I want to use the XML script design_script.xml in demos/design_raf_rac_interface/ to design the interface of a complex structure.
the syntax of "ProteinInterfaceDesign" used in the example xml is typically like:
<ProteinInterfaceDesign name=design repack_chain1=1 repack_chain2=1 design_chain1=1 design_chain2=0 interface_distance_cutoff=8/>
Does the attribute "repack_chain1" mean "to repack sidechains of residues in first chain"?
While my complex structure has 4 chains, the first two chains form the partner A and the last two chains form the partner B, what I want to do is to design the interface residues on partner B not on A. So how to assign such attributes for chain 3 and 4? Is there something like "design_chain4=1"?
Is there a way to make "ProteinInterfaceDesign" to only work on a set of specific residues rather than whole interface, for example by loading sort of .res file?