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[ccp4bb]: refining two conformations related by crystallographic symmetry
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We have a heme molecule with its quasi-2-fold axis on a crystallographic
2-fold axis; i.e. we have a half heme in the asymmetric unit which is
complemented by a half heme in another asu. Apparently the heme is an equal
mixture of molecules in two orientations related by the 2-fold axis.
We would like to refine positionally, but get bad nonbonded interaction
with symmetry related atoms. Is there a refinement program which ignores
clashes when occupancy is 0.5, or can be made to do so?
An alternative is to use a lower symmetry spacegroup in which the 2-fold
becomes local, and refine two alternate positions of the heme. Then return
to true symmetry, fix the heme atoms, and refine only the protein. In this
case what should we do to avoid corrupting the R-free set when we expand
the data to lower symmetry and return to true symmetry?