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On Tue, Feb 7, 2012 at 6:29 AM,
The average B-factors for the protein and solvents are: Main chain [snip] Yes, the water molecules were identified automatically by phenix.refine programme.
Okay, so the 1.6A structure with significantly fewer waters has slightly higher B-factors overall. Since many of the waters will be defined largely (entirely?) by high-resolution data, and the cutoffs used by phenix.refine are relatively conservative, it wouldn't surprise me if it's just missing a lot of weaker sites - and there probably really are fewer to find anyway. At the end of refinement I don't think you should rely on phenix.refine to find all of the waters anyway; try using the water-picking in Coot, filter out the obviously wrong ones, and refine a final time without solvent update. (This applies to the other datasets as well, at least the two at 1.6A - it wouldn't surprise me if there are more waters to be found.) For the obsessive-compulsive or just curious, there is now a standalone tool in the nightly builds for looking at difference maps: mmtbx.find_peaks_holes model.pdb data.mtz write_pdb=True This is basically recycled from phenix.refine but since the idea wasn't to add waters, but to make it possible to cycle through the map peaks in Coot, it's slightly more aggressive and thorough. (The novel features are incorporation of the anomalous difference map if available, and identification of "waters" with suspicious mFo-DFc peaks.) We'll probably merge this with phenix.refine at some point. -Nat