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 

-------- Original message --------

From: Pavel Afonine <[email protected]>

Date: 2018-03-09 10:50 AM (GMT-06:00)

To: "Flath, Ben" <[email protected]>, [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