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On 19/02/15 11:00, Emilia C. Arturo (Emily) wrote: > Hello all. Hello Emilia (Emily), > I'd like to understand what it is I'm looking at when I use Coot's > density fit analysis tool. I recognize that there was a post related > to this topic on the Coot bb a while ago --the discussion was on how > to interpret the red-ness or green-ness of the density fit plot > (https:[log in to unmask]) > <https:[log in to unmask]> --but > it doesn't seem the issue was resolved then (i.e. what does 'red' > really mean? is it ...bad?). I failed to fix this for 0.8.1 I will add it to the list now for 0.8.2. The colours were set for "typical" (~2.1A on the absolute scale). > Now I have more to ask that involves my using phenix-generated FEMs to > build in Coot. > > So what I've done is the following: I adjust my model in Coot, using a > phenix-generated FEM as the map for fitting, then refine with phenix, > and using the refined pdb and reflections file, I use phenix to > generate a new FEM. Then I repeat. At some point I learned about > Coot's density fit analysis tool and took a look at how my model fits. > If the map that is selected in the sidebar of Coot is a FEM, then the > density fit analysis plot looks mostly green everywhere - fine. If, > however, I select as my map in the Coot sidebar the 2Fo-Fc that phenix > had generated along with the latest refined model--the one I'm > examining with the density fit analysis tool--then Coot's density fit > analysis plot looks red (with values ~ < 0.3), with splashes of > orange, barely any green or yellow (with values ~ > 0.3), almost > everywhere. :-( yes - this doesn't work for FEM maps. > > So these are my questions: What are the units of the density fit values? electrons/A^3 with volume normalization. I think FEM maps are normalized (so that the mean is 0 and standard deviation is 1.0) and this is not typical for maps generated from structure factors on the absolute scale - where you'd expect density values smaller than this by a factor of 2 or 3 (or so)). So the density values from FEM maps are higher and the validation graph greener. > i.e. What is the calculation that's done? The map is sampled at the atoms and weighted by occupancy. > I'm surprised that the FEM-dependent density fit graphs look so > different (i.e. so green) relative to the graphs generated if my map > is set to the 2Fo-Fc from the loaded model; I know less about FEM maps than I should, but I can refer you to Section 7.9.1 of the documentation: https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#Validation-Graphs After you've rescaled, I'd be interested in your reflections of the differences. Regards, Paul.