The Ramachandran Plot Window plots only values for the currently selected amino-acids of the current layer. The name of the current layer is drawn at the bottom left of the window. Amino-acids appear as a little cross with the exception of Gly that appears as a square. To know to which amino-acid a point belongs, simply place the mouse pointer onto a point or a group of points. Its (their) name(s) will appear at the top of the Window.
Omega, Phi, Psi and secondary structure assignment of the currently displayed points can be saved as a tabulated text-file for further analysis (Cmd + s on a Mac, Ctrl+s on a PC). Moreover, an image can also be exported (Mac only). Core and allowed regions as defined by Morris et al. ref  are also framed, and it is possible to select amino-acids that are outside of these regions in one operation with the appropriate item of the select menu.
Note: The Ramachandran plot can be used to directly modify a Phi/Psi angle of a residue with a direct feedback of the modification. All you need to do is drag a point at its new location. You can constrain the rotation around either of the Phi or Psi axis by holding down the "9" or "0" key while moving the point. By default it is the C-terminal part of the protein that will move, as a little 'c' drawn just below the help icon reminds you. If you want the N-terminal part to move, click on the 'c' that will be changed into a 'n'. If you want to move only a part of the backbone (and not the whole backbone up to the C-terminal), you must break the backbone between the last amino-acid you want to move and the first you want to stay fixed. This is done with the appropriate item of the tool menu.