On Mon, Nov 22, 2004 at 02:49:56PM -0500, 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
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