I am Dung. I am currently using Chimera to do the refinement for my protein because it has some large missing residues segments. I use Tools/ Loops- Model refinement of Chimera software to do that task. As it was failed to generate models if I performed refinements for all missing residues segments. Thus, I decided to refine them not at once. The problem is that I could not find how to combine the  separated loops from models after refinement. I am new to Chimera so I hope that my description can be useful for you to imagine my problem. 

I hope that you could support me to solve this problem. I really appreciate it. 

Thank you for spending your valuable time. 

Yours sincerely, 

Dung