Sivaram I wrote: > I have a sequence.Its has about 300 aminoacids.The first 200 aa share > sequence homology with one protein and the rest 100 share with other > protein .Is there a way to build Homology model using the two protein > structures .If yes how do I do it?

Of course. Simply provide an alignment of all three sequences (your target, and the two templates). Modeller will use both templates in the modeling procedure. There is an example in the advanced tutorial at http://salilab.org/modeller/tutorial/advanced.html

Ben Webb, Modeller Caretaker