[phenixbb] Unmasking cavities

Pavel Afonine PAfonine at lbl.gov
Fri Oct 3 18:17:32 PDT 2008

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 

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.


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
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