It appears that one should be able to assign the rotation and translation values of jump 1 in pose1 to jump 1 in pose2 (even if poses 1 and 2 possess different numbers of residues) with the following:
pose2.jump(1).set_rotation(pose1.jump(1).get_rotation())
pose2.jump(1).set_translation(pose1.jump(1).get_translation())
Although I find that these commands suitably alter the translation and rotation values obtained with the commands
pose2.jump(1).get_rotation()
pose2.jump(1).get_translation()
I do not find the coordinate values in pose2 reflect the changed jump values, even if I force an update by diddling with a backbone angle. I would like to have pose2 reflect the new jump values that I am trying to assign.
Post Situation:
If you have a copy of the C++ code, the contents of src/protocols/moves/RotateJumpAxisMover may be valuable. They show (well, not with enough comments) how to separate the two "stubs" (coordinate frames) out of the Jump, modify one of the Stubs, and then reassemble it into a Jump. Maybe you need to take the downstream Stub of pose1/jump1 and insert it into pose1/jump1 while leaving the upstream stub of pose1/jump1 unmodified. (By upstream and downstream I mean w/r/t the direction of folding in the atom tree).
I have no idea if this is applicable in python or not.