Francesco Pietra wrote: > I was trying to widen the script model-single.log of tutorial "Basic > example' to treat also a ligand > > from modeller import * > from modeller.automodel import * > > env = environ() > env.io.hetatm = True > a = automodel(env, alnfile='xxx.ali', > knowns='XXX', sequence='yyy', > assess_methods=(assess.DOPE, assess.GA341)) > a.starting_model = 1 > a.ending_model = 5 > a.make() > > The five model were built without the ligand. Much obliged for getting > a correction of this script.

Most likely you haven't actually put the ligand in your model sequence in the alignment file. But it's impossible to say for sure without seeing that alignment file.

Ben Webb, Modeller Caretaker