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[modeller_usage] Modeling ligands in the binding site

Hi Modeller users,
I have a problem of Modeling ligands in the binding site, I have read the manual online, but I still can't understand exactly!
my question is what the differences of alignment between that of with and without ligand! Is it just the value of env.io.hetatm? And how to set the atoms with restraint? Could somebody share the all python scripts used during the entire process of  Modeling ligands in the binding site? Any response will be highly appreciated!
All the best,
Qinghua Liao