I'm trying to dock three chains with RosettaScripts with Rosetta 3.3. Docking chain C to chains AB. I.E. the partner string would be AB_C. It appears that no matter what jump number I use in the docking tag in RosettaScripts, it always tries to dock the second and third chains to the first chain of the structure (always 1_23) corresponding to a jump number of 1. Is this a known issue with the docking mover in Rosetta Scripts?
I can solve this problem by including the commandline flag -docking:partners AB_C. But I'd like to call it to everyone's attention if it is indeed an issue with the code for RosettaScripts and/or Docking.