[phenixbb] Refinement of a complex with a symmetric inhibitor lying on the axis of symmetry
Ralf W. Grosse-Kunstleve
rwgk at yahoo.com
Wed Dec 1 08:44:01 PST 2010
> I try to refine a crystal structure of a protein - inhibitor complex. The
> protein is a homodimer and the two molecules have a crystallographic
> symmetry. The space group is P6122. The symmetric inhibitor binds
> symmetrically to the protein so that I refine the half of it. The core of the
>inhibitor is a five-membered ring with a nitrogen lying directly on the axis of
>symmetry. I achieved to refine this by setting the occupancy to 1.0.
> And now, here is my problem:
> Two C atoms of this ring system are bound across the symmetry axis - how could
>I include this in the refinement? Is there any possibility to generate
>restraints to the other part of the inhibitor (of the symmetry equivalent)??
It is possible but cumbersome. With a reasonably recent version of phenix
(dev-268 or later) it is much simpler to have the entire inhibitor in the pdb
file, with occupancy 0.5. All the rest is taken care of automatically.
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