It seems I am looking for the the compute_box option in polder maps. Ben Sent from my Android -------- Original message -------- From: "Flath, Ben" Date: 2018-03-09 11:15 AM (GMT-06:00) To: Pavel Afonine , "Flath, Ben" , [email protected] Subject: Re: [phenixbb] View Solvent Mask 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