[phenixbb] Modifications for Ca-binding site

Pavel Afonine pafonine at lbl.gov
Mon Dec 28 18:59:17 PST 2015

Hi Jacob,

this is not expected to happen (moving side chains away from their 
proper densities towards heavier blobs). Could you please send me data 
file, and two PDB files (before and after refinement) and indicate 
residues that are in trouble? In case there are ligands, please send 
ligand CIF files too (so that I can actually run refinement myself!). I 
will investigate once I have files.

Regarding residual map features around Calcium, there may be a number of 
reasons, listed here

- page 8-14 here:

- page 6 here:

Needless to say - please send files to me directly (not entire mailing 


On 12/28/15 18:44, Keller, Jacob wrote:
> I am getting a lot of problems with my calcium binding sites--there is clear density for the calciums and the protein side chains, but Phenix keeps sucking the side chains out of their density towards the calciums and also the calciums show some positive difference density, perhaps due to too-high b-factors (or potentially partial occupancy by Na?). I think what might work best is to turn off the Ca-O bond length restraints somehow, but don't see where/how to do that. I tried releasing them from geometrical restraints, but that made things worse, since things went haywire in the sidechains themselves.
> Is it possible to make Phenix ignore the Ca-O bond distance restraints?

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