Volume 2 Chapter 3 3D-Constrain Sub-menu ATOM-LABEL

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ATOM-RADIUS

Function

ATOM-RADIUS is used to define any atom in the fragment so that its covalent radius is saved in the parameter table. The CSD covalent radii are listed in Volume 4, Appendix 1 of the main documentation set, Volume 3, Appendix 10, and in Appendix E of the "Getting Started" Manual.

CSD covalent radii assignments are updated from time to time in the light of new structures. Hence minor discrepancies between tabulated values and the printed lists can occur.

Graphics QUEST3D Procedure

The mode of operation is identical to that for ATOM-LABEL

The default parameter name for ATOM-RADIUS is RADn, where n is the atom number in the fragment.

Applications

The ability to manipulate covalent radii together with interatomic distances (through the TRANSFORM functions) is useful in certain research applications. It permits interatomic distances to be normalised with respect to sums of covalent radii. For two atoms i,j having covalent radii Ri, Rj and interatomic distance Dij, the normalised distance Dnorm is:

Dnorm = Dij - [Ri+Rj]

If we have the simple fragment:

TR N

and we are interested in comparing the TR-N distance across the full range of elements contained within the TR definition, then Dnorm may be a useful method of quantifying this comparison. The (different) sums of covalent radii for each instance provide the yardstick for the comparison.

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Volume 2 Chapter 3 3D-Constrain Sub-menu *CREMER.