[phenixbb] Filtering ordered solvent molecules based on secondary map

Pavel Afonine pafonine at lbl.gov
Tue Jan 4 14:50:20 PST 2011

>           So the default value for the poor_map_value_threshold is 1, 
> which I assume is 1 sigma.  So if the electron density for a putative 
> water is less than 1 sigma in the 2mFo-DFc map OR if the calculated 
> correlation coefficient is less than the poor_cc_threshold value 
> (default 0.7), then the water is removed, right?


>                 For my own education, what would be the best way of 
> calculating the correlation coefficient values for all the waters or 
> ligands in a given model?  What I want to do is get a sense for the 
> relationship between electron density and correlation coefficient 
> values for waters in my structure to understand how "strict" the 
> default poor_cc_threshold value is and whether/how much I might want 
> to raise it.

You can use

phenix.model_vs_data model.pdb data.mtz --comprehensive

and that will list map CC for all atoms or per residue,




if you need more fine-tuning.

I have to run now - otherwise I miss my flight to London -:)

All the best!

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