Crystals User Guide

Chapter 6: Regularisation

6.1: EXAMPLE 1

As explained above (Part 4), Fourier techniques provide a powerful way for initiating the refinement of a structure. When the geometry of fragments are well known from previous analyses, for example phenyl groups, the initial refinement can be speeded even futher by forcing the observed fragment to adopt an idealised geometry. This process, common in protein crystallography, is known as regularisation, and can be used not only to tidy up a poor geometry, but also to postulate sites for missing atoms.

Regularising a cyclopentadienyl ring. The idealised coordinates are from the literature.

 \REGULARISE REPLACE
 GROUP 5
 OLD C(1) C(2) C(3) C(4) C(5)
 ATOM 0 0 0
 ATOM .846  1.165 0
 ATOM .846 -1.165 0
 ATOM 2.216  0.72 0
 ATOM 2.216 -0.72 0

Completing and regularising a phenyl ring. C(3) is very poorly placed, and so will first be deleted, and C(6) has not been found at all. New atoms will be generated for them.

 \EDIT
 DELETE C(3)
 \REGULARISE REPLACE
 OLD C(1) C(2) C(3) C(4) C(5) C(6)
 PHENYL
 END

p BE SURE THAT THE GIVEN ATOMS ARE ALL IN THE SAME MOLECULAR FRAGMENT, OTHERWISE YOU WILL NEED TO GIVE SYMMETRY OPERATORS.