Hi Ben,

For what purpose do you want to prevent the bulk solvent mask of entering pockets?
For omit maps, use polder maps. If the ligand is placed, use the default option. If nothing is placed yet, you can use the box option (https://www.phenix-online.org/documentation/reference/polder_box.html) or place a dummy ligand in the area.  

Best wishes,

Dorothee

On Fri, Mar 9, 2018 at 10:11 AM, Pavel Afonine <pafonine@lbl.gov> wrote:

How can I modify the mask so it doesn't enter pockets within my model?

 This is what polder map is for: stop solvent entering the region in question.

Pavel

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