It is not exactly what you asked but this may do the trick:
Look for a program named ribosome - it makes regular protein structures given the sequence.
At 09:15 AM 10/26/2010, Modeller Caretaker wrote: >On 10/25/10 3:30 PM, Orhan Ertughrul wrote: > > Iâve been using a standard script to build an alpha helix from an > > alanine chain. Modeller generates the restrained structure but it isnât > > alpha-helical when viewed in PYMOL.
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