[phenixbb] View Solvent Mask

[Flath, Ben]

It seems I am looking for the the compute_box option in polder maps.

Ben



Sent from my Android


-------- Original message --------
From: "Flath, Ben" <bef206 at mail.usask.ca>
Date: 2018-03-09 11:15 AM (GMT-06:00)
To: Pavel Afonine <pafonine at lbl.gov>, "Flath, Ben" <bef206 at mail.usask.ca>, phenixbb at phenix-online.org
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 <pafonine at lbl.gov>
Date: 2018-03-09 10:50 AM (GMT-06:00)
To: "Flath, Ben" <bef206 at mail.usask.ca>, phenixbb at phenix-online.org
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


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