Hi Gottfried, I was wondering what happens if you make a Polder omit map for
the HEPES? I am also curious, if the extra positive density is for missing bulk
solvent with ligand of occupany 0.5, do you observe the density with ligand
present at 0.5 occupancy to be more diffuse than with no ligand present? If we
take the example of amino acid side chains modeled with dual conformations,
generally an abundance of extra positive density is not observed due to
side-chains having partial occupancy and missing bulk solvent.
Regards,
John
On Thursday, December 14, 2023 at 01:55:20 PM CST, James Holton
<jmhol...@lbl.gov> wrote:
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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