The operation of the graphics software system is summarized in the flowchart below.

CSDS : Graphics Software System

(Note: GSTAT can still be used as per the Basic System.)

By comparison with the flowchart for the basic software system, the following changes have been made:

Query input to the QUEST3D program is now via an extensive set of graphical menus. Query construction and program operation are now fully interactive.
QUEST3D, as its name implies, can now calculate and test a wide variety of 3D geometrical parameters: the geometrical calculations and selection facilities of GSTAT are upgraded and transferred to QUEST3D to add to the existing 1D and 2D search capabilities.
The integration of 1D, 2D and 3D search facilities is a direct result of the integrated 2D and 3D connectivity representations that are now available in the Version 5 database.
QUEST3D can now display 1D,2D, 2D/3D and 3D diagrams for hit entries, in addition to the alphanumeric information output by basic QUEST.
The 3D diagrams can be generated either at the molecular level, or at the crystal structure (packing) diagram level.
QUEST3D will output all of the interface files of the basic QUEST program. In addition QUEST3D will output files containing:
- (a) A FRAGMENT file recording the CSD atoms that correspond to the atoms of a 2D/3D search query
- (b) A TABLES file recording the user-defined geometry that has been calculated for each hit fragment
- (c) A MODEL file recording the integrated 2D/3D chemical/structural information for each molecule or fragment that satisfies the search constraints input to QUEST3D
- (d) A Postscript file containing any give combination of the display types for each entry that satisfies the search constraints input to QUEST3D
VISTA, a menu-driven data analysis package operates on the FRAGMENT and TABLES files generated for hits by QUEST3D. This program is has a graphical interface and allows the user to save created plots as postscript files.
GSTAT can still be used and it retains all of its original functionality in full. However, the program can now read the FRAGMENT file output by QUEST3D, thus bypassing the fragment location procedures. Volume 4 of the documentation describes how this improves the precision of subsequent data analyses. GSTAT will also generate a TABLES file in a format identical to that generated by QUEST3D.

The interactive menu system of QUEST3D will now permit the user to:

Compose Text, Numerical, Chemical Formula and Crystallographic Unit Cell searches.
Build a 2D substructure search query, using elements or groups of elements selected from the Periodic-Table sub-menu.
Apply 2D Constraints to the basic substructure, e.g. restrictions on hybridization state or coordination number, ranges of permitted bond types, atomic charges, numbers of terminal hydrogen atoms, etc. All of the facilities of basic QUEST are available and any input errors can rapidly be corrected using the Edit menu.
Use the 3D-CONSTRAIN sub-menu to:
- (a) Establish geometric objects
- (b) Define, name and calculate a wide variety of 3D geometrical parameters derived from atomic coordinates and geometric objects
- (c) Select hit fragments on the basis of limiting values of any or all of these geometric parameters

The QUEST3D program will present hits as 2D and 3D diagrams. The 3D diagram can be a molecular diagram or a packing diagram and can be interrogated to display geometrical data on the screen.

QUEST3D will also generate a final tabulation of geometrical parameters defined by the user via the 3D-CONSTRAIN sub-menu.

These processes are illustrated below for the cyclopropyl-carbonyl fragment that was used to exemplify the operation of the basic software system.

NFRAG   REFCOD        D1      D2      D3   DMEAN     TAU               *
     1  ACMEPT     1.416   1.529   1.522   1.489 176.205               *
     2  ACMEPT     1.416   1.530   1.528   1.491 176.188               *
     3  ACMEPT10   1.416   1.529   1.522   1.489 176.205               *
     4  ACMEPT10   1.416   1.530   1.528   1.491 176.188               *
     5  ACOHKT     1.497   1.524   1.525   1.515  21.613               *
     6  ACOHKT     1.524   1.525   1.497   1.515  75.168               *
     7  AIMCTY     1.512   1.517   1.497   1.509 146.695               *
     8  ARITOL     1.500   1.535   1.506   1.514 150.295               *
     9  BARTUS10   1.477   1.536   1.516   1.510  10.475               *
    10  BAXTID     1.519   1.531   1.542   1.531  19.962               *
 
        Nobs         494     494     494     494     494               *
        Mean       1.496   1.519   1.522   1.512  74.425               *
        SDSample   0.024   0.017   0.021   0.011  67.395               *
        SDMean     0.001   0.001   0.001   0.001   3.032               *
        Minimum    1.416   1.454   1.440   1.473   0.000               *
        Maximum    1.592   1.582   1.580   1.539 179.980               *

1.5.2 VISTA

This is the new CSDS program available to users of the Graphical version of the CSDS. VISTA stands for VIsualization of STAtistics and allows interactive examination of the numerical results of 3d searches. The current release allows the production of histograms, scattergrams and principle component analysis plots. In all these cases it is possible to select any combination of bins, examine the list of refcodes in these bins and examine all 1D, 2D, 2D/3D and 3D displays for any selected entry. It also contains a postscript editor allowing plots to be customised before they are saved.

1.5.3 GSTAT

Operation of the GSTAT program within the graphics software system is exactly as for the basic software system. QUEST3D will generate an FDAT file for the hits and the user must generate an alphanumeric instruction set as described in Volume 4 of this Documentation.

However, the most difficult function of GSTAT is the re-location of substructural fragments within the limited information available in the crystallographic connection table (see Volume 4, Chapter 5). The crystallographic connection table lacks much of the chemical information available to QUEST3D and search precision is therefore reduced.

Thus, in the graphics software system, QUEST3D will generate an additional file (Fragment) which contains the list of CSD atoms that satisfy the 2D/3D search constraints for each hit entry. GSTAT can now read this file, in addition to the FDAT file, so avoiding the imprecisions noted above.

QUEST and QUEST3D have always output an alphanumeric version of the user's search query at the head of the print file. It is now a simple matter to edit in a few additional instructions (in bold type in the example below) to generate a valid GSTAT instruction set. This method is used in the example to generate histograms and scattergrams following a QUEST3D run.

GSTAT instruction file:

GET T1
>> T1 *CONN
NFRAG   1
AT1 C 2 T4                                         :XY   100   625
AT2 C 2 T4                                         :XY   100   37
AT3 C 3 T4                                         :XY   353   505
AT4 C 2 T3                                         :XY   716   505
AT5 O 1 E                                          :XY   900   396
BO 1 2 1
BO 2 3 1
BO 1 3 1
BO 3 4 1
BO 4 5 2
GEOM
DEFINE D1 1 2
DEFINE D2 1 3
DEFINE D3 2 3
TRANSFORM ?ADD1 = D1 + D2
TRANSFORM ?ADD2 = ?ADD1 + D3
TRANSFORM DMEAN = ?ADD2 / 3.0
SELECT DMEAN 1.47 1.54
SETUP X1 2 3
DEFINE ?TAU 5 4 1 X1
TRANSFORM TAU = ABS ?TAU
C OVERLAP OF CRYSTAL FRAGMENTS PERMITTED
C SEARCH FOR ALL CRYSTAL FRAGMENTS
NFRAG -99
ENANT NOIN
HIST D3
SCAT D3 TAU
END
 
D3         10   20   30   40   50   60   70   80   90  100        D3
       .....I....I....I....I....I....I....I....I....I.....
  1.40 -                                                 -
       .                                                 .
       .**                                               . (  4)
       .**                                               . (  4)
       .***                                              . (  7) MEAN:
  1.45 -*********                                        - ( 19)      1.495
       .*******                                          . ( 15)
       .****************                                 . ( 32) SDEV:
       .************************************             . ( 72)      0.025
       .*******************************************      . ( 86)
  1.50 -****************************************         - ( 80) MINIMUM:
       .************************************             . ( 73)      1.416
       .**********************************               . ( 68)
       .*************                                    . ( 27) MAXIMUM:
       .****                                             . (  8)      1.592
  1.55 -*                                                - (  3)
       .**                                               . (  4)   504 VALS
       .*                                                . (  1) PLOTTED:
       .                                                 .
       .*                                                . (  1)
  1.60 -                                                 -
       .....I....I....I....I....I....I....I....I....I.....
D3         10   20   30   40   50   60   70   80   90  100        D3
 
 
    1.375    1.420    1.465    1.510    1.555    1.600
       +I--------I--------I--------I--------I--------I+  D3
  180.0-        4    1  2  4122922  32                - ACROSS      DOWN
       I           1    1  12 15634641 1           1  ID3          TAU
       I                  1 5445461252121             I        MEAN:
       I                   13322156141421 21          I   1.495    74.059
  140.0-                     222 12  21  1  1         -        SDEV:
       I                      1111  111               I   0.025    67.386
       I                       1 2    1               I      MINIMUM:
       I                           211 2              I   1.416     0.000
  100.0-                        1                     -      MAXIMUM:
       I                 1      2 1 11 1  1           I   1.592   179.980
       I                        111 1 3211 1          I
       I                         2 1 11  11 1   1     I  504 VALS PLOTTED
   60.0-                    12  1 24231               -    0 VALS OMITTED
       I          1         1 113286A22               I
       I                  1 1211 3  21      11        I  CORREL. COEFF.
       I                    12333122221               I       0.162
   20.0-            2 1  122238752332431 1            -
       I            21 83422A456A4532313  1           I
       I            2 1623259847743232                I
       I                                              I
  -20.0-                                              -
       +I--------I--------I--------I--------I--------I+
TAU

1.5.4 PLUTO

Again, since QUEST3D will generate an FDAT file for hit entries, then PLUTO will operate in an identical manner in both graphics and basic software systems.

However, it should be noted that some of the functions of PLUTO are now available in the hit display menus of QUEST3D and that this area of the QUEST3D code will develop further in due course.

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Volume 1 Chapter 1 Guide to the Documentation .

1.5 The Graphics Software System