The previous puzzle demonstrated how to apply a building block to the protein. This puzzle shows how to remove or replace a building block.
As in the previous puzzle, open the Blueprint tool. Pick one of the building blocks, and drag its template over to the sequence. (These are the same actions as in the previous puzzle.)
The protein changes shape, but the puzzle does not complete.
There are two ways to complete this puzzle.
One way is to remove the template from the sequence. Click inside the box that highlights the template and drag. The box disappears, but the protein retains the shape created by the template. Shake to complete the puzzle.
Replacing the template is the other way to complete the puzzle. This is the method suggested by the help popups. Apply one template, then drag a second template over it. The second template must be the same size or larger than the first template, and it must completely cover the first template. When you completely cover the first template, the puzzle completes.
Applying different templates can be useful as you're designing a protein. But removing templates is a key to producing a successful design. The templates have invisible constraints that are similar to bands. The constraints hold the parts of the protein covered by templates tightly in place, not allowing them to move or change shape very much. That's fine to start out, but the sections covered by templates will probably need to move at least a little.
Removing templates lets the corresponding parts of the protein move around when you wiggle the protein. If the protein is fairly stable, the template sections should only change slightly when you wiggle after removing the templates.
The building block shapes are found in natural proteins, but no two proteins will have exactly the same shape. The building block shapes are averages based on similar shapes found in different experiments on different proteins. These shapes are a useful starting point for proteins you design, but they'll change as you apply finishing steps to your work.