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.
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