For phenix maps: the sum is over the entire unit cell. Ralf
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