deepti nayar wrote: > I am new to modeller. I am using modeller 9v2. I am trying to model > structure for a protein using two templates. Can anyone tell me > whethermodeller first builds its own alignment among the templates and > then build a model???

You can certainly build models with multiple templates. There is even an example in the manual: http://salilab.org/modeller/9v4/manual/node21.html

Modeller never 'automatically' builds an alignment - it takes the one you give it. There are functions in Modeller to do alignments, however, so you can use these to make your alignment if you want.

> Is there a way by which we can get the model based on our wished > alignment. I tried this but it seems it doesnt work.

Sure, that's the default. Try running the example above to see for yourself. What do you mean by "it doesn't work"?

Ben Webb, Modeller Caretaker