Dear Modeller caretaker, I used mutate_model.py to introduce a single point mutation into the structure of my protein with a ligand bound into the active site. The mutation I introduced was near the ligand, and when I had a look at the resulting structure, I saw that the mutated residue has been located in too strict proximity with the ligand (i.e. the mutated residue and the ligand collide with each other). My suspicion is that this script does not take into account the presence of ligands or other elements marked as HETATM in the original protein. Is this true? In order to encompass this problem, if this is true, can I simply replace HETATM with ATOM in order to make mutate_model.py correctly functioning? Many thanks in advance and best regards Anna Marabotti