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? 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. 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. 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? Cheers Clemens -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
