Looks to me like those two waters are just close enough to push the bulk
solvent mask out of that region. Have you tried optimizing your bulk
solvent parameters? (keyword "solvent optimize" in refmac;
"optimize_mask=True" in phenix).
Also, try exporting your bulk solvent mask (MSKOUT in refmac; use
phenix.fmodel with "solvent_radius" and "shrink truncation radius" taken
from phenix.refine log), and looking to see where it begins and ends.
-James Holton
MAD Scientist
On 3/4/2020 6:04 PM, Jessica Besaw wrote:
Hello friends,
I have a "blob" of density in an active site of my protein.
I am struggling to determine if I should place a water in this spot,
if I should model it as a disordered water, if the density may be a
ligand that I have not considered, or if it should be left as
unaccounted for density. I would like to publish this structure
without compromising the science.
I have attached several possibilities that I have considered below.
Any suggestions would be appreciated.
Cheers!
Jessica Besaw
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