Hi

I have added missing loop residues to my existing pdb file using the refining only part of the model method (I want to keep the rest of the coordinates unchanged) and then loop optimisation method to optimise the added residues.
During this process atoms missing from other residues within the protein chain are also added. My question is how is this done? I have not found any reference to this in the manual. After these atoms are added do they undergo any energy minimisation?

I would really appreciate any help with this question as I am confused why after energy minimising these residues myself in another program and then reanalysing my model with the evaluate_model.py script, the dope score I obtain is significantly worse than for the original model from modeller.

Many thanks
J