Hi,
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?
Note, I have tried loop refinement; it worked on a couple of my short helices, but has failed to fix my last one.
Any suggestions are appreciated. Thanks.
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
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
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Jacob Glanville -
Modeller Caretaker -
Shawna Frazier