Dear Albert, It will be really a big mess to select best decoy. Use this line in your modeling script in the loop like this, and use redirectional operator while running the modeller as model_mult.py > modeling.log. That will solve your purpose.

knowns=(........), sequence='.....', assess_methods=(assess.DOPE,assess.GA341,assess.normalized_dope)) a.starting_model=1

This will solve your purpose. Take care of loop closure.

Good Luck, Ashish

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA