[phenixbb] Question about scale of ED maps from phenix vs map coeffs when displayed in COOT
Ralf W. Grosse-Kunstleve
rwgk at cci.lbl.gov
Sat Mar 21 20:11:53 PDT 2009
For phenix maps: the sum is over the entire unit cell.
> Is the sum over the asymmetric unit or the portion of space that
> happened to be covered by the map? The result of this calculation
> depends greatly on the amount of solvent region that is included in
> the sum.
> Dale Tronrud
> Ralf W. Grosse-Kunstleve wrote:
> >> That was (and is) always a mystery for me: when I look at two maps (both
> >> coming from phenix.refine):
> >> - one is computed in COOT from phenix.refine map coefficients, and
> >> - another one displayed in PyMol using X-plor formatted map.
> >> To make both maps looking identical I have to draw them at different
> >> sigma levels, sometime very different. This is true for both fo-fc and
> >> 2fo-fc maps.
> >> I have some ideas but no any proofs so I don't want to put my
> >> speculations to the bb. So, I have no answer... May be Ralf or Paul E...?
> > Our "sigmas scaled maps" are simply divided by the "biased standard
> > deviation":
> > sqrt(sum((value-mean)**2) / n)
> > The mean of our maps is usually zero, as we don't usually include F000.
> > Ralf
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