2.2 QUEST3D: Searchable Information Fields
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.
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
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.
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.
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
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.
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.
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.
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.
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.
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
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.
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