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.