[Chimera-users] join models C-N peptide bond

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 17 11:38:52 PDT 2013

I assume you have already also chosen the "C-N peptide bond" option in Join Models and that the C is the backbone C of the last residue in a peptide chain in one model and the N is the backbone N of the first residue in a peptide chain in a different model.

If all of the above are true, the most likely problem is that you have selected more than 2 atoms.  For example, if you just select on the ribbon with the mouse, it selects the whole residue, not just an atom in the residue.  You can see how many atoms you have selected by clicking the green magnifying glass near the bottom right corner of the Chimera window.  The resulting dialog will show how many atoms are selected.

To select only two atoms, display atoms instead of ribbons and then use the mouse to select them.  For example, to show only peptide backbone atoms, you could use commands:

show protein & @n,ca,c,o

The selection could be done with the mouse (Ctrl-click on one atom, Shift-Ctrl-click on the other) or with commands, for example:

sel #0:368.A at C #1:1.A at N

(of course, the exact command would depend on the residue numbers and chain IDs in your structures)
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 17, 2013, at 2:44 AM, A Amiri <atefeh_amiri23 at yahoo.com> wrote:

> Hello.
> I have a problem with chimera! i want to join two pdb file together by C-N peptide bond. Actually this is a modeling of a fusion protein that one part of its, is a protein and another part  is a linker. I need a complete structure.
> I select the carbon atom from one model and nitrogen atom from another model. I use the "build structure<join modesl" menu for this purpose but  the "apply" button is inactive still and i don't know how i can  activate it!
> please help me.

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