Tables for
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F. ch. 24.3, pp. 665-666

Section Quest3D

F. H. Allena* and V. J. Hoya

aCambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
Correspondence e-mail: Quest3D

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Quest3D is the main search engine and information-retrieval program for the CSD. It permits interrogation of all information fields: (a) 19 text fields, (b) 38 individual numerical fields, (c) element symbols and element counts, (d) full or partial molecular formulae, (e) direct access to over 150 bit screens, (f) extensive 2D chemical substructure search capabilities, and (g) 3D substructure searching at the molecular level or at the extended crystal-structure level. A search of a specific information field is termed a test of that field, and is constructed graphically via the menu system; menu components correspond to the categories of searches identified above. A complete query is then constructed by combining a number of separate test components using Boolean logic.

Substructure searching is the most important and frequently used facility. At the molecular level, the substructure (chemical fragment) query is entered graphically and is defined using the formal covalent bond types present in the 2D chemical connectivity tables of the CSD. The process can be extended to locate non-bonded contacts in the complete crystal structure. Here, the individual atoms or chemical groups involved in the contact must be specified, and a limiting non-bonded contact distance must be provided, along with any other geometrical criteria required to define the contact more precisely.

All substructure searches begin with the user drawing the required chemical unit(s) via the BUILD menu. Chemical variability and precision are controlled through (a) the PERIODIC TABLE sub-menu, which allows for specification of variable element types at specific atomic sites, (b) the 2D-CONSTRAIN menu, which allows further chemical restrictions to be specified, such as cyclicity/acyclicity of bonds, exact hydrogen-atom counts, total coordination numbers for atoms etc., and (c) the 3D-CONSTRAIN menu, which permits the user to specify a list of geometrical parameters to be calculated by the program for each instance of the fragment located in the CSD; any of these geometrical parameters may be used as criteria to limit the scope of the search, especially at the intermolecular level. A file of calculated geometrical information is output by Quest3D and may be read by Vista, or by external data analysis software. Other Quest3D output files allow CSD search results to be communicated rapidly to proprietary modelling software.

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