In the Side Panel of both linear and secondary structure 2D
views, you can choose to color structure symbols and sequence
residues according to the probability of base pairing / not base
pairing, as shown in figure 22.4.
In the linear sequence view (), this is found in Nucleotide info under Secondary structure, and in the secondary structure 2D view (), it is found under Residue coloring.
For both paired and unpaired bases, you can set the foreground color and the background color to a gradient with the color at the left side indicating a probability of 0, and the color at the right side indicating a probability of 1.
Note that you have to Zoom to 100% () in order to see the coloring.