Re: [modeller_usage] making ideal alpha-helix

[Modeller Caretaker <>]

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
--
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