restraining sec. structure elements

Dear All I have a theoretical model structure in hands with some regions structurally meaningful and others not. I'd like to use Modeller to modify only some regions of this model, I mean, those elements of sec. structure that looks like an helix but have some distortions on it. I guess that some EM/MD steps in Modeller could fix that. Would be nice if Modeller could re-design these regions considering the presence of the rest of the protein (without modifying obviously the rest of the model - only the chosen elements). I was looking through the manual and tutorials but couldn't find nothing very helpful. Any hont will be very welcome. Frank Alarcon www.lncc.br