[Chimera-users] Joining fragments in a peptide bond

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 14 12:05:38 PDT 2010

Hi Sujata,
If you get a newer version of Chimera (1.5, so a daily build -- these are lower down on the download page) there is a new tab in the Build Structure tool, Join Models.  (Build Structure is under Tools... Structure Editing in the menu).

With this new section it is much nicer.  You don't have to move the two pieces together manually, but instead just enter the desired bond length and torsion angle and it will reposition one piece as needed.  The two peptides should be open as separate models.  You might need to add hydrogens first, as mentioned in the documentation linked above.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 14, 2010, at 11:48 AM, Sujata wrote:

> Hi All,
> I have two peptide fragments that I want to join with a peptide bond.
> So I move the 2nd fragment towards the C terminal of the 1st one and bring the C of 1st and N of 2nd manually closer such that the distance is 1.34 A. I combine the two PDB files into one and I have a peptide I want but in the process of bringing them closer, the angles around the peptide bond CA-C-O and C-O-N are not what they should be?
> My question is - is there a way to fix these angles while I am fixing the distance?
> What is the right way to join fragments in a peptide bond? Is there a cleaner way?
> Thank you.
> Appreciate your help.
> Sujata

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