On 2/23/17 6:55 AM, Shyam Saladi wrote: > In the process of using model.loops to identify regions that I will need > to model in a multi-chain situation, I have noticed that it returns > insertions between chains as a single loop.
Yes, this is the default behavior of the model.loops() method: https://salilab.org/modeller/9.18/manual/node177.html
If you don't want it to do that, set include_termini to False. (It would also be pretty easy to write a function to split loops in the way you describe too, although I think it would make little difference to the loop modeling algorithm other than a different starting conformation.)
I can't run your test case because it looks like you've confused two examples (5xki vs. 2abx).
Ben Webb, Modeller Caretaker