[Chimera-users] Joining fragments in a peptide bond

Sujata sujata.sovani at gmail.com
Tue Sep 14 11:48:55 PDT 2010

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
What is the right way to join fragments in a peptide bond? Is there a
cleaner way?

Thank you.
Appreciate your help.
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