[phenixbb] phenix.refine special positions
folmerf at gmail.com
Thu Aug 13 11:23:20 PDT 2009
2009/8/13 Simon Kolstoe <s.kolstoe at ucl.ac.uk>:
> Dear Pavel et al.
> Is there any way of defining a residue for rigid body refinement if a
> couple of the atoms are sitting on a symmetry axis? i.e. can I define
> the rigid body to be chain L but not the atoms that are giving the
> problems? I keep on getting the error:
> ================== Extract refinement strategy and selections
> Some atoms selected for rigid body refinement are in special positions
> below). Please remove these atoms from the rigid body selection and
> refinement again.
> "ATOM 4 C4 A12 L 2 .*. C "
> Atoms at special positions are within rigid groups.
I think you can define this with the refine.sites.rigid_body scope.
phenix.refine data.mtz model.pdb strategy=rigid_body
refine.sites.rigid_body="chain L and not resid 12"
What I do not know, however is if this will accomplish what you want.
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