Dear Modeller users!
I have a question regarding loop refining. Following modeller advanced tutorial I've tried to do such task on my receptor model consisted of 6 loops (with 2 S-S bridges in one of the loop) which should be refined.
1)Does it possible to make some corrections in the below script to refine all 6 loops at one task keeping intact interloop S-S bonds. E.g I'd like to refine regions 51-58, 87-94, 127-141, 163-195, 228-233 and 260-270
class MyLoop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # 10 residue insertion return selection(self.residue_range('127', '139'))
2) What are the most trivial way to rank refinement for all N models? E.g usage of the model_energies.py leading to looping all of the models result in the .profile file. How I could estimate dope scores within the loop selections on all N models ?
Thanks for help,
James