Defining the Contour Plane

By default, the contour plane is defined as the view’s XY plane. The plane can be defined in the Contour dialog’s Plane area. It is defined as the plane perpendicular to the vector defined by the specified Normal and Origin points in the dialog. The default origin point is (0,0,0), and the default point defining the normal vector is (0,0,1).

More complex plane definitions can be specified by clicking on the Define Plane button, which brings up the dialog seen below. There are two methods for defining the plane: Normal Vector (as described above) and Three Points (illustrated in the figure). In the latter method, you define the origin and two other points to define the contour plane (traditionally referred to as O, P, and Q). The easiest way to define the points is to specify atoms for them, but you can also enter lists of atoms (the average of their coordinates will then be used) or completely arbitrary Cartesian coordinates.

d_cplane.tif

Specifying the Desired Contour Plane

In this example, we are defining the contour plane as the one containing the carbon atoms, using the 3-points-definition method. The green lines in the View window indicate the normal vector (labeled N) at the origin (O) and the line OQ. The OP line is not visible in this view, as it mirrors the C-C bond between atoms 1 and 5.

The drop-down that defaults to Translate plane along ON allows the user to specify how much to shift the contour plane along a specified vector or how much to rotate it along a specified axis. This is useful if, for example, your target atoms define a relevant plane but it lies away from the molecule’s center of mass. The by text field allows you to specify the exact distance to shift the plane, or the slider allows you to see the plane update as you move it.