You are here

loop modelling on complex structure

2 posts / 0 new
Last post
loop modelling on complex structure


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,


Post Situation: 
Fri, 2020-09-18 07:24

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.

LOOP 23 30 26
LOOP 123 130 126
Mon, 2020-09-28 10:41