Hi Charlie,
Also from reading the manual, as I understand it, the phenix.refine command will automatically generate Coot compatible maps.
phenix.refine always outputs maps ready to visualize in Coot. The files is called xxx_map_coeffs.mtz and it contains various columns with Fourier map coefficients. When loading this file into Coot you need to choose which map to display (which map coefficients to use).
But if I take my autobuild.pdb file and the original mtz data file, how can I quickly obtain the same R/Rfree, what commands would I have to imput other than phenix.refine mtz pbd?
In addition to what Tom wrote, there is a specific command to do this: phenix.model_vs_data model.pdb data.mtz and it will give you complete model and data statistics, including R-factors.
Also, is it possible to make 3Fo-2Fc maps?
phenix.refine can create a map i*mFo-j*DFc or i*Fo-j*Fc, where i and j are any user provided numbers. Example: phenix.refine model.pdb data.hkl params.txt where params.txt file contains these lines: refinement.electron_density_maps { map { mtz_label_amplitudes = 3FO2FCWT mtz_label_phases = PH3FO2FCWT likelihood_weighted = True obs_factor = 3 calc_factor = 2 kicked = False fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = 1.5FO1.2FCWT mtz_label_phases = PH1.5FO1.2FCWT likelihood_weighted = False obs_factor = 1.5 calc_factor = 1.2 kicked = False fill_missing_f_obs_with_weighted_f_model = True } } Pavel.