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

Murpholino Peligro murpholinox at gmail.com
Mon Jun 24 15:49:49 PDT 2019


Thank you for the clarification.

El vie., 14 de jun. de 2019 a la(s) 14:50, Pavel Afonine (pafonine at lbl.gov)
escribió:

> 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..
>
> Pavel
>
> 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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