The final test starts with an extended chain, with a single objective: make more helices.
This puzzle presents a protein that's a straight extended chain, with all its segments in a line.
The goal is to add some secondary structure using the blueprint tool.
Follow the hints to open the Blueprint window. The related Building Blocks window opens at the same time.
The Blueprint window shows the secondary structure and current amino acid for each numbered segment.
The Blueprint and Building Blocks windows, with an outline of how to make more helices.
The entire protein is loop at the start. In the Objectives, the one objective gives a goal: "turn 15 more residues into helices".
The entire protein is also alanine, so the code A appears for every segment. This puzzle doesn't allow changing the primary structure, so everything is going to stay alanine.
The first step is to drag the helix shape, found at the top left of the Building Blocks window, over to the top line of the Blueprint window. Drop the helix shape at the left side of the top line in Blueprint.
The second step is to "paint" helix across the rest of the protein. In the Blueprint window, click on the right end of the helix shape, and drag across the top line. The top line changes to helix as you drag. You'll need to scroll to see all of the protein, so you'll need to click and drag more than once.
A single giant helix isn't very interesting, but you can just click "Idealize SS" at this point to finish the puzzle.
If you want to continue, the third step is to drag some helix-helix building blocks over to the Blueprint window. These building blocks are typical shapes found in real proteins where a section of loop connects two helices. The first building block has a single segment of loop connecting two helices.
A successful design, with four helices.
Click on one of the helix-helix building blocks, and drag it over to the Blueprint window. The tool will automatically change the connecting segments to loop. Try dragging two or three building blocks over, making three or four helix sections of roughly equal length.
After adding some building blocks, the fourth step is to click the "Idealize SS" button. Most of the segments marked as helix are actually still a straight chain. The "Idealize SS" button gives them the shape of a perfect helix.
Just the "Idealize SS" button may give you enough points to complete the puzzle. If not, the fifth step is to wiggle. In most cases, wiggling for a bit should gain the necessary points. If not, there's always resetting the puzzle and trying again.
