Cartoon smooth loops
This is a display setting. When set to off, the cartoon will follow a path that is splined between each alpha carbons. This sometimes yields representations that are pretty frizzy. Turning this setting on will make the cartoon follow a smoother (but less conservative) path so that the representation is easier on the eyes. Use with caution, since false conclusions can be drawn by solely examining a smoothed cartoon trace. It is always best (for non-representation purposes) to also have a line trace so that the backbone is precisely located.
Sticks and Smooth Loops
When cartoon_smooth_loops is turned on and sticks are shown for some residue selection, often times the sticks don't touch the backbone or cartooned elements. To fix this, turn this setting off or enable cartoon_side_chain_helper. See the images below for an example.
Also, of note for this problem is Cartoon_flat_sheets.
set cartoon_smooth_loops, 1
set cartoon_smooth_loops, 0
I do not know precisely how the smoothed trace is generated, probably by some splining mode. Could someone more knowledgeable than me edit to be more precise ?