Thanks Guys, would it be possible to implement the H-bonding criteria? From my experience with CNS it worked quite nicely. Right now I end up with ~350 waters in a 2.3 A structure of a 30kDa protein, which is a bit much. -----Original Message----- From: [email protected] [mailto:[email protected]] Sent: Monday, March 19, 2007 1:02 PM To: PHENIX user mailing list Subject: Re: [phenixbb] More stringent water picking 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 _____ _______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb http://www.phenix-online.org/mailman/listinfo/phenixbb