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Anonymous
The only of these questions I can address is 3). The nnmake functionality (it’s possible to run locally, it’s easier to run via robetta) is the only fragment-generating software I’m aware of that works with Rosetta.
Within Rosetta 3, there are some internal fragment generators online. These generators directly read the vall fragment database from the pdb (no, I don’t know what vall stands for). Anyway, they can create fragments as necessary on-the-fly. There’s one version included in 3.1, and a second version in development. I don’t know what the release plans for these are. It’s possible to generate your own fragments within Rosetta3.1 but it’s unlikely to be worth your trouble unless you’re already familiar with programming inside Rosetta.