Paul Emsley wrote:
What kind of maps are produced in coot when refmac is run from within
it? Sigma-weighted 2fo-fc's ?
SigmaA, yes, Standard refmac maps: 2mFo-DFc, mFo-DFc.
Well, maybe.
The maps from refmac are sigmaa-weighted 2mFo-DFc and mFo-DFc maps only
if you are not using phased constraints. If you are, the actual
coefficients are a bit more complex than that, although they are
conceptually equivalent.
This paper described the situation for density modification in parrot,
which is the same method as used in refmac, but I have attempted to
provide a non-mathematical explanation as well.
http://journals.iucr.org/d/issues/2010/04/00/ba5136/ba5136.pdf
