On Thu, Jan 17, 2013 at 8:10 AM, Phil Evans <p...@mrc-lmb.cam.ac.uk> wrote: > 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
I completely agree with this, although I still think the density fit graphs in Coot should work independently of scale. The main objection I've heard to attempting to put maps on an absolute scale is that it would (inaccurately) imply that the values really are accurate electron levels, which they are not, for the reasons I already mentioned. (The phrase "letting the perfect be the enemy of the good" comes to mind here...) Unfortunately this is not something I personally can fix, but I will bring it up at group meeting. (I should add that my hypothesis is only a guess, and I haven't actually tested it yet - however, it is consistent with the facts presented. I would need to look at the Coot source code to be sure, but I'm hoping Paul/Kevin/Bernhard will comment.) -Nat
