[phenixbb] Unexpected Occupancy refiniement for ligands...

Edward A. Berry BerryE at upstate.edu
Sat Aug 13 09:45:32 PDT 2011

Yuri wrote:
> HETATM 6875 HC22 MLA L 3 33.760 -29.776 6.943 1.00 30.56
> C H
> Each atom is getting an individual occupancy assigned, which physically
> is impossible :)
> Any light?
> Could it be my selection syntax?

Could be- What was your selection syntax?

For waters its probably not a good idea to refine occupancy - let the B factor
take care of it unless you have really high resolution.

For larger ligands I think it makes sense to refine occupancy (for the
whole ligand as a single occupancy group) and individual isotropic ADP.
The ADP's can only spread the electrons around, cannot correct if
the integrated electron density for the ligand is less than expected.

More information about the phenixbb mailing list