Subject: Re: [modeller_usage] remove short helices
From: Modeller Caretaker <>
Date: Wed, 19 Aug 2009 08:02:17 -0700
Cc:
Shawna Frazier wrote:
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?
See http://salilab.org/archives/modeller_usage/2009/msg00170.html for a
recent discussion. In short, there is no way to force Modeller to build
models with no secondary structure, but modifying the alignment so that
the model is not aligned with the template in that region will often
give the result you want.
Note, I have tried loop refinement; it worked on a couple of my short
helices, but has failed to fix my last one.