Qinghua Liao wrote: > 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!

You can find a full working example in the examples/automodel/ directory. The Python script is model-ligand.py and the alignment is align-ligand.ali. The alignment differs in that extra '.' residues are added for each HETATM residue that should be copied from template to target.

Creating restraints on ligand atoms is done in exactly the same way as protein atoms. If you can't figure out the numbering, first build a model without any additional restraints and look at the output PDB file to see the residue numbers and chain IDs.

Ben Webb, Modeller Caretaker