Re: [modeller_usage] remove short helices

[Jacob Glanville <>]

What are you using to view the structure? Some viewing programs try to  
make best guesses about secondary structure when rendering a ribbon  
view.

Jacob Glanville
Informatics associate
Rinat Biotherapeutics and Bioinnovation Center; Pfizer Inc.
(415) 497-3552


On Aug 19, 2009, at 8:02 AM, Modeller Caretaker < 
> wrote:

> 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.
>
> What makes you sure that your helices need to be "fixed"?
>
>    Ben Webb, Modeller Caretaker
> --
>              http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
> _______________________________________________
> modeller_usage mailing list
>
> https://salilab.org/mailman/listinfo/modeller_usage