Using cartoon view to present the protein secondary structures and tertiary structure is common and we also often see people present some sidechains of particular residues which may be important in some biological roles. In PyMOL, when sidechain atoms are presented in the “sticks mode” with the cartoon scaffold, we always see the backbone atoms (e.g. N, O) are also presented in the sticks mode.
Here is the example (PDB code: 2BTF) showing that the nitrogen (blue) of Val47 is displaying inside the helix.
By using a PyMOL commend “set cartoon_side_chain_helper”, we can quickly hide sticks of the nitrogen and oxygen atoms.
Command: set catoon_side_chain_helper, on
note: “on” for removing the sticks, “off” (default argument) is to keep all atoms in sticks view
Note (11/14/2011): PyMOLWiki has an example page of this command, see here.