[phenixbb] R factor

Pavel Afonine pafonine at lbl.gov
Sun Sep 19 09:18:56 PDT 2010

  Hi Hailiang,

> Never mind. The data.mtz is missing about 10% reflections, without which
> the Fc map (by model_vs_data --map=fc) looks weird (showing some big
> density like heavy metal not in the model). Thats why I wondered whether
> model_vs_data --map=fc involved something else.

This is because the computed Fcalc correspond to the data completeness 
in your reference data.mtz file.

If you want the complete set of Fcalc within certain resolution range, 
you need to use:

phenix.fmodel model.pdb high_resolution=1 low_resolution=25

> Just curious, why missing 10% reflections generated "heavy-metal" like
> density in solvent region?

Because data completeness affects the whole map, and you can't tell 
where the artifacts due to incomplete set will show up.


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