2.1 QUEST3D: Basics
All search queries are encoded via the interactive menu system described in
Section 2.3, Appendix A and in the various examples. Queries may be divided
into two broad types:
- Search any of the 1D, 2D or 3D information fields in the CSD (see Section
- Display search results as text and as graphical representations of 2D and
- Permit interaction with search results, i.e. manipulation of 3D graphics,
display of individual geometrical parameters on demand, etc.
- Generate summary tables of specified geometrical information for all hits.
- Prepare simple histograms and scattergrams of specified parameter(s).
- Create a variety of subfiles of CSD information for use by VISTA, PLUTO or
by external software packages.
Individual text and numerical fields in the CSD are referred to by search
field names in the relevant menus. These are of the form *FIELD and a full
list is given in Appendices B and C.
A search of an individual field involves either:
- Queries that interrogate one of the individual text and numerical
information fields: these searches are encoded via the main SEARCH menu and its
- Queries that interrogate the 2D and 3D information fields and depend upon
the encoding of a chemical substructure (fragment) in graphical form: these
searches are encoded via the main BUILD menu and its associated sub-menus.
Each interrogation of an individual *FIELD is referred to as a search TEST,
simple examples are:
- The matching of a query text string to the contents of a specified text
- The comparison of a numerical query value to the contents of a numerical
The logical operators that can be used in a numerical comparison are: .eq.
(default) .lt. .le. .ge. .gt. A numerical range may be specified by use
of n1 - n2.
- TESTn or Tn *SURNAME Smith
- TESTn or Tn *YEAR .eq. 1978
Searches based on the graphical encoding of a chemical fragment diagram all
involve the interrogation of the 2D chemical connectivity field (internally
known as *CONN in QUEST3D) and may also involve the use of the associated 3D
A complete CSD search often requires that a number of individual search TEST's
must be combined to generate the required results. Thus, many individual
TEST's may be encoded (limit 200) and these are numbered sequentially (n in the
Tn lines above).
When all necessary TEST's have been encoded, the search is initiated from the
QUEST sub-menu. All assembled TEST's are displayed for verification and for
inclusion (or not) in the final search QUESTION, where the individual TEST's
are combined using the logical operators .AND. .OR. and .NOT. Thus the two
tests given above could be combined to create the complete QUESTion:
that would locate all papers by Smith in 1978.
Chemical fragment queries are also assigned a TEST number and displayed
graphically by the QUEST sub-menu. They may be included in the logical
combination(s) of the QUEST instruction in exactly the same manner using their
assigned TEST number(s).
TEST's encoded during a QUEST3D session are always available for inclusion in
the final QUESTion line, but it is not necessary that all TEST's shall be
included in this process.
Each CSD entry contains a bitmap that records yes/no (bit setting of 1/0)
answers to simple questions about that entry, e.g. "Is this entry error-free
after CSD checks?", "Does this entry have an R-factor less than 0.075?", "Was
the absolute configuration determined for this entry?", "Is this a neutron
study?, etc. These bit settings are called search keys or SCREEN's in the CSD.
A total of 155 screens (Appendix D) are encoded for user-selection. SCREEN'ed
searches are rapid to set up and run (SCREEN sub-menu called from SEARCH menu).
One or more SCREEN's can form a very powerful complete query in their own
right, or may be used in combination with normal TEST's to further define a
more complex search query.
Any files that may be required for later use by CSD System programs or by
external software are specified to QUEST3D via the SEARCH or QUEST menus (see
Section 3.3). QUEST3D generates the following file types by default: .jnl
produced in all searches, and .fgd, .sum, .tab in 3D searches.
Search hits may be examined within one of four DISPLAY menus:
All 3D displays
can be manipulated interactively with control of atom labelling and options to
create crystallographic packing diagrams.
Search hits may be accumulated in two ways by use of the DISPLAY menus:
- 2D/3D DISPLAY (default): 2D chemical diagram, 3D molecular structure, 1D
- 2D DISPLAY: 2D chemical diagram, 1D information summary
- 3D DISPLAY : 3D molecular structure
- 1D DISPLAY : Complete 1D information for the entry
hit generates information in the output files created by QUEST3D.
- Stepwise: each hit is presented individually for examination and
the system pauses for you to decide whether to KEEP or REJECT the hit.
- Continuous: when you are satisfied that the query is generating the
expected results, then switch to FAST mode, this accumulates all hits until the
end of the database is reached but cannot be interrupted.