[phenixbb] Filtering ordered solvent molecules based on secondary map
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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