Hi Everyone, I think it would be sensible to change: - ordered_solvent.max_solv_macromol_dist to something smaller like 3.5A (i.e. only look in the first hydration shell). - ordered_solvent.secondary_map_cutoff to 1.5 sigma The CNS h-bond criteria might help, although it I would prefer something more sophisticated be done as part of a mechanism to distinguish water from ions. Cheers, Paul Pavel Afonine wrote:
Hi Carsten,
thanks for your question!
The main water picking criteria in phenix.refine are: 1) Fo-Fc map; 2) 2Fo-Fc map; 3) macromolecule - water distance; 4) water-water distance; 5) B-factors and occupancies max/min values; plus some more of expert level ...
There is no specific H-bonding criteria implemented. You can play with sigma cutoff for both maps and with the distances above. In most of the cases it the reasonable behavior.
I would be interested in Paul's (Adams) comments about his experience of usefulness of H-bonding criteria in CNS.
Thanks! Pavel.
Schubert, Carsten [PRDUS] wrote:
Hi,
is it possible to increase the stringency criteria for picked waters, besides increasing the sigma level? E.G. something on the order of the H-bonding criterion found in CNS? I find that the automated water-picking routine gives me quite a few waters, which are not necessarily justified by visual inspection of the maps.
Thanks
Carsten
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