On Thu, Jan 17, 2013 at 3:16 AM, Pedro M. Matias <[log in to unmask]> 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
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