3.1. A representation of crambin (PDB 3CNR) with a co-crystallized ethanol molecule  (p. 145) | html | pdf |
      • Fig. 3.6.6.1. The family of categories used to describe MAD phasing  (p. 155) | html | pdf |
      • Fig. 3.6.6.2. The family of categories used to describe MIR phasing  (p. 156) | html | pdf |
      • Fig. 3.6.7.1. The family of categories used to describe atom sites  (p. 165) | html | pdf |
      • Fig. 3.6.7.2. Alternative conformations in an HIV-1 protease structure (PDB 5HVP) to be described with data items in the ATOM_SITES_ALT, ATOM_SITES_ALT_ENS and ATOM_SITES_ALT_GEN categories  (p. 168) | html | pdf |
      • Fig. 3.6.7.3. The family of categories used to describe the chemical and structural features of the monomers and small molecules used to build a model of a structure  (p. 171) | html | pdf |
      • Fig. 3.6.7.4. The family of categories used to describe the links between chemical components  (p. 173) | html | pdf |
      • Fig. 3.6.7.5. The family of categories used to describe chemical entities  (p. 175) | html | pdf |
      • Fig. 3.6.7.6. The family of categories used to describe polymer chemical entities  (p. 176) | html | pdf |
      • Fig. 3.6.7.7. The family of categories used to describe the higher-level macromolecular structure  (p. 179) | html | pdf |
      • Fig. 3.6.7.8. The higher-level structure of the complex of HIV-1 protease with an inhibitor (PDB 5HVP) to be described with data items in the STRUCT_ASYM, STRUCT_BIOL, STRUCT_BIOL_KEYWORDS and STRUCT_BIOL_GEN categories  (p. 180) | html | pdf |
      • Fig. 3.6.7.9. The family of categories used to describe secondary structure  (p. 181) | html | pdf |
      • Fig. 3.6.7.10. The family of categories used to describe structural interactions such as hydrogen bonding, salt bridges and disulfide bridges  (p. 182) | html | pdf |
      • Fig. 3.6.7.11. The family of categories used to describe the structural features of monomers  (p. 184) | html | pdf |
      • Fig. 3.6.7.12. The family of categories used to describe noncrystallographic symmetry  (p. 185) | html | pdf |
      • Fig. 3.6.7.13. Noncrystallographic symmetry in the structure of trimeric haemerythrin (PDB 1HR3) to be described with data items in the STRUCT_NCS_ENS, STRUCT_NCS_ENS_GEN, STRUCT_NCS_DOM and STRUCT_NCS_DOM_LIM categories  (p. 185) | html | pdf |
      • Fig. 3.6.7.14. The family of categories used to describe β-sheets  (p. 188) | html | pdf |
      • Fig. 3.6.7.15. A hypothetical β-sheet to be described with data items in the STRUCT_SHEET, STRUCT_SHEET_ORDER, STRUCT_SHEET_RANGE and STRUCT_SHEET_HBOND categories  (p. 188) | html | pdf |
      • Fig. 3.6.7.16. The family of categories used to describe molecular sites  (p. 189) | html | pdf |
    • Tables
      • Table 3.6.4.1. Major category groups defined in the mmCIF dictionary  (p. 148) | html | pdf |
      • Table A3.6.1.1. Categories in the mmCIF dictionary  (p. 196) | 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 |
      • 3.7.2.1. The image data  (p. 199) | html | pdf |
      • 3.7.2.2. Array elements  (p. 200) | html | pdf |
      • 3.7.2.3. Intensities  (p. 200) | html | pdf |
      • 3.7.2.4. Organization and encoding of array data  (pp. 200-201) | html | pdf |
    • 3.7.3. Axes  (pp. 201-202) | html | pdf |
    • 3.7.4. The diffraction experiment  (pp. 202-205) | html | pdf |
      • 3.7.4.1. Frames of data  (p. 203) | html | pdf |
      • 3.7.4.2. The detector apparatus  (p. 203) | html | pdf |
      • 3.7.4.3. Apparatus and instrumentation at the crystal  (pp. 203-204) | html | pdf |
      • 3.7.4.4. The radiation source  (p. 204) | html | pdf |
      • 3.7.4.5. Intensity measurements  (p. 204) | html | pdf |
      • 3.7.4.6. Diffraction scans  (pp. 204-205) | html | pdf |
    • Appendix 3.7.1. Category structure of the CBF/imgCIF dictionary  (p. 205) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 3.7.2.1. ARRAY_STRUCTURE_LIST specification of linearly organized image elements  (p. 201) | html | pdf |
      • Fig. 3.7.2.2. ARRAY_STRUCTURE_LIST specification of `constant-angle' image elements in a cylindrical scan  (p. 201) | html | pdf |
      • Fig. 3.7.2.3. ARRAY_STRUCTURE_LIST specification of `constant-velocity' image elements in a cylindrical scan  (p. 201) | html | pdf |
      • Fig. 3.7.3.1. AXIS laboratory coordinate system  (p. 202) | html | pdf |
    • Tables
      • Table 3.7.1.1. Category groups defined in the CBF/imgCIF dictionary  (p. 199) | html | pdf |
      • Table A3.7.1.1. Categories in the CBF/imgCIF dictionary  (p. 205) | 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 |
      • 5.1.2.1. Markup languages  (p. 482) | html | pdf |
      • 5.1.2.2. Data-representation frameworks  (pp. 482-483) | html | pdf |
    • 5.1.3. Strategies in designing a CIF-aware application  (pp. 483-486) | html | pdf |
      • 5.1.3.1. Working with filter utilities  (pp. 483-484) | html | pdf |
      • 5.1.3.2. Using existing CIF libraries and APIs  (p. 484) | html | pdf |
      • 5.1.3.3. Creating a CIF-aware application from scratch  (pp. 484-486) | html | pdf |
    • 5.1.4. Conclusion  (p. 486) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 5.1.3.1. Example of using filters to make a PDB-aware application CIF-aware  (p. 483) | html | pdf |
      • Fig. 5.1.3.2. Example of using filters to make a general application CIF-aware  (p. 484) | html | pdf |
      • Fig. 5.1.3.3. Using QUASAR or cif2cif to reorder CIF data for an order-dependent application or filter  (p. 484) | html | pdf |
      • Fig. 5.1.3.4. Typical dataflow of a C-based CIF API  (p. 484) | html | pdf |
      • Fig. 5.1.3.5. Example of bison data defining a CIF parser (taken from CBFlib)  (p. 485) | 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 |
      • 5.2.2.1. Single and multiple values  (p. 488) | html | pdf |
      • 5.2.2.2. Loop packets and context within lists  (pp. 488-489) | html | pdf |
      • 5.2.2.3. Context in data sets  (pp. 489-491) | html | pdf |
    • 5.2.3. Star_Base: a general-purpose data extractor for STAR Files  (pp. 491-494) | html | pdf |
      • 5.2.3.1. Program features  (p. 491) | html | pdf |
      • 5.2.3.2. The Star_Base data request  (pp. 491-492) | html | pdf |
      • 5.2.3.3. The Star_Base conditional request  (p. 492) | html | pdf |
      • 5.2.3.4. The Star_Base branching request  (pp. 492-494) | html | pdf |
      • 5.2.3.5. Implementation issues  (p. 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 |
      • 5.2.6.1. OOSTAR  (pp. 495-496) | html | pdf |
      • 5.2.6.2. CIF++  (p. 496) | html | pdf |
      • 5.2.6.3. CIFOBJ  (p. 496) | html | pdf |
      • 5.2.6.4. starlib  (pp. 496-497) | html | pdf |
      • 5.2.6.5. StarDOM  (p. 497) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 5.2.2.1. Example quantum chemistry basis set functions in STAR File format  (p. 489) | html | pdf |
      • Fig. 5.2.2.2. Retrieval from the example file in Fig. 5.2.2.1 of the value of _basis_set_function_exponent with associated context  (p. 489) | html | pdf |
      • Fig. 5.2.2.3. Example STAR data structure where save frames encapsulate related data sets  (p. 490) | html | pdf |
      • Fig. 5.2.2.4. Context for the requested values of _atom_identity_symbol in the preceding example  (p. 490) | html | pdf |
      • Fig. 5.2.3.1. Examples of branching requests and the results returned by Star_Base from the example file of Fig. 5.2.2.1   (p. 493) | html | pdf |
      • Fig. 5.2.5.1. Hyperlinking markup generated by StarMarkUp  (p. 495) | html | pdf |
    • Tables
      • Table 5.2.3.1. Permitted constructions for a Star_Base conditional request  (p. 492) | html | pdf |
      • Table 5.2.3.2. Value-matching operators in Star_Base conditional requests  (p. 492) | html | pdf |
      • Table 5.2.6.1. Object classes for manipulating STAR data in starlib  (p. 497) | 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 |
      • 5.3.2.1. vcif  (pp. 499-501) | html | pdf |
        • 5.3.2.1.1. How to use vcif  (pp. 499-500) | html | pdf |
        • 5.3.2.1.2. Options to vcif  (p. 500) | html | pdf |
        • 5.3.2.1.3. Limitations of vcif  (p. 501) | html | pdf |
    • 5.3.3. Editors with graphical user interfaces  (pp. 501-507) | html | pdf |
      • 5.3.3.1. enCIFer  (pp. 501-504) | html | pdf |
        • 5.3.3.1.1. The main graphical window  (p. 501) | html | pdf |
        • 5.3.3.1.2. The interface toolbar  (pp. 501-502) | html | pdf |
        • 5.3.3.1.3. The task bar  (p. 502) | html | pdf |
        • 5.3.3.1.4. The main edit pane  (p. 502) | html | pdf |
        • 5.3.3.1.5. The dictionary browse pane  (p. 502) | html | pdf |
        • 5.3.3.1.6. The error notification pane and logging area  (pp. 502-503) | html | pdf |
        • 5.3.3.1.7. The loop editor  (p. 503) | html | pdf |
        • 5.3.3.1.8. The publication and chemical and crystal data wizards  (p. 503) | html | pdf |
        • 5.3.3.1.9. The visualization window  (pp. 503-504) | html | pdf |
      • 5.3.3.2. CIFEDIT  (p. 504) | html | pdf |
      • 5.3.3.3. HICCuP  (pp. 504-506) | html | pdf |
        • 5.3.3.3.1. Interactive use of the program  (pp. 505-506) | html | pdf |
          • 5.3.3.3.1.1. The control window  (p. 505) | html | pdf |
          • 5.3.3.3.1.2. The report frame and edit window  (p. 505) | html | pdf |
          • 5.3.3.3.1.3. Dictionary browsing  (pp. 505-506) | html | pdf |
        • 5.3.3.3.2. Options  (p. 506) | html | pdf |
      • 5.3.3.4. Platform-specific editors  (pp. 506-507) | html | pdf |
        • 5.3.3.4.1. beCIF  (p. 506) | html | pdf |
        • 5.3.3.4.2. printCIF for Word  (pp. 506-507) | html | pdf |
    • 5.3.4. Data-name validation  (pp. 507-509) | html | pdf |
      • 5.3.4.1. CYCLOPS  (pp. 508-509) | html | pdf |
        • 5.3.4.1.1. Operation  (p. 508) | html | pdf |
        • 5.3.4.1.2. Invocation of the program  (pp. 508-509) | html | pdf |
    • 5.3.5. File transformation software  (pp. 509-515) | html | pdf |
      • 5.3.5.1. QUASAR: a data extractor  (pp. 509-511) | html | pdf |
        • 5.3.5.1.1. Purpose  (p. 509) | html | pdf |
        • 5.3.5.1.2. Mode of operation  (p. 509) | html | pdf |
        • 5.3.5.1.3. The request list  (pp. 509-510) | html | pdf |
        • 5.3.5.1.4. Output from QUASAR  (p. 511) | html | pdf |
          • 5.3.5.1.4.1. Treatment of missing data  (p. 511) | html | pdf |
          • 5.3.5.1.4.2. Matching data names  (p. 511) | html | pdf |
          • 5.3.5.1.4.3. Case sensitivity  (p. 511) | html | pdf |
      • 5.3.5.2. cif2cif  (pp. 511-512) | html | pdf |
        • 5.3.5.2.1. Operation  (pp. 511-512) | html | pdf |
          • 5.3.5.2.1.1. Copying  (p. 511) | html | pdf |
          • 5.3.5.2.1.2. Constraining standard uncertainties to specified ranges  (p. 511) | html | pdf |
          • 5.3.5.2.1.3. Dictionary validation  (p. 511) | html | pdf |
          • 5.3.5.2.1.4. Serving a request list  (pp. 511-512) | html | pdf |
          • 5.3.5.2.1.5. Other features  (p. 512) | html | pdf |
        • 5.3.5.2.2. Invocation of the program  (p. 512) | html | pdf |
      • 5.3.5.3. ciftex: translating to a typesetting language  (pp. 512-515) | html | pdf |
        • 5.3.5.3.1. Basic operation of ciftex  (pp. 512-514) | html | pdf |
          • 5.3.5.3.1.1. Non-looped data  (p. 513) | html | pdf |
          • 5.3.5.3.1.2. Looped data  (p. 513) | html | pdf |
          • 5.3.5.3.1.3. The ancillary map file  (pp. 513-514) | html | pdf |
          • 5.3.5.3.1.4. The ancillary format file  (p. 514) | html | pdf |
        • 5.3.5.3.2. Invocation of the program  (p. 514) | html | pdf |
        • 5.3.5.3.3. Some general comments  (pp. 514-515) | html | pdf |
    • 5.3.6. Libraries for scripting languages  (pp. 515-517) | html | pdf |
      • 5.3.6.1. STAR::Parser and related Perl modules  (pp. 515-517) | html | pdf |
        • 5.3.6.1.1. STAR::Parser  (p. 515) | html | pdf |
        • 5.3.6.1.2. STAR::Dictionary  (p. 515) | html | pdf |
        • 5.3.6.1.3. STAR::DataBlock  (pp. 515-516) | html | pdf |
        • 5.3.6.1.4. STAR::Checker  (p. 516) | html | pdf |
        • 5.3.6.1.5. STAR::Writer and STAR::Filter  (p. 517) | html | pdf |
      • 5.3.6.2. PyCifRW: CIF reading and writing in Python  (p. 517) | html | pdf |
    • 5.3.7. Rapid development tools  (pp. 517-522) | html | pdf |
      • 5.3.7.1. ZINC: an interface to CIF for standard Unix tools  (pp. 518-519) | html | pdf |
        • 5.3.7.1.1. Description of the ZINC format  (p. 518) | html | pdf |
        • 5.3.7.1.2. ZINC-based utilities  (pp. 518-519) | html | pdf |
          • 5.3.7.1.2.1. cifZinc  (p. 518) | html | pdf |
          • 5.3.7.1.2.2. zincCif  (p. 519) | html | pdf |
          • 5.3.7.1.2.3. zincGrep  (p. 519) | html | pdf |
          • 5.3.7.1.2.4. cifdiff  (p. 519) | html | pdf |
          • 5.3.7.1.2.5. zb  (p. 519) | html | pdf |
          • 5.3.7.1.2.6. zincNl  (p. 519) | html | pdf |
          • 5.3.7.1.2.7. zincSubset  (p. 519) | html | pdf |
      • 5.3.7.2. CifSieve: automatic construction of CIF input functions  (pp. 520-522) | html | pdf |
        • 5.3.7.2.1. Overview of the process  (p. 520) | html | pdf |
        • 5.3.7.2.2. The augmented DDL dictionary  (p. 520) | html | pdf |
        • 5.3.7.2.3. Input to a C application program  (p. 521) | html | pdf |
        • 5.3.7.2.4. Input to a Fortran application program  (pp. 521-522) | html | pdf |
    • 5.3.8. Tools for mmCIF  (pp. 522-525) | html | pdf |
      • 5.3.8.1. CIFOBJ and related libraries  (p. 522) | html | pdf |
      • 5.3.8.2. OpenMMS  (pp. 522-523) | html | pdf |
        • 5.3.8.2.1. The OpenMMS toolkit  (p. 523) | html | pdf |
      • 5.3.8.3. mmLib: a Python toolkit for bioinformatics applications  (pp. 523-525) | html | pdf |
    • 5.3.9. Concluding remarks  (p. 525) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 5.3.2.1. (a) An example CIF with a number of syntax errors and (b) the report of the errors produced by vcif  (p. 500) | html | pdf |
      • Fig. 5.3.2.2. Verbose error listing from vcif when run with the `-v' option on the example of Fig. 5.3.2.1  (p. 500) | html | pdf |
      • Fig. 5.3.3.1. The enCIFer graphical user interface  (p. 501) | html | pdf |
      • Fig. 5.3.3.2. The enCIFer loop editor  (p. 503) | html | pdf |
      • Fig. 5.3.3.3. The enCIFer publication data wizard  (p. 503) | html | pdf |
      • Fig. 5.3.3.4. The enCIFer chemical and crystal data wizard  (p. 503) | html | pdf |
      • Fig. 5.3.3.5. Visualization of a molecular and crystal three-dimensional structure with enCIFer  (p. 503) | html | pdf |
      • Fig. 5.3.3.6. The use of CIFEDIT to display and alter the contents of a CIF  (p. 504) | html | pdf |
      • Fig. 5.3.3.7. Row-based loop editing with CIFEDIT  (p. 504) | html | pdf |
      • Fig. 5.3.3.8. Control window of the HICCuP application  (p. 505) | html | pdf |
      • Fig. 5.3.3.9. HICCuP edit window and error description  (p. 505) | html | pdf |
      • Fig. 5.3.3.10. HICCuP dictionary browser window  (p. 505) | html | pdf |
      • Fig. 5.3.3.11. A category view in the beCIF editor of a CIF with navigation by tabs  (p. 506) | html | pdf |
      • Fig. 5.3.3.12. Representation by the beCIF editor of looped data within a category (here ATOM_SITE) in spreadsheet style  (p. 507) | html | pdf |
      • Fig. 5.3.3.13. The dual RTF/CIF editing windows in the printCIF for Word application  (p. 507) | html | pdf |
      • Fig. 5.3.4.1. Sample output from CYCLOPS  (p. 509) | html | pdf |
      • Fig. 5.3.5.1. An example request list for QUASAR  (p. 510) | html | pdf |
      • Fig. 5.3.5.2. Example CIF for demonstrating the use of QUASAR  (p. 510) | html | pdf |
      • Fig. 5.3.5.3. Result of running QUASAR with the example request list of Fig. 5.3.5.1 on the CIF listed in Fig. 5.3.5.2  (p. 510) | html | pdf |
      • Fig. 5.3.5.4. Sample CIF data input to ciftex  (p. 513) | html | pdf |
      • Fig. 5.3.5.5. Output from ciftex run on the data of Fig. 5.3.5.4  (p. 513) | html | pdf |
      • Fig. 5.3.5.6. markup for typesetting a table of atomic coordinates  (p. 513) | html | pdf |
      • Fig. 5.3.5.7. Example map file for use with ciftex  (p. 514) | html | pdf |
      • Fig. 5.3.5.8. Example format file for ciftex  (p. 514) | html | pdf |
      • Fig. 5.3.6.1. Skeleton version of an application to format a CIF dictionary for publication  (p. 516) | html | pdf |
      • Fig. 5.3.6.2. Structure of the imgCIF dictionary (Chapter 4.6 ) as described by the get_keys method of the STAR::DataBlock module  (p. 517) | html | pdf |
      • Fig. 5.3.7.1. ZINC transformation of CIF  (p. 518) | html | pdf |
      • Fig. 5.3.7.2. Two example files in CIF format differing greatly in layout but little in content: (a) sample1.cif, (b) sample2.cif  (p. 519) | html | pdf |
      • Fig. 5.3.7.3. Output from cifdiff comparing files sample1.cif and sample2.cif of Fig. 5.3.7.2  (p. 519) | html | pdf |
      • Fig. 5.3.7.4. Extracts from an augmented DDL1 dictionary (version 1.0 of the core CIF dictionary)  (p. 520) | html | pdf |
      • Fig. 5.3.7.5. Header file cifvars.h for a C application built by BuildSiv from the augmented DDL dictionary of Fig. 5.3.7.4  (p. 521) | html | pdf |
      • Fig. 5.3.7.6. An example C program designed to read CIF data as tagged in the augmented DDL dictionary of Fig. 5.3.7.4  (p. 521) | html | pdf |
      • Fig. 5.3.7.7. Fortran include file forcif.inc for an application built by BuildSiv from the augmented DDL dictionary of Fig. 5.3.7.4  (p. 522) | html | pdf |
      • Fig. 5.3.7.8. An example Fortran program designed to read CIF data as tagged in the augmented DDL dictionary of Fig. 5.3.7.4  (p. 522) | html | pdf |
      • Fig. 5.3.8.1. The OpenMMS metamodel and data flow  (p. 523) | html | pdf |
      • Fig. 5.3.8.2. Sample XML output from the OpenMMS XML generator  (p. 524) | html | pdf |
      • Fig. 5.3.8.3. A snippet of code illustrating mmCIF/PDB file format conversion with the mmLib toolkit  (p. 524) | html | pdf |
    • Tables
      • Table 5.3.6.1. Object methods provided by the STAR::DataBlock Perl module  (p. 516) | html | pdf |
      • Table 5.3.8.1. The modules provided by the mmLib toolkit  (p. 524) | 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 |
      • 5.4.6.1. General monitor variables  (p. 528) | html | pdf |
      • 5.4.6.2. General control variables  (p. 528) | html | pdf |
      • 5.4.6.3. Input monitor variables  (p. 529) | html | pdf |
      • 5.4.6.4. Output control variables  (p. 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 |
      • 5.4.11.1. Fatal errors: array bounds  (pp. 532-534) | html | pdf |
      • 5.4.11.2. Fatal errors: data sequence, syntax and file construction  (p. 534) | html | pdf |
      • 5.4.11.3. Fatal errors: invalid arguments  (p. 534) | html | pdf |
      • 5.4.11.4. Warnings: input errors  (p. 534) | html | pdf |
      • 5.4.11.5. Warnings: output errors  (pp. 534-535) | html | pdf |
      • 5.4.11.6. Warnings: dictionary checks  (p. 535) | html | pdf |
    • 5.4.12. Internals and programming style  (pp. 535-538) | html | pdf |
      • 5.4.12.1. Programming style  (p. 536) | html | pdf |
      • 5.4.12.2. Memory management  (p. 536) | html | pdf |
      • 5.4.12.3. Use of INCLUDE  (p. 536) | html | pdf |
      • 5.4.12.4. Use of ENDDO  (p. 536) | html | pdf |
      • 5.4.12.5. Names of internal routines  (pp. 536-537) | html | pdf |
      • 5.4.12.6. Use of the underscore character  (p. 537) | html | pdf |
      • 5.4.12.7. Names longer than six characters  (p. 537) | html | pdf |
      • 5.4.12.8. File management  (p. 537) | html | pdf |
      • 5.4.12.9. Case sensitivity  (p. 538) | html | pdf |
      • 5.4.12.10. Management of white space  (p. 538) | html | pdf |
    • 5.4.13. Distribution  (p. 538) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 5.4.7.1. Example application accessing aliased data names  (p. 530) | html | pdf |
      • Fig. 5.4.9.1. Sample program CIF_IN  (p. 531) | html | pdf |
      • Fig. 5.4.9.2. Example CIF read by the sample program CIF_IN shown in Fig. 5.4.9.1  (p. 532) | html | pdf |
      • Fig. 5.4.9.3. Printout from the example program CIF_IN run on the test file of Fig. 5.4.9.2  (p. 532) | html | pdf |
      • Fig. 5.4.10.1. Sample program to create a CIF  (p. 533) | html | pdf |
      • Fig. 5.4.10.2. Sample CIF created by the example program of Fig. 5.4.10.1  (p. 533) | html | pdf |
    • Tables
      • Table 5.4.6.1. CIFtbx variables  (p. 528) | html | pdf |
      • Table 5.4.12.1. Parameter statements in CIFtbx  (p. 536) | 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 |
      • 5.5.2.1. PDB format  (p. 539) | html | pdf |
      • 5.5.2.2. Ontology representation of macromolecular structure data   (pp. 539-540) | html | pdf |
      • 5.5.2.3. Supporting other data formats and data delivery methods  (p. 541) | html | pdf |
    • 5.5.3. Integrated data-processing system: overview  (pp. 541-543) | html | pdf |
      • 5.5.3.1. ADIT: functional description   (pp. 541-542) | html | pdf |
      • 5.5.3.2. Generalized database support  (p. 542) | html | pdf |
      • 5.5.3.3. Building a structure-determination data pipeline  (pp. 542-543) | html | pdf |
    • 5.5.4. Access  (p. 543) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 5.5.2.1. Excerpt of records from a PDB data file  (p. 539) | html | pdf |
      • Fig. 5.5.2.2. Files at different levels of the mmCIF metadata architecture  (p. 540) | html | pdf |
      • Fig. 5.5.3.1. Functional diagram of the ADIT system  (p. 541) | html | pdf |
      • Fig. 5.5.3.2. Schematic diagram of ADIT editing, format translation and validation functions  (p. 541) | html | pdf |
      • Fig. 5.5.3.3. Example ADIT data-input screen  (p. 542) | html | pdf |
      • Fig. 5.5.3.4. Schematic diagram of ADIT database loading functions  (p. 542) | html | pdf |
      • Fig. 5.5.3.5. Schematic diagram of a structure-determination data pipeline  (p. 543) | 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 |
      • 5.6.2.1. Low-level CBFlib functions  (pp. 546-549) | html | pdf |
      • 5.6.2.2. High-level CBFlib functions  (p. 549) | html | pdf |
      • 5.6.2.3. General high-level functions  (pp. 549-551) | html | pdf |
      • 5.6.2.4. Goniometer geometry functions  (p. 551) | html | pdf |
      • 5.6.2.5. Detector geometry functions  (pp. 551-552) | html | pdf |
    • 5.6.3. Compression schemes  (p. 552) | html | pdf |
      • 5.6.3.1. Canonical-code compression  (p. 552) | html | pdf |
      • 5.6.3.2. CCP4-style compression  (p. 552) | html | pdf |
    • 5.6.4. Sample templates  (pp. 552-554) | html | pdf |
    • 5.6.5. Example programs  (pp. 555-556) | html | pdf |
      • 5.6.5.1. convert_image  (p. 555) | html | pdf |
      • 5.6.5.2. makecbf  (pp. 555-556) | html | pdf |
      • 5.6.5.3. cif2cbf  (p. 556) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 5.6.1.1. Schematic data structure of a CBF or imgCIF data set accessed through a handle  (p. 544) | html | pdf |
      • Fig. 5.6.1.2. Flow chart for a typical application reading CBF/imgCIF data  (p. 545) | html | pdf |
      • Fig. 5.6.1.3. Flow chart for an application writing CBF/imgCIF data  (p. 545) | html | pdf |
      • Fig. 5.6.4.1. Template imgCIF for use with an ADSC Quantum 4 detector  (pp. 553-554) | html | pdf |
      • Fig. 5.6.4.2. Part of the template file for a MAR345 detector  (p. 554) | html | pdf |
      • Fig. 5.6.5.1. An extract of program code for the conversion of image data to CBF format  (p. 555) | html | pdf |
      • Fig. 5.6.5.2. Code fragment to illustrate the creation of the DIFFRN_FRAME_DATA category  (p. 555) | html | pdf |
      • Fig. 5.6.5.3. Listing of the main code fragment in the program cif2cbf for conversion of an ASCII CIF to a CBF file  (p. 556) | html | pdf |
    • Tables
      • Table 5.6.1.1. Return values from CBFlib functions  (p. 544) | html | pdf |
      • Table 5.6.2.1. Formal parameters for low-level CBFlib functions  (p. 546) | html | pdf |
      • Table 5.6.2.2. Values for headers in cbf_read_file  (p. 547) | html | pdf |
      • Table 5.6.2.3. Values for headers in cbf_write_file  (p. 547) | html | pdf |
      • Table 5.6.2.4. Values for encodings in cbf_write_file  (p. 548) | html | pdf |
      • Table 5.6.2.5. Values for the parameter compression in cbf_get_integerarrayparameters and cbf_set_integer­array  (p. 549) | html | pdf |
      • Table 5.6.2.6. Formal parameters for high-level CBFlib functions  (p. 550) | html | pdf |
      • Table 5.6.3.1. Structure of compressed data using the canonical-code scheme  (p. 552) | html | pdf |
      • Table 5.6.3.2. Structure of compressed data using the CCP4-style scheme  (p. 552) | 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 |
      • 5.7.2.1. Assembling the complete article  (pp. 557-558) | html | pdf |
      • 5.7.2.2. Reporting multiple structures and using templates  (p. 558) | html | pdf |
      • 5.7.2.3. Adding extra information to an article  (pp. 558-559) | html | pdf |
      • 5.7.2.4. Previewing the article  (pp. 559-560) | html | pdf |
      • 5.7.2.5. Data validation  (pp. 560-561) | html | pdf |
      • 5.7.2.6. Automated data validation: checkcif  (pp. 561-562) | html | pdf |
      • 5.7.2.7. Submission and review  (p. 562) | html | pdf |
      • 5.7.2.8. Publication  (p. 562) | html | pdf |
    • 5.7.3. CIF and other journals  (pp. 562-564) | html | pdf |
      • 5.7.3.1. Including CIF data in an article  (p. 563) | html | pdf |
      • 5.7.3.2. CIF and XML  (pp. 563-564) | 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 |
    • Figures
      • Fig. 5.7.2.1. Structure of a CIF describing several crystal structures  (p. 559) | html | pdf |
      • Fig. 5.7.2.2. Examples of authors' request-list extensions for items not normally printed in a paper  (p. 560) | html | pdf |
      • Fig. 5.7.2.3. Extracts from a checkcif report for a `publication check' on a CIF to be submitted to an IUCr journal  (p. 561) | html | pdf |
      • Fig. 5.7.3.1. Typesetting of structural data  (p. 563) | html | pdf |
      • Fig. 5.7.3.2. Part of a file used to print the article shown in Fig. 5.7.3.1(b)  (p. 564) | html | pdf |
      • Fig. 5.7.3.3. Part of the SGML file used to print the article shown in Fig. 5.7.3.1(b)  (p. 564) | html | pdf |
    • Tables
      • Table A5.7.1.1. Request list for Acta Crystallographica Section C  (pp. 565-566) | html | pdf |
      • Table A5.7.2.1. List of data-validation tests applied by checkcif  (pp. 566-567) | html | pdf |
      • Table A5.7.2.2. List of data-validation tests applied by PLATON  (pp. 567-568) | html | pdf |