In the tutorial on the loop modeling, loop is defined by the fold tree in the loaded from pdb-file pose that already have residues that are “loop” and are normally missing. If I have a structure, where the loop is missing, how do I define it? As far as I understand, there’s no way to do this from sequence, Do I have to make a “fake” loop structure before obtaining a possibility to really model it?
You can add missing loop residues before loop modeling fairly easily with RosettaRemodel. See the application documentation as well as this thread: https://www.rosettacommons.org/node/3840
There may be other ways, but I have found that this works fairly well and is documented enough to actually get it to work.
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