MODELLER based on your constructed alignment file
parsing the reliable template residues mapped against the target
ones, constructs and fixes the average alpha carbon backbone
Actually all atoms that have the same name in target and template will
be simply copied into the model in this case. Usually this means all
backbone atoms, not just alpha carbons.
On increased sampling,
MODELLER tries best to satisfy the Lennard Jones and all the
energetic equations composing its DOPE energy function.
In fact the optimization tries to minimize the molecular PDF, which
includes contributions from soft sphere (not Lennard Jones). DOPE is a
separate, atomistic pairwise statistical potential. It is not used in
comparative modeling.