Generate Contours

Contours are two dimension projections of cube data into a plane. They also use the cubes generated in the Surfaces and Contours dialog. You can use the items on the Contour Actions menu to create a new contour (New Contour), to display or hide a contour (Show Contour and Hide Contour), and to remove a contour (Remove Contour). The figure below illustrates an example contour display.

r_contour.tif
Example Contour Plot
This contour projects the HOMO into a
plane perpendicular to the C=O bond.

The figure below illustrates the dialog that results from selecting Contour Actions=>New Contour.

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The Generate Contours Dialog

This dialog will generate a contour from an existing cube created or loaded previously via the Cube Actions menu in the Surfaces and Contours dialog. It contains four subareas:

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 in the figure 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.

Once the contour plane is defined, you can move it further using the popup and other controls in the bottom part of the dialog. The plane can be translated or rotated about the various defined axes.