loop modelling on complex structure

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- September 18, 2020 at 2:24 pm #3578
  Anonymous
  Hi,
  
  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,
  
  Tianyang
- September 28, 2020 at 5:41 pm #15529
  Anonymous
  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
```
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