Hi mchldln, I have a question about your second reply post. If the .fasta sequence containing both protein 1 and 2 when uploaded to generate the fragment libraries. And if they have to be continuous, which seems really odd to me, will the docking-loop modeling still work appropriately if you feed it this weird fragment libraries? I mean, how does rosetta distinguish between those two separate subunits?
I have read several of your posts, and it seems to me that you have a lot of “trial and error” experience in using Rosetta 2.* version, which is very valuable, given the incomplete Rosetta documentation.