The cartoon representation of cyclic peptides does not appear on PyMol. Could someone help with the commands for making cyclic peptides Cartoon on PyMol?
Unfortunately, PyMol doesn't allow to build cyclic peptide in the cartoon representation. But you can build a covalent amide bond between N and C terminus of your peptide using the "bond" command. The N-C terminal amide bond can only be displayed in "sticks" mode.
Here is the instruction:
1. You can create a new bond by selecting two atoms, each with the Command + middle-mouse-button. In your case, press the keyboard COMMAND + MIDDLE-MOUSE-BUTTON and select N-terminal amino and C-terminal carboxyl.
2. Typing "bond" on the command line. You will see a bond showing up.