[modeller_usage] Hydrogen Atom Preservation

Hello!

I have been attempting to use Modeller to refine the loops of some generated protein structures. When performing loop refining, Modeller seems to remove all hydrogen atoms from the structure. I have not been able to find any way to change this behavior. Are there any such options? That is, to stop Modeller from removing the Hydrogen atoms from the structures it refines?

Thanks for your time, and any help that anyone can provide.