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. Pavel.