Re: [modeller_usage] Modelling multiple chains

[Modeller Caretaker <modeller-care@ucsf.edu>]

On Mon, Nov 22, 2004 at 02:49:56PM -0500, gerald.quon AT 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
-- 
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