[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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