the input antigen-Fab compelx: chain A, B: antigen chain H, L: Fab chains in order: A, B, H, L A = jump1 = B = jump2 = H = jump3 = L so set jump=2, and design_chain1=0, design_chain2=1 when calculating ddg and other properties. (Here "chain1" and "chain2" simply mean "those residues before the jump" and "those residues after the jump". For a 4-chain protein, you have three jumps, one between (at least in the before/after sequence sense) A and B, the second between B and C, and the third between C and D. If you want to do designs between the AB complex and the CD complex, you need to specify the "jump=2" parameter for ProteinInterfaceDesign to tell it to work off of jump 2 instead of the default jump 1.) DDG filter computes binding score for the complex (threshold=0 only allows complexes with negative binding score) (repeats=3 calculates binding score three times and returns average) (repack=1 repack complex in both bound and unbound states to calculate binding score) SASA filter computes interface solvent-accessible surface area (threshold=800 only allows complexes with greater than 800 Å^2 as per Janin et al., Quarterly Reviews of Biophysics, 2008) Read .resfile set partner2 to be designed Reads command line options Runs local refinement stage of full atom docking Runs protein interface design Runs full atom side-chain and backbone minimization Runs movers and filters in this order