Hi<br>
<br>
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.<br>
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? <br>
<br>
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.<br>
<br>
Many thanks<br>
J<br>