I am a molecular computer modeller from Cardiff University and we have the Rosetta software installed on our cluster. I've been running ab initio 3D protein structure prediction tests on an unknown toxin (over 700 residues long) and have filtered some interesting structures, though they seem to be very different to the structures produced by Robetta server. To be sure we can produce similar structures to the Robetta system, is it possible anyone could tell me the setup details that Robetta server uses, such as : -kill_hairpins true or false, -use_filters true or false, as I found for this toxin I needed the -kill_hairpins option to be false, otherwise I kept getting failed structures (-F0000001) on most of the decoys produced?
One thing to make sure of is that the file for input to ss is correct. It changed somewhere between 3.4 and 3.5 and this was not documented anywhere. (It is now documented on the abinitio page. ) https://www.rosettacommons.org/content/killhairpin-error
I would love to have the full options of what Robetta uses as well. In the meantime, this may help in correcting your failed structures.