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On 13 December 2011 17:59, James Holton <[log in to unmask]> wrote: > A small but potentially important correction: > > FC_ALL PHIC_ALL from REFMAC are indeed the calculated structure factor of > the coordinates+bulk_solvent, but AFTER multiplying by the likelihood > coefficient "D" (as in 2*m*Fo-D*Fc ). So, if you subtract ( FC_ALL PHIC_ALL > ) from ( FC PHIC ) you will NOT get the bulk solvent contribution alone. > AFAIK there is no way to obtain just the bulk solvent contribution from > REFMAC. James, I agree completely! But I would venture to go further and say that the FC/PHIC values really have no business being in the output MTZ file in the first place, so if they weren't there then the question of subtracting them would never arise. They are the result of intermediate calculations, the kind of things I print out when I'm debugging a program to aid in checking the logic. The FC_ALL/PHIC_ALL values represent the final definitive result of the refinement, so in all applications where Fcalc is required (e.g. density correlation stats) DFc/phi(DFc) should always be used - and why would one want to omit part of the model anyway (unless maybe for an omit map - but that doesn't seem to be relevant here)? Fc/phic is the transform of the refined atomic model parameters as output in XYZOUT which essentially is just a snapshot of the model. DFc/phi(DFc) represents the transform of an ensemble average of a distribution of models generated by the random co-ordinate (and other parameter) errors, and of course everyone knows that X-ray diffraction measures the ensemble average, not a shapshot. Also we know that (2mFo-DFc)/phic (or mFo/phic if centric) is the best estimate of the true phased F. The best estimate of the difference Ftrue-Fmodel is the difference coefficient 2(mFo-DFc)/phic (or mFo-DFc)/phic if centric). So the best estimate of Fmodel is clearly (Ftrue - (Ftrue - Fmodel))/phic = (2mFo - DFc - 2(mFo - DFc))/phic = DFc/phic (and the same result for centric). Cheers -- Ian