cleanATOM() for non-ideal amino acids

Hello People,

I am trying to clean this protein 3HZ7.pdb using pyrosetta.toolbox.cleaning.cleanATOM('3HZ7.pdb') in order to use it within PyRosetta.

The protein has MSE (Selenomethionine?) instead of MET at different parts of the sequence, therefore when applying cleanATOM() it just deletes these amino acids and I end up with a broken backbone (attached figure).

Any idea how I can overcome this issue? is there a method within cleanATOM that I should be calling? or running the protein through a different class before applying cleanATOM() on it?