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I’m trying to use an NMR structure as template for fixbb and want to use all 20 models as template, e.g. -nstruct 10 for each model = 200 designs. Is there a option to tell rosetta3.1 to read all models and use them one at a time?
No – you’ll have to split them up into 20 separate inputs. You should be able to use one resfile for all of them, though. fixbb will take the -s or -l option.