Basic Threading. The Alignment panel is displayed. A ball-and-stick model shows the shape of the template, while the protein is greyed out. Clicking the 'play' button threads the protein to the shape of the template.
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.
Madde's "Basic Threading" video
Loci's "Basic Threading" video
In the Alignment Panel, the primary structure of the protein is shown as a sequence of one-letter amino acid codes at the top. Also, the segment number is shown above each code.
Alignment Panel. The amino acids D, E, and N have a blue background, which means they are similar.
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.