Hi Dale,

this was one of my suspicions... Since Coot computes maps dynamically in a box around the point you click on, I was thinking that it normalizes the map in that box and not in whole unit cell, therefore the difference. I don't know, just a guess. It would be helpful if Paul E. could comment on this...

Pavel.


On 3/21/09 8:11 PM, Ralf W. Grosse-Kunstleve wrote: 
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
      
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