The first step in this puzzle is to click on "Show Alignment" in the Actions menu. This opens the Alignment Panel. The protein becomes a translucent grey ghost, and a ball-and-stick model appears.
The primary sequence of the ball-and-stick template is shown below the current protein's sequence. The amino acid codes for segment 1 through 38 are the same in the protein and the template. The template has two additional amino acid at the end.
When you click on the "play" button (the small triangle) in the Alignment Panel, the protein "threads" to the shape of the template.
After you thread the protein, all that's necessary to shake and wiggle.
Technical stuff: the alignment tool shows the amino acid codes with a colored background. Amino acids with the same color are similar, and might be used to substitute for each other. For example, "D" (aspartate) is dark blue, and so are "E" (glutamate) and "N" asparagine.