[phenixbb] Ordered solvent distances

Abhinav Kumar abhinavk at slac.stanford.edu
Wed Aug 1 16:13:29 PDT 2012

Thanks Pavel.


(650) 926-2992

On 08/01/2012 12:50 PM, Pavel Afonine wrote:
> 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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