[modeller_usage] modelling proteins with multiple chains...

["Himanshu Grover" <>]

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