Thank you all for your input.
On Wednesday, May 30, 2012, Paul Emsley <[email protected]> wrote: > 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. > -- Dayana Nisbar
