I'm trying to get something like the domain insertion mode in 3.2. For example, I have a 100 residue protein and I'd like to remodel the 50 residues between residues 25 and 75. Should I add a jump between residues 25 and 75 and have rosetta read a movemap to fix the backbone angles of residues 1-25, and 75-100?
There are (at least) two domain insertion protocols I'm aware of in developer's trunk.......
....and none in the release.
I would suggest using an unadvertised semi-secret mode of the FloppyTail executeable. You aren't required to have the "end" of the tail actually be a C-terminus, so you can have your flexible region be mid-protein and it will flex the two domains around each other and look for reasonable docking conformations.
I wrote FloppyTail so I can support it pretty well, but it wasn't really meant for domain insertion so you might find you don't like its results.
Don't forget to change the if statement on line 447 (I think this is out of date in the documentation) to false. The create_extra_output function is used to duplicate the publication's results, but it will crash if you aren't trying to do that. (I changed it for 3.3 to have a boolean for "publication mode", which it probably should have been in the first place...)