Hopefully a fairly simple foldtree problem:
I have a two chain protein complex where the end of the floppy tail of domain B also happens to be the root of domain B.
Since the interaction with domain A is significant I'd like to re-root and sample according to something like:
FOLD_TREE EDGE 1 645 -1 EDGE 1 646 1 EDGE 646 1500 -1
FOLD_TREE EDGE 1 645 -1 EDGE 1 646 1 EDGE 1400 646 -1 EDGE 1400 1500 -1
So I use:
ft = FoldTree()
Two problems immediately come up from this though:
(1) that torsional changes in residues 1400-646 now affect chain A for some reason.
(2) the structure resulting from the above code is not the same as the input structure.
Basically all I want is to re-root my second kinematic chain somewhere inside of Domain B and continue to let domain A move completely independently both kinematically and as a rigid body.
Also, why does a new fold_tree not preserve structure?