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On 21/01/13 14:21, Clemens Vonrhein wrote: > Dear all, > > On Thu, Jan 17, 2013 at 07:48:34AM -0800, Nat Echols wrote: >> If I had to guess, I'd say that the output from Refmac is on an >> approximately absolute scale, i.e. the volume-scaled density values >> resemble the actual electron densities expected for the model. (I say >> "approximately" because the absence of F(0,0,0) and various FFT >> artifacts pretty much guarantee that the values are not actually >> accurate, just on the same order of magnitude.) This is presumably >> done by scaling F(obs) to F(calc). Maps from Phenix are definitely >> *not* on an absolute scale, however, and I guess the same must be true >> for BUSTER. > Just for the record: the map-coefficients written by BUSTER > (amplitudes 2FOFCWT and FOFCWT in the final 'refine.mtz' file) are on > the same scale as the model (amplitude FC) ie. on approximate absolute > scale. > > As far as we can tell, Coot uses the actual map-values (e/A^3) as a > 'score' in those 'density fit' graphs - is that right? Yes - for the moment at least. If I can make it fast enough, it will not be the case for 0.8. > So it is not > something with a known range (like a real-space correlation value from > -1 to +1) - especially not if the maps are sometimes on roughly > absolute scale and sometimes they aren't. Yes. > > It seems as if the determination of apropriate range for drawing those > bars within coot is affecting if one sees only red (false negative) or > only green (false positive) bars. Yes. > > Maybe Paul/Kevin/Bernhard can comment on how this is done? How does > one avoid getting frustrated by too many red bars and (equally > important) over-excited by bogus greenery? > No good answer at the moment. The graph is only relative :-( I can only refer you to Bernhard's answer (above). Paul.