[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

Hi Ina,

> 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.


P.S.: http://www.phenix-online.org/pipermail/phenixbb/2009-December/003070.html

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