Subroutine 'select_atoms' might be what you need. FAQ 2 in manual...
> 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
Bozidar Yerkovich, PhD
New York, NY, 10021, USA