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3.1.3.4 2D-CONSTRAIN Sub-menu

The 2D-CONSTRAIN sub-menu was formerly known as the CONSTRAIN-STRUCTURE sub-menu. This sub-menu allows you to specify additional constraints for fragment-based searches. Such constraints include:

These commands allow you to make your search more "precise".

The commands associated with SIMILARITY searches are also located in the 2D-CONSTRAIN sub-menu. This is where you decide whether you will use the TANIMOTO or DICE coefficients in the similarity search.

3.1.3.5 3D-CONSTRAIN Sub-menu

This is the sub-menu that allows you to formulate 3-dimensional searches.

The first step in the formulation of many "3D searches" is to define the items you require to be tabulated at the end of the search. For example, you may want to inspect all torsion angle values in a six-membered ring.

In some cases, this tabulation may be all that is required. In other cases, however, you may wish to use the SELECT command to restrict `hits' to those database entries for which one or more calculated parameter values lie within a specified range.

In addition, you may use the SPHERE of INCLUSION command to insist that there must be at least one atom within a given range of a Dummy atom, or the SPHERE of EXCLUSION command to insist that no atoms may lie within a given range of a Dummy atom.

Note also that the set of commands entitled "NON-BONDED" allow you to perform searches for non-bonded interactions between two fragments. This very powerful functionality is a completely new feature within the CSD System.

3.1.3.6 *MASK Sub-menu

This sub-menu, accessed from the 3D-CONSTRAIN sub-menu, allows you to specify that certain items of information, stored for each database entry, must be included in the tabulation at the end of the 3D search. For example, you may wish to correlate basic chemical class with a calculated geometrical parameter.

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