Hi Abhinav,

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 
density?

Currently not, but would be good to have, I agree.

Pavel

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