12 Jan
                
                    2018
                
            
            
                12 Jan
                
                '18
                
            
            
            
        
    
                6:03 p.m.
            
        I want to keep my ligand positions rigids during phenix refine, so that its position wont affected after phenix refine.
I suggest you exclude the ligand from positional refinement in phenix.refine. You can do this using atom selection for coordinate refinement in GUI or CL. Pavel