I am having a trouble with making an alpha helix example (
http://salilab.org/modeller/wiki/Make%20alpha%20helix).
It works fine for shorter helices, but if I increase helix length and do
e.g. m.build_sequence('AAAAAAAAAAAAAAAAAA') then the resulting helix is
far from perfect
Modeller's secondary structure restraints are used to help 'persuade' a
model to adopt a given secondary structure - they don't force it at the
expense of conforming to the template restraints and/or stereochemistry.
So they don't constrict the conformational space enough to always result
in perfect helices, and so I wouldn't expect to see such helices,
particularly for longer sequences.