I have experienced the same issue with 0.9.5 for Mac.
Most strikingly, this seems to occur randomly: some waters are refined
as usual but other are shifted dozens of Å to stick to a carbon of the
model.
A similar effect is observed when refining solvents with the "x" key.
On 1/6/21 21:45, David M Dranow wrote:
Hi All,
Does anyone have a decent set of refinement parameters for Coot 0.9.5 in linux? My
colleagues and I find that using the "r" shortcut causes most waters to fly off
and center on carbons, sometimes as far away as 45 Å! I've tried to change the overall
weight and Lennard-Jones epsilon, and Geman-McClure alpha and I find no combination that
keeps all waters within the density that they already are in. I'd be happy to provide a
model and map to demonstrate this phenomenon. Our current work-around is to use R, but
this is not ideal. If anyone has any idea how to fix this, we would greatly appreciate
any advice.
Thank you!
-David
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