[modeller_usage] remove short helices

[Shawna Frazier <sfrazier AT caltech.edu>]

Hi,

When I view my structural model as a cartoon, it contains several  
short 'helices', composed of only three residues each. The template  
pdb shows each of these regions as unstructured loops. Therefore, I  
would like to remove these short helices from my model. Is there a  
simple way to remove secondary structure?

Note, I have tried loop refinement; it worked on a couple of my short  
helices, but has failed to fix my last one.

Any suggestions are appreciated.
Thanks.