On 7/9/13 11:30 PM, Jan Kosinski wrote: > 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.
Ben Webb, Modeller Caretaker