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