thanks for getting back. I do have templates (crystal structures) which are aligned with all the target sequence apart from this 46 aa. long part. As a result, the predicted structures from Modeller have a spaghetti-like conformation which extends from residue 84 to 161 (this region includes the unaligned part). So I was think if it is possible to feed a Modeller-generated structure to Rosetta and tune it to repack residues 84-161? If not then I could predict the whole structure ab-initio and use the Rosetta-predicted structure as a template for Modeller (by tuning it to read only the 77 disordered amino acids to avoid bias towards the Rosetta-generated structure – obviously because the sequence identity between the latter and the target sequence is 100%). Any other suggestions are welcome.