Volume 1 Chapter 7 Further Examples of Non-Bonded Searches

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7.15 Commands in the 3D-CONSTRAIN Sub-menu

The 3D-CONSTRAIN sub-menu (see below) contains buttons that correspond to the foregoing description. The buttons are arranged in groups that can be correlated directly with individual descriptions in this chapter.

The group command button has a special colour and in most groups there are also a number of white 'keyword' buttons. In these cases, the group command button has no action - it merely acts as a group label and all instructions are input by selecting the keyword buttons. In some groups (TRANSFORM, SELECT), the group command is the only button. Here, selection of the group command button is mandatory and must be followed by further input as requested in the dialogue area.

Instructions are displayed as they are composed, using the left-hand side of the screen - the summary area. The instructions are displayed, minus the group command, but in the colour of the group command.

The 3D-CONSTRAIN sub-menu is illustrated above. The command group colours are indicated and the appropriate section of descriptive material in this chapter is indicated.

Full notes on the operation of individual group and keyword command buttons are included in chapter 3, Vol.2; brief summary notes are provided here by way of introduction.


The default settings of these commands define EXHAUSTIVE fragment location with atomic OVERLAP of fragments permitted.

The EXHAUSTIVE button can be toggled between two states:

The OVERLAP button toggles between 'atomic overlap permitted' and 'atomic overlap not permitted'

The state of the EXHAUSTIVE and OVERLAP settings is incorporated in the "home" prompt in the dialogue area.

7.15.2 SETUP Commands

The SETUP group permits the addition of complex geometric objects to the basic atoms of the fragment diagram.

The description of each SETUP operation is displayed in red in the summary area.

Available geometric objects are:

The geometric objects are established in terms of the atoms, centroids and dummy atoms of the fragment and, in the case of dummy atoms, by providing numerical information via the keyboard.

7.15.3 DEFINE Commands

The DEFINE group is used to specify and name the numerical parameters chosen to characterise the 3D structure of each fragment.

The operation of the keyword commands may be summarised as:

As a result of repeated use of DEFINE commands, we establish Np parameters each having a unique name.

These parameter names and their definitions are displayed in green in the summary area.

The values of each of the Np parameters will be calculated for each occurrence of the chemical fragment in the 3D crystal structures of the CSD. If we have Nf occurrences of the fragment over the complete CSD search, then we establish a data matrix of Np columns and Nf rows.

The DEFINEd parameters may be used, by parameter name, to add further columns to this matrix via use of the TRANSFORM commands.

7.15.4 TRANSFORM Command

The TRANSFORM command allows 'composite parameters' to be formed from those parameters already DEFINEd. A parameter name is required for the new composite parameter.

On activating the magenta TRANSFORM button, a list of available transformation operators appears in the top-right hand corner of the display area.

A composite parameter is specified by encoding the correct arithmetic expression to generate the parameter required from the displayed parameters and TRANSFORM operators.

Since only a single operation can be carried out by each TRANSFORM command, multiple use of the command is often necessary to obtain the desired composite parameter.

Thus, to obtain the mean of 3 bond lengths B1, B2, B3, it is necessary to proceed stepwise as:

SUM1 = B1 + B2

SUM2 = SUM1 + B3

MEAN = SUM2 / 3.0

In this case, SUM1 and SUM2 are 'intermediate' parameters and we may not wish to include them in the final data matrix. This can be effected by using a question mark '?' as the first character of the parameter name for such intermediates.

In some cases, a DEFINEd parameter itself is only generated as an intermediate, and the '?' convention can also be used in naming DEFINEd parameters. Thus, if we only wished to display the MEAN value in the geometrical descriptors, then the bond lengths could have been named ?B1, ?B2, ?B3 at the DEFINE stage.

7.15.5 SELECT Commands

The SELECT command is used to specify limiting lower and upper bounds for a named geometrical parameter. Multiple use of SELECT is required to place geometric constraints on more than one parameter in the same QUEST3D search.

The operation of SELECT with respect to torsion angles is illustrated below.

Torsion Angles

Torsion angle a-x-y-f is angle by which a-x must be rotated to overlie y-f.

Clockwise rotation is positive

Anti-Clockwise rotation is negative

In the above example a-x-y-f is -60°.


1. W. Klyne and V. Prelog, Endeavour, 16, 521, 1960.

2. M.S. Newman, J. Chem. Educ., 32, 344, 1955.

The selection range for torsion angle parameters will be interpreted as including those torsion angles within the segment formed by a clockwise rotation from the first-given value to the second.

Limiting values must be given with the second value greater than the first, e.g. -160 -140.

Any of the parameters established using DEFINE or TRANSFORM may be used in a SELECT instruction. Parameters are indicated by clicking on the appropriate parameter name in the summary area.

The SELECT group of the sub-menu also permits specification of spheres of inclusion or exclusion around a given point (centroid or dummy).

The commands INCLUSION/EXCLUSION require that other atoms of the molecule are required/not permitted within a sphere of specified radius about the point, in order for the fragment to be a hit.

7.15.6 ENANTIOMER Commands

The inclusion, or not, of 3D structural inverses in the search proces has been covered in detail in section 7.13 of this chapter. The functions of the settings NOINVERT (default), INVERT, and NORMAL are fully described there.

7.15.7 NON-BONDED Commands


This button permits the specification of an atomic group in terms of atom numbers from the sub-fragments drawn using the 2D menu system.

The button can be used to set up a maximum of 20 groups. Atoms may be included in more than one group.

Only atom numbers may be used in group specification. Centroids (X) and dummy atoms (D) that may have been established using SETUP cannot be used in the specification of a group.


This button permits specification of van der Waals radii for element types that will be used in the search. A small set of pre-defined van der Waals radii are included within the program for the common elements; full details are given in chapter 3 of Vol.2.


This button is the main control button for all non-bonded searches. The user is prompted for a variety of information which is provided by button clicks on selected atoms, or by direct input from the keyboard.

The information requested is :

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Volume 1 Chapter 7 Bit Screens for 3D Searching.