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[modeller_usage] Modeling ligands in the binding site

Hi modeller users,
I want to build a model with a ligand in the binding sites, but I have problems. I read the manual on-line, but I don't find any python script for aligning the sequence to the structure with ligand. I don't know the differences when compared to structure without ligand. Could somebody give me some example of these python script, or give me some suggestion on how to edit the python script which is used to align to structure without ligand?  Thanks very much!
ALl the best,