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michael nelson wrote: > Hi,all: > I want to tidy up waters to finish a structure and I have a few > concerns so far. > How do I decide if a peak correspond to a water, not something else, > like an ion such as Mg2+? Mg++ itself has 10 electrons, like water, but in solution it forms a hydrated complex. Mg sometimes will bind to an oxygen functional group, and the distance should be about 2.1 Å. There should be six ligands in total; usually five or more are waters. Waters should be around 2.8 Å from their H-bonding partners and again about 2.1 Å from the Mg++. If you don't have ca. 2.0 Å data, you won't resolve the octahedrally coordinated ligands for Mg++, so it gets a bit harder. A spherical blob centered ca. 4.5 Å might be a hydrated Mg++. > How do I decide if a water is decent enough to be kept?Any hard > criteria in this case?Forming hydrogen bonds is definitely one, any > other? Coot implements two different, and complementary water tests, and this greatly facilitates culling the fictional ones out. But manual inspection is imperative, so that you keep only (a) those that are chemically reasonable and (b) have non-embarrasing density in a 2Fo-Fc map. > Sometimes, I'll have big unmodelled bulbs, which is too big to be > waters but they're not like any precipitant or ligand that might be > present in the solutions?How do I model these bulbs? With caution. You could try putting in a model of your buffer if the case is compelling, but unmodelled blobs are less problematic to your audience than guesses. > Many thanks! > Mike > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com
