Hi Ahmad, Probably you need to add the covalent bond between the carbonyl carbon at the end of one chain and the backbone nitrogen at the start of the other chain. Show all the atoms so that you can see them, select those two atoms, and then add a bond, e.g. with “bond” command or in the “Adjust Bonds” section of the Build Structure tool. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#bond> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Feb 4, 2019, at 10:53 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:

After merging two structures in Coot, chimera is showing a chain break at one end where I merged my molecule. The other end is displayed correctly. How can I fix that?