chem cryst
CRYSTALS manual
University of Oxford

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.


[The Crystals User Guide | Getting Started | Atoms And Peaks, Parameters, And Parameter Values. | Fourier And Patterson Functions | Generalised Fourier Sections | Regularisation | Hydrogen Placing | Refinement | Results | Conclusion ]