Question

How to combine different protein model from modeller?

Answer 1

While modelling programs can give you helpful results you should be careful how you interpret them. Domains may form interfaces with each other that can be hard to predict from the structures of individual domains in isolation. Ideally to make a model of a complete stretch for protein you want to be able to make two homology models that overlap. When I did this for LTBP1 I made models using modeller