I am trying to use flexbb-interfacedesign.xml from rosetta 3.9 to do the design of a protein interface.
I have two questions:
1) The top of flexbb-interfacedesign.xml reads as the following, is there a missing open bracket before "ProteinInterfaceDesign...", as highlighted in red?
2) How does rosetta define "chain1" and "chain2", as highlighted in yellow? I have tried many times by changing either "1" or "0" and even changing the chain name in the pdb (e.g. A->B, B->A) but still I cannot control which chain to design.
<TASKOPERATIONS> You can control which parts you want to change from here
ProteinInterfaceDesign name=pido repack_chain1="1" repack_chain2="1" design_chain1="1" design_chain2="0" interface_distance_cutoff=10/> task operation that designates which residues are designable and repackable at the interface