[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
Fri Mar 20 17:12:04 PDT 2009
> 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
sqrt(sum((value-mean)**2) / n)
The mean of our maps is usually zero, as we don't usually include F000.
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