Hi Emily, It could be a scaling issue. Coot has a parameter under Extensions...Refine...Set Density Fit Graph Weight... Making this value smaller will make the bars shorter and greener. So if the two maps (or coefficients) are on different scales, you will need different values of the Set Density Fit Graph Weight to make the two sets look similar.
Jack On Feb 20, 2015, at 9:11 AM, Emilia C. Arturo (Emily) wrote: Thank you for the multiple kind off-list responses I received regarding how to interpret map colors in Coot. I'm very grateful for the references, but it seems that I did not state my issue clearly :-) What I was referring to was the tool that Coot has under Validate > Density Fit analysis. The tool outputs graphs like the ones I'm pasting below. Both sets of graphs were generated from the same pdb file, but the very-red bar graphs were calculated using the map coefficients phenix had generated along with this model, while the mostly green bar graphs pasted separately below, showing bars for the same stretch of residues in each chain, were generated using the feature enhanced map that phenix generated from this same model.<Screen Shot 2015-02-20 at 9.56.22 AM.png><Screen Shot 2015-02-20 at 9.56.49 AM.png> How do I interpret the fact that the FEM and 2Fo-Fc maps give such different fits for the same model using this type of analysis? ...or are the fits really that different (and maybe green versus red is not as big as the visual cue would have me assume)? Emily. On Thu, Feb 19, 2015 at 11:00 AM, Emilia C. Arturo (Emily) <ec...@drexel.edu<mailto:ec...@drexel.edu>> wrote: Hello all. 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://www.mail-archive.com/coot@jiscmail.ac.uk/msg02995.html)<https://www.mail-archive.com/coot@jiscmail.ac.uk/msg02995.html)--but> --but it doesn't seem the issue was resolved then (i.e. what does 'red' really mean? is it ...bad?). 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. So these are my questions: What are the units of the density fit values? i.e. What is the calculation that's done? 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; both maps came from the same model. In fact, I got worried, but then I realized that I don't actually understand the red-ness and green-ness. I'm quite new to the business of crystallography so any input is welcome regarding the use of FEMs and density fit analyses. Emily. Ph.D. program in Biochemistry, Drexel Univ. College of Medicine Jaffe lab, Fox Chase Cancer Center Philadelphia, PA
