Dear Ed and Pavel, Some background, 1.5A, 0.14/0.16, P 63 2 2. 1- I figured out the occupancy problems. I had to define the ligands as group occupancy rather than individual atoms...(duh!!...) It looks better now. 2- Is there any case/resolution when one should try anisotropic refinement for a ligand? I would think if its covalently attached maybe... 3- About the waters occupancies/B-factors I definetely see some density peaks that correspond to waters (good distance and angles for H-bond interactions with protein backbone on the surface) Obviously they are weaker than peaks for waters that are ordered near the active site. I modelled those in and I got some negative peaks in the mFo-DFc map after isoptropic B refinement. That is what led me to think I should try occupancy refinement. 4-Still on the same topic B-factors, I am also encountering the same problem with surface side chains especially (D, E, Q). I am confident they should be where they are. backbone density looks great. But no matter where I put their side chains, I get negative peaks in the diff. map. Their B-factors usually refine to ~55 vs ~25 for ordered side chains. Yuri On Sat, 13 Aug 2011 12:45:32 -0400, Edward A. Berry wrote:
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.
-- Yuri Pompeu