Go to preferences->3d graph preferences, or click the "Graph Settings" button on the 3D display. You'll be greeted by a window similar to that on the right. Positions Per Tickmark are the number of positions to go before placing another tickmark. The same goes for the label, energy, and window sizes. The Edge Cutoff is used to decide where to draw the line edges for cliffs. The algorithm analyzes the local heights around each position. If a difference is above the cutoff, it draws the edge line (for the appropriate direction/height). In general, a lower edge cutoff will yield a graph with more edge lines. The "Show Mesh" option enables and disables the mesh -- the lines from energy point to point which are laid on top of and below the color polygons for entire energy graph.