Now the important question How can I modify the mask so it doesn't enter pockets within my model? Add HOH with occupancy set to zero and ignore_zero_occupancy_atoms=False? Or is running polder maps more effective? Thanks again Ben Sent from my Android -------- Original message -------- From: Pavel Afonine Date: 2018-03-09 10:50 AM (GMT-06:00) To: "Flath, Ben" , [email protected] Subject: Re: [phenixbb] View Solvent Mask Hi Ben, I was watching the YouTube tutorial on Polder Maps and noticed that the bulk solvent mask was visualized in coot. How can I visualize my bulk solvent mask? phenix.mask model.pdb will calculate the mask. Pavel

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 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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