Reply To: Using rosetta 3 to make a fragment library and then use it to model loop of a protein structure

I’ve contacted one of the fragment developers, he said he’d post a deeper reply when he had time. I’ve already told you all I know about it…

Robetta makes fragments of length 3 and 9 (and possibly 1 or 13, I forget). Someone determined those were optimal for ab initio a long time ago and it’s never been changed. You may be able to get away with trimming the 9mer library to 8mers.

I’m not aware of any deep documentation for the fragment picker that’s in 3.1 (as I said, src/core/fragment). You can play around with that code. What you want to do will certainly require writing C++ code in 3.1. If you wait for 3.2, then it will probably become easier…but it’s still fairly likely you’ll need to write stuff in C++.

I’ve attached a bit of code that ought to be mostly-compatible with the 3.1 release. It’s from a module that wasn’t in 3.1 (and won’t be out until 3.3), but it uses the most basic of the fragment-picking commands which ought to get you started. (You can ignore the parts about loops and anchors – those are related to the application, not the fragment picking)