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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