On 4/3/19 5:22 PM, Alex Lian wrote: > I have a few questions about the mutant_model script. I am trying to do > a single mutation modeling using this script. > > optimize(s, sched) > s.energy() > > Where S represents a group of selected atoms (Mutation position). If I > understand correctly, The optimize function will do a conjugate gradient > to the selected atoms to find the local energy minimum. However, after > doing the minimization step, the energy function results in a small > positive value which is unusual. I also tried selecting the whole > structure which is about 300 residues, did the optimized step and energy > computing. This time the energy function showed up with an extremely > large positive value. Besides this, I tried to compute the DOPE for both > nature structure and the whole sidechain refined structure and found > that the DOPE for the refined model is even larger than the one for the > native structure which made me so confused.

You didn't ask any questions, but this behavior sounds normal to me. The mutate model protocol is designed to work with everything but the mutated residue held fixed, so I would not expect it to work particularly well on the entire model.

Ben Webb, Modeller Caretaker