What's the difference between a dummy water and a real one?
Paul
On 22/11/2021 14:34, Schreuder, Herman /DE wrote:
Dear Paul,
I agree with Oliver and Norbert, in the early phases of refinement,
when a lot of rebuilding has to be done, the coot RSR is not very
helpful and in general I leave it to buster do refine the rebuilt
regions. Knowing now that (dummy) waters may be the culprit, I will
remove them. However, it would be much more convenient if the
repulsions with water molecules would not be taken into account.
Thank you,
Herman
*Von:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *Im Auftrag von
*Norbert Straeter
*Gesendet:* Sonntag, 21. November 2021 12:24
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* Re: [ccp4bb] COOT RSR
Dear Paul,
I agree to Oliver. In situations where you want to fit a "dummy water"
to a difference density peak (to determine distances to the
environment) or try the fit of solvent molecules to yet unexplained
density, it would be nice to first obtain an optimal fit and next
think about the environment and possible bumps and partial occupancy.
I had this problem already several times, that I could not get a good
fit because of the model repulsions. Even if two partially occupied
waters are at closed distance the repulsions appear to be active in
RSR. It is not about the old method being better.
Best wishes,
Norbert
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