There is no command for “Join Models”, but the Python equivalent isn’t too difficult.  Let’s assume you’ve selected the C and N atoms by whatever means (and only those atoms), then this Python code would be the “Join Models” equivalent:

from chimera.selection import currentAtoms

a1, a2 = currentAtoms()

if a1.element.name == “C”:

c, n = a1, a2

else:

c, n = a2, a1

length = 1.33

dihedral = 180.0

phi = -120

from BuildStructure import cnPeptideBond

cnPeptideBond(c, n, n, length, dihedral, phi=phi)

If you put the above Python code into a file whose name ends in .py, then you can run it simply by opening the file.  So if you named the file peptide.py, then something like this:

sel something-that-selects-just-C-and-N

open peptide.py

I have attached the Python file because my mail program changes simple quotation marks into fancy ones that aren’t correct in Python.

—Eric