[phenixbb] Why the correlation coefficient of the electron density with the model is never 1?

Pavel Afonine pafonine at lbl.gov
Fri Jun 14 12:50:24 PDT 2019

Hi Murpholino,

reasons are similar to why crystallographic R factor never goes to zero.

Model-map CC is calculated between the map (the data, in case of cryo 
EM, or sort of data in case of Crystallography) and a model. As you know 
data always has errors and model is just an approximation to reality. So 
you have no chance to match them perfectly, unless overfit. Something 
along these lines..


On 6/14/19 12:42, Murpholino Peligro wrote:
> The links below show a plot of the results of 
> phenix.real_space_correlation* for a nice lisozyme crystal and also 
> the coot view.
> https://drive.google.com/open?id=0B9tqXyDsq9YIdkRhcVFXU2dEdnhINXR6Y3hza2Y5NGpNM1hV
> https://drive.google.com/open?id=0B9tqXyDsq9YIREd1OFZhNGZtRnN4aldtVU1mdk84NExVX2Vn
> As you can see the electron density fits very well the model.
> Why not a single residue gets a perfect correlation coefficient? (i.e. 1)
> Just curious.
> Thanks
> * phenix.real_space_correlation pdbfile mtzfile --detail="residue" > outpu
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