(hesitating to restart an old flame war) There has been a long-standing argument about scaling of electron density maps, with many people deprecating "sigma-scaling", for two reasons
1) in 2Fo-Fc type maps, "sigma" = RMS density is a function among other things of the solvent content (smaller with high solvent content) 2) in difference maps Fo-Fc type, as the model improves, sigma gets smaller (ideally = 0). Sigma contouring is useful to pick out the largest features though. Scaling even approximately to e/A^3 (i.e. scaling Fobs to Fcalc) is consistent across solvent content and model quality, though still affected by resolution and other things, and generally should be preferred in my opinion. Sharpening map coefficients may also affect the scale Phil On 17 Jan 2013, at 15:48, Nat Echols <[email protected]> wrote: > On Thu, Jan 17, 2013 at 3:16 AM, Pedro M. Matias <[email protected]> wrote: >> To clarify my previous e-mail, in both cases the maps are being calculated >> from weighted coefficients from an MTZ file output by the program. >> I tried calculating a weighted 2Fo-Fc map in CCP4i using the PHENIX MTZ file >> and the end-result (red bars) was the same. > > 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. Since everyone is used to looking at sigma-scaled maps > this has not been a problem in the past; I don't think older versions > of Coot had this problem either. > > You are not the first person to complain about this, for what it's worth. > > -Nat
