Ramachandran plots are “dynamic”. When you edit the molecule (i.e. move the coordinates of some of atoms) the Ramachandran plot gets updated to reflect those changes. Also the underlying \phi/\psi probability density changes according to the selected residue type (i.e. the residue under the mouse in the plot). There are 3 different residue types: GLY, PRO, and not-GLY-or-PRO 1.
When you mouse over a representation of a residue (a little square or triangle 2) the residue label pops up. The residue is “active” i.e. it can be clicked. The “graphics” view changes so that the C\alpha of the selected residue is centred. In the Ramachandran plot window, the current residue is highlighted by a green square.
The underlying distributions are taken from the Richardson's Top500 structures http://kinemage.biochem.duke.edu/databases/top500.php.
The probability levels for acceptable (yellow) and preferred (red) are 0.2% and 2% respectively.
You can change the contour levels:
(set-ramachandran-plot-contour-levels 0.025 0.003)
You can change the “blocksize” (the default is 10 degrees) of the contours using
(set-ramachandran-plot-background-block-size 5)
These comes into effect when a new plot is created (it doesn't change plots currently displayed).