[Chimera-users] Beta-turns and hairpins

Eric Pettersen pett at cgl.ucsf.edu
Tue Jul 3 17:37:54 PDT 2012

Hi Kyle,
	Alternatively, if what you mean is that you have a structure that is missing loops, or that you want alternate loop conformations, then you should download the daily build and use the Model/Refine Loops tool in the Structure Editing category.  That tool can be used to build models with loops filled in / refined by the Modeller program (which you can install locally, or use via a web service that we host).


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Jul 3, 2012, at 5:29 PM, Elaine Meng wrote:

> Hi Kyle,
> You can build peptides with specified phi,psi angles using Build Structure.  This tool is under Tools... Structure Editing.  Start it, then go to the "Start Structure" tab, choose "peptide sequence," and proceed:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>
> Alternatively, you can add amino acids one by one to an existing peptide with the "addaa" command:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Jul 3, 2012, at 2:57 PM, Kyle Morris wrote:
>> Dear all,
>> Is there a simple way to model beta-turns and hairpins in polypeptide chains in Chimera?
>> Thanks in advance for any assistance,
>> Kyle
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> Chimera-users at cgl.ucsf.edu
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