On Mon, Nov 22, 2004 at 02:49:56PM -0500, gerald.quon@utoronto.ca wrote: > I'm interested in modelling a dimer composed of two chains. I would > definitely like to avoid modelling each chain separately, then combining > the PDB files - is it possible to model them together in MODELLER? I > would try just concatenating the two chains into one, but i'm guessing > the discontinuity of the backbone will mess around with the minimization...

Sure - Modeller can do that. Just be sure to use a chain break character (/) in your alignment, between the two chains. This way, the minimizer knows to expect such a discontinuity.

BTW, there's no need to relabel the chains - Modeller can read multi-chain PDBs just fine.

Ben Webb, Modeller Caretaker