On 6/12/10 3:47 PM, sdh wrote: > I want to model a big fibrous protein using several templates. The > templates do not overlap (gap is no longer then 1-3 residues) or overlap > over few residues. > > I found the following sentence in the FAQ: "If no additional information > is available about the relative orientation of the two domains the > resulting model will probably have an incorrect relative orientation of > the two domains when the overlap between A and B is non-existing or > short. To obtain satisfactory relative orientation of modeled domains in > such cases, orient the two template structures appropriately before the > modeling." > > My questions are: how precisely the templates have to be oriented? Would > be cursory placing enough?
Orientating the templates will only affect the initial (unoptimized) model. Since there are no constraints on the domain-domain interaction, the final (optimized) model may not respect that orientation. So you would obtain better results if you can add simple additional restraints between the domains: http://salilab.org/modeller/9v8/manual/node27.html
Ben Webb, Modeller Caretaker