[phenixbb] no density on the anchored proteins

Pavel Afonine pafonine at lbl.gov
Thu Jun 2 09:31:47 PDT 2011

Hi Hailiang,

> I am using phenix.refine to calculate the map of the 50S RNA (1FFK). It is
> weird that there is no density on the anchored proteins even for the Fc
> map. Following is the code I am using:
> phenix.refine ${f}.pdb ${f}.mtz main.number_of_macro_cycles=0
> xray_data.high_resolution=${res} xray_data.r_free_flags.generate=True
> export_final_f_model=mtz

using phenix.refine is possible but not the best way of calculating a 
map. In the example above you need to have main.number_of_macro_cycles=1 
(not 0) otherwise you do not do bulk-solvent correction and anisotropic 
scaling and therefore the map quality you will be getting will range 
from poor to extremely poor. Also, export_final_f_model=mtz is not 
really necessary: the maps will be generated automatically and output 
into *.mtz file. And if you specify main.number_of_macro_cycles=1 you 
also need to make sure that no refinement is going to happen by using 

A more streightforward way of computing a map is to use the tool that is 
specifically designed for doing this, phenix.maps:

Good luck!

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