Re: [phenixbb] Question about scale of ED maps from phenix vs map coeffs when displayed in COOT

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