On Thu, Jan 17, 2013 at 8:27 AM, Pedro M. Matias <mat...@itqb.unl.pt> wrote: > Excuse me if I'm wrong but should't the correlation coefficient between Fo > and Fc (which is what the Density Fit analysis is looking at) be independent > of this issue, provided Fo and Fc are on the same scale ? And since the map > is calculated from weighted 2Fo-Fc amplitudes and phases the scaling problem > should not occur.
Cross-posting again (sorry, I use different accounts for mailing lists and Phenix stuff): """I think it will be dependent on having F(obs) already on an approximately absolute scale. This can be accomplished by scaling them during conversion from intensities, based on the Wilson plot (I think). I should note that while the CCP4 conversion tools usually take care of this, if you supply Phenix with intensities it will simply take the square root (the French-Wilson correction doesn't affect the overall scale). It would probably be useful to do the same thing in our code; I think it's pretty straightforward but I'm not sure about the math. My guess would be that some of the MTZ files you used were either a) already on an absolute scale, or b) accidentally ended up being approximately correct. However, if you're willing to send me the inputs and outputs for Phenix and Refmac for the structures you've had a problem with, I can confirm my guesses.""" Note that what happens internally in Phenix is actually that Fc is scaled to Fo, not the other way around! (No, I don't know why this is done; ask Pavel.) So the Fc values from Coot are on a different scale. -Nat
