Hi Frank, I just want to add to Ralf's very comprehensive reply... The parameters solvent_radius, shrink_truncation_radius and grid_step_factor are explained in the original paper: Jiang, J.-S. & Brünger, A. T. (1994). J. Mol. Biol. 243, 100-115. "Protein hydration observed by X-ray diffraction. Solvation properties of penicillopepsin and neuraminidase crystal structures." The details of PHENIX implementation of this are described here: P.V. Afonine, R.W. Grosse-Kunstleve & P.D. Adams. Acta Cryst. (2005). D61, 850-855. "A robust bulk-solvent correction and anisotropic scaling procedure" Also, the negative peaks you observe can easily be Fourier series truncation ripples. I think Ralf's suggestion to place some dummy atoms there with zero occupancy is a good idea. I wouldn't even do any refinement (since moving atoms may cancel these artifacts), but just compute two maps - with and w/o the dummy atoms and see what happens to these negative peaks. Cheers, Pavel. On 9/28/2008 3:25 PM, Frank von Delft wrote:
Hi
After being through phenix.refine, I see in my hydrophobic core a big space (a few atoms wide) that is filled with strong negative difference density. I suspect the culprit is the bulk solvent mask, which is defined too tightly.
The online manual mentions three parameters, but not what they do. solvent_radius, shrink_truncation_radius, grid_step_factor
What *exactly* do they do?
(I thought I'd elicit a contribution for the online docs this way :) Cheers phx _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb