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 liga
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 solve
Dear Gottfried
Assuming your modelling is correct you can always try occupancy refinement of
your ligand (or simply test alternative values). Maybe that will help.
You can also play with bulk solvent mask parameters. Keywords (both occupancy
and mask parameters) can be found in
https://www2.mrc-
Dear all,
I have a modelling problem, which probably has something to do with
the solvent mask.
There is a positive density blob at the surface of my protein, which I
can more or less satisfy with a Hepe (EPE). Hepes is in the buffer,
the sulfonic acid H-bonds to a lysine side chain and a
Dear all,
I have a modelling problem, which probably has something to do with
the solvent mask.
There is a positive density blob at the surface of my protein, which I
can more or less satisfy with a Hepe (EPE). Hepes is in the buffer,
the sulfonic acid H-bonds to a lysine side chain and a mai
