Subject: Re: [modeller_usage] remove short helices
From: Jacob Glanville <>
Date: Sat, 22 Aug 2009 13:51:59 -0700
Cc: "" <>
What are you using to view the structure? Some viewing programs try to
make best guesses about secondary structure when rendering a ribbon
Rinat Biotherapeutics and Bioinnovation Center; Pfizer Inc.
On Aug 19, 2009, at 8:02 AM, Modeller Caretaker <
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.htmlfor 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.