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2.2 QUEST3D: Searchable Information Fields


1D Information: Text Fields (TEXT sub-menu called from SEARCH)

Locate a `query text string' in a named CSD text field. A full list of allowed *FIELDS is in Appendix B. Example 6 of Section 3.2 covers text searching.

1D Information: Numeric Fields (NUMERIC sub-menu called from SEARCH)

Compare a numerical query value with values in named CSD numeric field. A full list of allowed *FIELDS is in Appendix C. Example 7 of Section 3.2 covers numeric searching.

1D Information: Element Searching (ELEMENT sub-menu called from SEARCH)

The ELEMENTS sub-menu brings up the periodic table and CSD pre-set element groups. Searches using individual elements, the pre-set groups, or user defined groups, can be encoded interactively using this sub-menu. Example 8 of Section 3.2 covers element searching.

1D Information: Molecular Formula (Use FORMULAE button in SEARCH menu)

Searches for element type / element count combinations within the molecular formula records. Element can be an individual element symbol or one of the CSD pre-set element groups. Example 8 of Section 3.2 covers formula searching.

1D Information: Reduced Cell (REDUCED-CELL sub-menu called from SEARCH)

Interactive choice of Lattice Type, Crystal System, Cell-Parameters and a Search Tolerance. Searches are conducted in terms of the reduced cell calculated from the input values. Example 9 of Section 3.2 covers reduced-cell searching.

1D Information: Peptide Sequences (PEPTIDE-SEQ sub-menu called from SEARCH)

Interactive construction of amino-acid sequences (with user-defined variants at a given position, or 'any' option) for matching against CSD peptide sequence information. Example 10 of Section 3.2 covers peptide sequence searching.

1D Information: Search Screens (SCREENS sub-menu called from SEARCH)

Search screens encode yes/no information about a CSD entry in the form of an on/off [1/0] settings in a bit-map. Screens 1-155, defined in Appendix D, are specifically for setting by users as part of a CSD search. Uses of the SCREENS menu are illustrated in Section 3.4 of this Guide.

2D Information: Chemical Connection Tables (BUILD, 2D-CONSTRAIN etc.)

The chemical connection tables are searchable for chemical substructures (fragments) or complete molecules. Fragments are sketched using the BUILD menu and further defined by use of the 2D-CONSTRAIN and PERIODIC-TABLE sub-menus. Examples 1 and 2 of Section 3.2 of this Guide covers 2D substructure searching.

2D Information: Similarity searching (BUILD, 2D-CONSTRAIN)

A 2D drawing of a complete molecule is constructed using BUILD, PERIODIC-TABLE and 2D-CONSTRAIN. The SIMIL button in 2D-CONSTRAIN can then be used to initiate a 2D similarity search for that molecule, based on the algorithm described by Willett, et al., J.Chem.Inf.Computer Sci., 26,36,1986). Hits are ranked and presented in order of their similarity (maximum 1.0, minimum 0.0) to the input molecule. Section 3.6 covers similarity searching.

3D Information: Geometric Searching (BUILD, 2D-CONSTRAIN, 3D-CONSTRAIN etc.)

A 2D chemical fragment is constructed (and further defined if required) as indicated above. The 3D characteristics of the fragment can then be defined by placing restrictions on user-selected geometrical parameters. Examples 3, 4 and 5 of Section 3.2 of this Guide covers 3D fragment searching.

3D Information: Intermolecular Geometry (NON-BONDED button in 3D-CONSTRAIN)

Locates non-bonded interactions between atoms or groups of atoms that lie within interatomic distance limits (given explicitly, or relative to sums of van der Waals radii). Example 5 of Section 3.2 of this Guide covers non-bonded searching.

PDB Sequence Information (PDB-SEQUENCE button in SEARCH)

Construction of residue sequence queries (with user-defined variants at a given position, or `any' option) for matching against Protein Data Bank (PDB) entries. Section 3.7 covers PDB searching.

Reference Code Retrieval

Often you will accumulate a set of CSD reference codes and would like to view these entries in QUEST3D or create subfiles for use by VISTA or PLUTO. These refcodes can be searched in QUEST3D by use of a `Virtual Database', see Section 3.8.


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