[phenixbb] refinement with alternative molecules?

Su-Chang Lin sul2005 at med.cornell.edu
Thu Jan 28 01:15:44 PST 2010

Hi Ralf, 
   I've done the refinement with alt. conf..  The occupancy is 0.58 for Mol A, 0.42 for Mol B.
The maps look OK. R-factors drops a little bit.

Before when I put Mol A in that region for refinement, I saw additional densities (a helix) for Mol B.
When I put Mol B in the region for refinement, I saw additional densities (loops) for Mol A.
Now with alt. conf. there are no additional densities.

Can I use the occupancies for publication? Or do I need to do/check something else?


> Hi Su-Chang,
> > I will try to refine the structure without NCS restraints.
> I'd be interested to know how it goes, although I'm too busy to get
> into the NCS code right now.
> If the resolution is low I'd think it is better to use NCS, without
> alt. conf. The mismatches you saw between related molcules may
> be pure artifacts. But trying is better than guessing!
> Ralf
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