Re: [modeller_usage] remove short helices

[Jacob Glanville <dr.jake@gmail.com>]

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
Jacob.glanville@pfizer.com

On Aug 19, 2009, at 8:02 AM, Modeller Caretaker <modeller-care@salilab.org 
> 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
> --
> modeller-care@salilab.org             http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
> _______________________________________________
> modeller_usage mailing list
> modeller_usage@salilab.org
> https://salilab.org/mailman/listinfo/modeller_usage