21 Jun
                
                    2007
                
            
            
                21 Jun
                
                '07
                
            
            
            
        
    
                8:31 p.m.
            
        Will it recognized NAS-ASN, beta1-4, alpha1-4, etc linkages between sugars?
This is not automated (mainly out of fear of accidentally doing the wrong thing). You have to specify the linkages using the refinement.pdb_interpretation.apply_cif_link scope as explained here: http://www.phenix-online.org/download/cci_apps/ o phenix.refine [Documentation] Ralf