In RosettaScript, the mover "RepackMinimize" has attributes "design_partner1" and "design_partner2" to define which partner will be designed, but it does not have attribute like "jumps" or "partners" (just like "DockingProtocol") to let you set the jump in fold tree. It assumes to use jump=1, this is OK for two-chain complex. But it is not OK for more than two chains.
I applied this mover on a 4-chain complex with "minimize_rb=1":
<RepackMinimize name=des1 scorefxn_repack=soft_rep scorefxn_minimize=soft_rep minimize_bb=0 minimize_rb=1/>
But the program halted with errors:
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER RepackMinimize=======================
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph
core.pack.pack_rotamers: built 6972 rotamers at 79 positions.
core.pack.pack_rotamers: IG: 17487320 bytes
ERROR: min_rb.size() == pose.num_jump()
ERROR:: Exit from: src/protocols/protein_interface_design/design_utils.cc line: 365