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Re: [ccp4bb]: refining two conformations related by crystallographic symmetry



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Edward Berry wrote:
> 
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> 
> Dear CCP4'ers,
> 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?


 You can set the occupancies of the 2 hemes to 0.5 then refine both -
geometry should stay OK.
> 
> 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?


 Generate FreeRfalgs for true asymm unit, then use CAD to expand
everything
Cad hklin1 true.mtz hklout extended.mtz
outlim spacegroup lower_symm
labi file 1 allin
end
> 
> Thanks,
> Ed
> --

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Eleanor J.Dodson, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 42 44 49, work:  +44 (1904) 43 25 65
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