[phenixbb] Unmasking cavities

[Frank von Delft]

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