hi, i need some help with modelling a protein comprised of multiple chains.

Firstly, is it possible to model the entire protein in one go, or diff. chains need to be modelled separately...

Secondly, I want to provide my own alignment with the template, and am not using modeller's alignment routine... if I have to model 2 chains of the protein together, how do I provide the alignment... as the chains might not be contiguous... Moreover, when I do so, the resultant structure of modeller sticks together the loose ends of the 2 chains, as if they were continuous strands. This affects the model at the ends of the chains...How do I tell that this is the first chain and that is the second??

thanks, your sincerely, himan