Cuts act like a band, pulling the cut ends together when you wiggle the protein. A blue cut means the cut ends are too far apart, so the cut can't be closed. A yellow cut can be closed by clicking on it. To close the cut, wiggle until the cut turns yellow, then click on the cut. This should solve the puzzle. You can also try making your own cuts. Right-click (or control-click) on a segment, then select "Cut" from the wheel menu to insert a cut. Try inserting a cut between each segment, then wiggle and shake. Close the cuts again. This technique should get a high score.