[phenixbb] real_space_correlation

[Pavel Afonine]

Hi Jianghai,

when you run

     phenix.real_space_correlation m.pdb d.mtz

it will calculate and output map correlation coefficients (map CC) 
between two maps: map_1=Fmodel map and map_2=2mFo-DFmodel, where Fmodel 
= k_total * (Fcalc + Fbulk), and 2mFo-DFmodel is what's called sigmaa 
map. These maps are calculated using the model from input PDB file, and 
reflection data (Fobs or Iobs) and R-free-flags from input reflection file.

You can define map_1 and map_2.

Depending on data resolution, the map CC will be reported per individual 
atom or per entire residue.

Pavel

On 2/27/13 1:17 PM, Jianghai Zhu wrote:
> Hi All,
>
> I was trying to use "phenix.real_space_correlation *.pdb resolve_composite_map.mtz" to get some real space cc for my ligand against the SA composite omit map.  But I am not sure that the map used here was the SA composite omit map.  Will phenix use the omit map I provided or will it just simply calculate a sigmaA weighted 2Fo-Fc map based on the pdb?
>
> Thanks.
>
> --Jianghai
>
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