Volume 2 Chapter 3 3D-Constrain Sub-menu OVERLAP

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PERMUTE is used to force the program to calculate geometric and other PARAMETER's for all permutational isomers (topological equivalents) of the fragment.


The PERMUTE button can be toggled ON and OFF. PERMUTE operates when it is highlighted (but see applications and warning below).


Many small fragments have topological (atomic permutational) symmetry in 2D, i.e. it is impossible to assign a unique set of numbers to the atoms of the fragment. In order to carry out certain numerical analyses (e.g. Principal Component Analysis in VISTA), it is advisable to include geometrical data (particularly torsion angles) derived from all possible enumerations of the atoms of the 3D fragment.

The application (or not) of permutational symmetry in structure correlations and conformational analyses is a complex topic. The subject is well covered in the literature and will not be further described here. Note clearly that PERMUTE will generate geometrical parameters for all possible mappings of the 2D fragment onto the 3D structure. To include enantiomorphic 3D structures as well, the ENANT button must also be used.


For many apparently simple fragments, the PERMUTE button can generate a very large number of permutational isomers and, hence, an explosion of information in the TAB and SUM files. Cyclohexane has 12 permutational isomers, and triphenylphosphine has 48, both before the doubling caused when enantiomorphic structures are considered.


J.D.Dunitz & H.-B.Buergi, Chapter on "Symmetry Aspects of Structure Correlation", in Structure Correlation (Eds. H.-B.Buergi & J.D.Dunitz) VCH Publishers, Weinheim, Germany, 1994. Contains many leading references.

F.H.Allen, M.J.Doyle & R.Taylor, Acta Cryst., B47, 29-40, 1991, and F.H.Allen & R.Taylor, Acta Cryst., B47, 404-412, 1991, describe the cyclohexane example in some detail.

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