Re: [modeller_usage] model.loops crosses chains

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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