You guessed right. Bulk solvent does not get a localized "occupancy".
It is set to "0" anywhere near modeled atoms, even if those atoms have
an occupancy of 0.01. Yes, it might seem sensible to do "occupancy" for
the bulk, but in practice it is tricky. I tried my hand at a "fuzzy"
bulk solvent mask, which can be read in by refmac. It tends to perform
better than the default masks, but is rather computationally intensive
to make. Script here:
https://github.com/bl831/fuzzymask
This is perhaps a closer approximation to what you are thinking a bulk
solvent mask should be?
You might also want to try the Babinet inverse type of bulk solvent
model. refmac supports this if you use "scale type bulk".
-James Holton
MAD Scientist
On 12/14/2023 2:40 AM, Palm, Gottfried wrote:
I can only guess that the solvent at the place of the EPE is set to 0
(instead of 0.5)
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