[phenixbb] ligand refinement

Dear Phenix developers I have a covalently bound ligand in my structure and I would like to use phenix to refine the structure. The ligand is bound to the sulfur of a cysteine. What is the best method for defining the ligand. Should I generate a cif file for the whole amino acid and the ligand, or can I make one for just the ligand and add in some restraint somewhere which tells phenix to make a bond between the ligand atom and a nearby sulfur in a cysteine. If I generate a cif file with the whole amino acid and ligand, I assume I will I have to follow some convention in atom naming so that the main chain bonds and angles will form and refine OK? Regards Christine