I need to predict missed loop fragments in a part of a multi-chain complex corresponded to GPCR bound to heteromeric G-protein (pdb id 8HTI). In this structure the chain A (a subunit of the G-protein) contain missed loop fragments. So the following commands were executed in command line to reconstruct the entire structure of this subunit:

open 8hti

seq chain /A

ui tool show "Model Loops"

modeller refine 1/A:1:internal-missing numModels 5 fast false adjacentFlexible 1 protocol standard

which very slowly produces 5 models of the chain A.

The problem was that the modeller considered the chain A in isolation from the rest of the structure and predicted loops overlapped with other chains of the G protein. Would it be possible to reconstruct the missing fragments in the chain A considering also the presence of other chains to build the full complex ?

Many thanks in advance

Enrico