International Tables for Crystallography (2026). Vol. G. Early view chapter
https://doi.org/10.1107/97809553602060001008

Chapter 3.11. Classification and use of macromolecular data

Contents

  • Classification and use of macromolecular data | 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| html | pdf |
    • 3.11.2. Considerations underlying the design of the dictionary| html | pdf |
    • 3.11.3. Overview of the mmCIF data model| html | pdf |
    • 3.11.4. Content of the macromolecular CIF dictionary| html | pdf |
    • 3.11.5. Experimental measurements| html | pdf |
      • 3.11.5.1. Crystal cell parameters and measurement conditions| html | pdf |
      • 3.11.5.2. Data collection| html | pdf |
      • 3.11.5.3. Growth, description and analysis of the crystal| html | pdf |
        • 3.11.5.3.1. Crystal properties| html | pdf |
        • 3.11.5.3.2. Crystal growth| html | pdf |
    • 3.11.6. Analysis| html | pdf |
      • 3.11.6.1. Phasing| html | pdf |
        • 3.11.6.1.1. Overall description of phasing| html | pdf |
        • 3.11.6.1.2. Phasing via molecular averaging| html | pdf |
        • 3.11.6.1.3. Phasing via isomorphous replacement| html | pdf |
        • 3.11.6.1.4. Phasing via multiple-wavelength anomalous dispersion| html | pdf |
        • 3.11.6.1.5. Phasing via multiple isomorphous replacement| html | pdf |
        • 3.11.6.1.6. Phasing data sets| html | pdf |
      • 3.11.6.2. Refinement| html | pdf |
        • 3.11.6.2.1. Overall description of the refinement| html | pdf |
        • 3.11.6.2.2. Analysis of the refined structure| html | pdf |
        • 3.11.6.2.3. Restraints and refinement by shells of resolution| html | pdf |
        • 3.11.6.2.4. Equivalent atoms in the refinement| html | pdf |
        • 3.11.6.2.5. History of the refinement| html | pdf |
      • 3.11.6.3. Reflection measurements| html | pdf |
        • 3.11.6.3.1. Individual reflections| html | pdf |
        • 3.11.6.3.2. Groups of reflections| html | pdf |
    • 3.11.7. Atomicity, chemistry and structure| html | pdf |
      • 3.11.7.1. Atom sites| html | pdf |
        • 3.11.7.1.1. Individual atom sites| html | pdf |
        • 3.11.7.1.2. Collections of atom sites| html | pdf |
        • 3.11.7.1.3. Atom types| html | pdf |
        • 3.11.7.1.4. Alternative conformations| html | pdf |
      • 3.11.7.2. Molecular chemistry| html | pdf |
        • 3.11.7.2.1. Molecular chemistry in the core CIF dictionary| html | pdf |
        • 3.11.7.2.2. Chemical components| html | pdf |
        • 3.11.7.2.3. Chemical links| html | pdf |
      • 3.11.7.3. Distinct chemical species| html | pdf |
        • 3.11.7.3.1. Description of entities| html | pdf |
        • 3.11.7.3.2. Polymer entities| html | pdf |
      • 3.11.7.4. Molecular or packing geometry| html | pdf |
      • 3.11.7.5. Molecular structure| html | pdf |
        • 3.11.7.5.1. Higher-level macromolecular structure| html | pdf |
        • 3.11.7.5.2. Secondary structure| html | pdf |
        • 3.11.7.5.3. Structural interactions| html | pdf |
        • 3.11.7.5.4. Structural features of monomers| html | pdf |
        • 3.11.7.5.5. Noncrystallographic symmetry| html | pdf |
        • 3.11.7.5.6. External databases| html | pdf |
        • 3.11.7.5.7. [\beta]-sheets| html | pdf |
        • 3.11.7.5.8. Molecular sites| html | pdf |
      • 3.11.7.6. Crystal symmetry| html | pdf |
      • 3.11.7.7. Bond-valence information| html | pdf |
    • 3.11.8. Publication| html | pdf |
      • 3.11.8.1. Literature citations| html | pdf |
      • 3.11.8.2. Citation of software packages| html | pdf |
      • 3.11.8.3. Citation of related database entries| html | pdf |
        • 3.11.8.3.1. Related database entries| html | pdf |
        • 3.11.8.3.2. Compatibility with PDB format files| html | pdf |
      • 3.11.8.4. Article publication| html | pdf |
        • 3.11.8.4.1. Journal housekeeping and citation entries| html | pdf |
        • 3.11.8.4.2. Contents of a publication| html | pdf |
    • 3.11.9. File metadata| html | pdf |
      • 3.11.9.1. History of a data block| html | pdf |
      • 3.11.9.2. Links between data blocks| html | pdf |
      • 3.11.9.3. Other category classifications| html | pdf |
    • Appendix 3.11.1. Category structure of the mmCIF dictionary| html | pdf |
    • Appendix 3.11.2. The Protein Data Bank exchange data dictionary| html | pdf |
      John D. Westbrook, Ezra Peisach, Kyle L. Morris, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar and Stephen K. Burley
      • A3.11.2.1. Extensions for improved data representation| html | pdf |
      • A3.11.2.2. Dictionary extensions to support data processing, management and validation| html | pdf |
      • A3.11.2.3. Dictionary extensions to emerging experimental methods| html | pdf |
      • A3.11.2.4. Dictionary extensions to support related dictionaries| html | pdf |
      • A3.11.2.5. Supporting software| html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 3.11.3.1. A representation of crambin (PDB 1CBN) with a co-crystallized ethanol molecule| html | pdf |
      • Fig. 3.11.6.1. The family of categories used to describe MAD phasing| html | pdf |
      • Fig. 3.11.6.2. The family of categories used to describe MIR phasing| html | pdf |
      • Fig. 3.11.7.1. The family of categories used to describe atom sites| html | pdf |
      • Fig. 3.11.7.2. 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| html | pdf |
      • Fig. 3.11.7.3. 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| html | pdf |
      • Fig. 3.11.7.4. The family of categories used to describe the links between chemical components| html | pdf |
      • Fig. 3.11.7.5. The family of categories used to describe chemical entities| html | pdf |
      • Fig. 3.11.7.6. The family of categories used to describe polymer chemical entities| html | pdf |
      • Fig. 3.11.7.7. The family of categories used to describe the higher-level macromolecular structure| html | pdf |
      • Fig. 3.11.7.8. 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| html | pdf |
      • Fig. 3.11.7.9. The family of categories used to describe secondary structure| html | pdf |
      • Fig. 3.11.7.10. The family of categories used to describe structural interactions such as hydrogen bonding, salt bridges and disulfide bridges| html | pdf |
      • Fig. 3.11.7.11. The family of categories used to describe the structural features of monomers| html | pdf |
      • Fig. 3.11.7.12. The family of categories used to describe noncrystallographic symmetry| html | pdf |
      • Fig. 3.11.7.13. 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| html | pdf |
      • Fig. 3.11.7.14. The family of categories used to describe [\beta]-sheets| html | pdf |
      • Fig. 3.11.7.15. A hypothetical [\beta]-sheet to be described with data items in the STRUCT_SHEET, STRUCT_SHEET_ORDER, STRUCT_SHEET_RANGE and STRUCT_SHEET_HBOND categories| html | pdf |
      • Fig. 3.11.7.16. The family of categories used to describe molecular sites| html | pdf |
    • Tables
      • Table 3.11.4.1. Major category groups defined in the mmCIF dictionary| html | pdf |
      • Table A3.11.1.1. Categories in the mmCIF dictionary| html | pdf |
      • Table A3.11.2.1. Selected category groups added to the PDBx/mmCIF dictionary| html | pdf |