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 "strategy=none" A more streightforward way of computing a map is to use the tool that is specifically designed for doing this, phenix.maps: http://phenix-online.org/documentation/phenix_maps.htm Good luck! Pavel.