So I guess my basic question is: *Is it possible to set backbone
dihedral angles to a specific value? Or is there any other way to
use mdl.build_sequence to get an alpha helix?*
build_sequence builds the 3D coordinates from the internal coordinates
given in the CHARMM topology file. These are per-residue-type and for an
extended chain, so you'll always get an extended chain using that
function. There are no functions in Modeller to exactly set backbone
dihedral angles, sorry. You could query the current values (see e.g.
http://salilab.org/modeller/9.15/manual/node353.html) and then rotate
the model about the central bond to get the desired value, or you could
add dihedral restraints and then optimize the model - but both
approaches are probably no better than your current solution.