Hope this helps Thomas. You can manually set the max rounds by editing the main file, line 159, where it says this: self.SliHigh=Scale(self.main, orient=HORIZONTAL, to=100, resolution=1) by changing the ‘to’. Later I can do options and all that fun stuff.
Decoy of 0 will return your pose. More then that return the last pose from the job distributor after outputting your decoys.
Loops have to be added in order, N-term to C-term and in the order the chains are seen by rosetta (beginning to end of pdb file) for now. Clear the loops to reset. Cheers.