Reply To: Modeling circular permutation and domain insertion

[Anonymous]

With loops that long, you have another option besides relax; you may be able to do docking on your two rigid domains, then do loop modeling between fixed endpoints once you have the domains in place. (You’ll still need fixbb separately to do design). What you really need is a custom program; you could look into writing yourself exactly what you want with RosettaScripts or PyRosetta.