Hi,
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...
Gerald
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