On 1/3/21 5:07 PM, Casey Becker via modeller_usage wrote: > I'm currently trying to model a hemoglobin monomer that has a heme group > as a ligand. If I run Modeller through the chimera interface, the ligand > carries over to the models. However, if I run through IDLE, which I > prefer to do because I'm using parallel jobs, the ligand does not carry > over. Any help appreciated.

The only explanation I can think of is that you're using a different alignment file in the two cases (which you didn't post here). Ligands are specified there, not in your Python script (you just need to tell Modeller in your Python script to read HETATM residues from your template by setting env.io.hetatm=True, which you are doing).

Ben Webb, Modeller Caretaker