I have a pretty small question. Is there a way in MODELLER where i
can completely use a single template along with its side-chain
topology?
Where you have a 1:1 alignment, the initial model is exactly the same as
the template. If you don't want Modeller to optimize this, you can
override select_atoms():
In normal modelling scripts, it simply harness the peptide backbone
localization information from the template and then fixes the
side-chains with its own algorithms.
No, the initial model is simply copied from the template where the atom
names are the same (this usually means the backbone and part of the
sidechain, depending on the type of the aligned residue). Side chain
dihedrals are not strongly restrained though, so during optimization
they can certainly move from these initial positions.