[phenixbb] how to make covelent link of BME with Cys and refine

Thanks Nigel, I am using phenix 1168 but when i type intra_chain = True command with phenix.refine it gives error message as "intra_chain = True is unknown command". The actual command i used was " phenix.refine .pdb .mtz .cif intra_chain = True". can you please explain how to resolve it. Raj