Thomas, Sorry for the bugs. It’s just me testing everything when I have some extra time. N-Term and C-Term ends use a different fold-tree then the one that is setup in the program for loops. This can be changed. Its code is in the InitializeLoops definition in file LoopClassAB.txt. The tutorial for PyRosetta talks about the fold tree. I would program in the option if I had more time at the moment. Do you know Python?
Bug 2 is fixed. Bug 3 I noticed when using my main program to do modeling of a missing stretch from a protein last week too. In the previous version, i would CCD the loop, but it looks like the loop not breaking would use ccd to completely mess the whole structure up. So I have to put in a conditional CCD for if the loop gets broken during the step. I think I saw a check somewhere in the bound classes to check for a broken loop, but I’ll have to find it.
Relaxation is the Classic Relax or Fast Relax of Rosetta (This is the standard rosetta refinement protocol) (Bradley, Misura, Baker 2005); while Minimization, as I used it, is the MinMover from PyRosetta. The MinMover makes slight tweaks to the backbone. From the tutorial: The MinMover carries out a gradient-based minimization to find the nearest local minimum in the energy function, such as that used in one step of the Monte-Carlo-plus-Minimization algorithm of Li & Scheraga. Both do Minimization.
dfpTolerance refers to the Tolerance setting of the MinMover, probably minimize_set_tolerance, but im not 100 percent sure.
Sorry that there were some issues. Hope this helped. My email is email@example.com if you want to contact me directly.