Hi all. Recently I've been using the FloppyTail application to try and model the N-terminal floppy region of my protein. I ran into (and solved) two issues, one that I'm sure is a genuine bug, and another that may be known but is nonetheless very serious. I am running rosetta 3.3 on a machine running MacOS server 10.5. All tests used the '-C_root' option, and had my protein listed first in the pdb.
The first issue involves the option '-packing:repack_only'. While this option is on in the integration demo, it is not described in the documentation and I couldn't find any information on it in any other application or context. Without this option, FloppyTail randomly changes the sequence of about 90% of the defined flexible region, as well as sporadic point mutations throughout the rest of the protein. The application also takes much, much longer to run, finishing about 17 times slower. I would assume this behaviour doesn't happen with a C-terminus tail, but haven't tested it. With the option turned on, the application runs just fine and outputs expected results.
The second issue is with the numbering of the flexible region, with '-flexible_start_resnum' and '-flexible_stop_resnum'. My region is about the first 40 amino acids or so, so I had the start and stop as 1 and 40, respectively. This worked fine when I was modelling the protein on its own. But my protein has a docking partner that the N-tail may be interacting with, and when I included this docking partner into the pdb things got strange. The docking partner was being held still, as was the first amino acid of the tail, but the rest of my protein was moving and flying around that first amino acid. This is obviously an issue, as it completely destroys the docking conformation between my two proteins. Also, the tail was arbitrarily placed, so I certainly don't want it constrained by that starting position. This behaviour disappeared when I changed the start and stop numbers to 0 and 40; both proteins stayed in their pre-defined docking conformation, and the tail was the only thing moving around.
These two things took me a couple days to solve, and I wasn't able to find any other previous cases or information on them. I wanted to post so hopefully someone else having those issues could find a fix, and so the developer could see these and either fix or add them to the documentation.