Collections of atom sites

Fitzgerald, P. M. D.; Westbrook, J. D.; Bourne, P. E.; McMahon, B.; Watenpaugh, K. D.; Berman, H. M.

doi:10.1107/97809553602060000738

International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

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International Tables for Crystallography (2006). Vol. G. ch. 3.6, p. 167

Section 3.6.7.1.2. Collections of atom sites

P. M. D. Fitzgerald,^a ^* J. D. Westbrook,^b P. E. Bourne,^c B. McMahon,^d K. D. Watenpaugh^e and H. M. Berman^f

^a Merck Research Laboratories, Rahway, New Jersey, USA,^bProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA,^cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,^dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,^eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and ^fProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA
Correspondence e-mail: paula_fitzgerald@merck.com

3.6.7.1.2. Collections of atom sites

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The data items in these categories are as follows:

(a) ATOM_SITES [Scheme scheme88]

(b) ATOM_SITES_FOOTNOTE [Scheme scheme89]

The bullet ( $[\bullet]$ ) indicates a category key. The arrow ( $[\rightarrow]$ ) is a reference to a parent data item. Items in italics have aliases in the core CIF dictionary formed by changing the full stop (.) to an underscore (_) except where indicated by the $[\sim]$ symbol.

The ATOM_SITES category of the core dictionary, which is used to record information that applies collectively to all the atom sites in the model of the structure, is incorporated without change into the mmCIF dictionary, and Section 3.2.4.1.2 can be consulted for details.

In practice, the data names in the PHASING categories are preferred to the aliases to the core CIF data items _atom_sites.solution_primary, *_secondary and *_hydrogens. The data items in the mmCIF PHASING categories are designed to allow a much more detailed description of how a macromolecular structure was solved.

The data item _atom_sites.entry_id has been added to the ATOM_SITES category to provide the formal category key required by the DDL2 data model.

The ATOM_SITES_FOOTNOTE category can be used to note something about a group of sites in the ATOM_SITE coordinate list, each of which is flagged with the same value of _atom_site.footnote_id. For example, an author may wish to note atoms for which the electron density is very weak, or atoms for which static disorder has been modelled. Example 3.6.7.2 shows how an author has used these data items to describe alternative orientations in part of a structure. However, the very large number of data names describing specific structural characteristics in the mmCIF dictionary mean that these rather general data names are rarely needed.

Example 3.6.7.2. Footnotes for particular groups of atom sites in an HIV-1 protease structure (PDB 5HVP) using data items in the ATOM_SITES_FOOTNOTE category. [Scheme scheme90]

References

International Tables for Crystallography (2006). Vol. G. ch. 3.6, p. 167