[phenixbb] Ordered solvent distances
pafonine at lbl.gov
Wed Aug 1 12:50:48 PDT 2012
> The default minimum distance that a water gets placed near
> protein/water atoms using 'ordered_solvent=true' option in
> phenix.refine is 1.8.
> Isn't this too close?
Possibly. Though we pick waters into Fourier maps (which are different
from exact electron density distribution due to finite number of Fourier
coefficients = finite resolution) so the peaks may be shifted. The
smaller threshold distance is meant to account for this. As a side
effect it increases the risk of interpreting bad pick. How big this risk
(given all other peak selection criteria) - that I don't know: can take
a few days to investigate.
Also, it's a parameter - you can change it to match your taste.
> Also, if two waters can't get placed in the density due to distance
> criterion, can phenix place one water in dual conformations in that
Currently not, but would be good to have, I agree.
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