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On 29/05/12 19:49, Dayana Nisbar wrote: > I need help with finding water in my protein structure using Coot. > > I tried to find water with peaks above 1.6 sigma for both the 2Fo-Fc and mFo-DFc maps. > > The result were 253 water molecules found for 2Fo-Fc map and 563 water molecules found for mFo-DFc map. > > My question is.... > > 1) Why is it the number of water molecules are different? Because the map you are searching are different. The peaks have different positions, shape and distance to protein atoms. > 2) Which map should we use to correctly place the water molecules? I prefer the 2Fo-Fc style map. You could create a weighted average of these maps if you wish. > 3) What is the sigma cut-off for finding water? How "deep" do you want to delve into you map? There is a lot of shape at 0.1 rmsd - do you want to model that? (Most people do not). Most people are happy to model density features around 1 rmsd for 2FoFc-style map and around 3 rmsd for the difference map. (Not to say, of course, that 1 rmsd has much meaning for 2FoFc-style map, but as a rule of thumb, it is not bad at about 1.8-2.2A and solvent content 55+/-7% in my experience). > 4) How can I validate these water molecules? > Other than the water validation built into Coot of course, you could also try Whatcheck. HTH, Paul.