On 6/27/11 10:43 AM, Pavel Afonine wrote:
In this case one of the waters needs to be shifted towards green density, and you need to add another water to empty blob (I don't know why phenix.refine did not add it automatically - I will investigate once I get a chance).
Dear Pavel, This has been my experience with Na sites as well. Phenix.refine water-update would always move/delete my waters out of coordination spheres (so I would turn off solvent updates, and strictly restrain these waters). I always assumed that since Mg and Na coordinate water with very short distances (2-2.4 Angstroms) compared to water to N and O atoms, they were disliked by solvent updates. Since I have not looked at the code (and haven't used the recent versions for Mg/Na containing structures), I cannot confirm this, but does solvent-update assume waters should be within 2.3-3.5 A? If that is the case, that may kill some true water sites. Cheer, Engin -- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111