Mauricio Carrillo Tripp wrote: > I'm trying to do a loop refinement calculation with the dopehr_loopmodel > class, modeller 9v4. > Here's the python script I'm using: ...
You're only building one loop model. I'd recommend building several, so that you can sample the conformational space more effectively. This also allows for the possibility that some of the models are not produced due to optimizer failure, as you have discovered.
... > check_inf__E> Atom 31754 has out-of-range coordinates (usually infinity). > The objective function can thus not be calculated.
Most likely the loop conformation is distorted in such a way that the optimizer cannot recover. In the case of GB/SA (used by dope_loopmodel) this may result in very large forces, thereby causing very distorted models. The older loopmodel class is more stable because it does not use GB/SA.
Otherwise, it looks like what you are doing is fine.
Ben Webb, Modeller Caretaker