I'm using next-generation kIC to model one loop , which interacts with another subunit in the hetero-trimer complex.
I'd like to input the whole 3-chain structure for loop modelling as adjacent subunit could stabilize the loop conformation because of the interaction.
But I've got no idea where I can designate the chain for loop modelling if I input multi-chain structure?
Could anyone please give me some ideas?
Thanks a lot,
Loops files use Rosetta numbering, which is continuous throughout the full structure. So there is a unique numeric identifier for each position. You need to create a mapping from the individual chains, in order, to Rosetta numbering.
For your complex scenario, it sounds like you'd want a loop file with multiple loops (see example below). Then both loops will be conformationally sampled.