6 Oct
                
                    2015
                
            
            
                6 Oct
                
                '15
                
            
            
            
        
    
                10:56 p.m.
            
        Someone more familiar with the Phenix commandline may be able to tell you how to generate maps from the commandline in a more scriptable way.
Command line tools include: - phenix.mtz2map will convert Fourier map arrays into real-space maps; - phenix.maps will compute maps given model and diffraction data; - I can provide any customized Python/CCTBX scripts to do all this at even lower level. Pavel