Structure Mode is a set of tools that allow the user to manipulate the secondary structure of a protein.
When you download a protein puzzle from FoldIt, they will sometimes be a collection of helices (spiral fat balloons), sheets (flat tiles) and loops (thin tubes). These "secondary structures", as they are called are not "real", they are just a convention used to depict certain common structures regularly found in proteins. The game allows you to override those choices of secondary structure and force them to be shown as something else instead.
It is common, for example, to change everything to loops to make local-wiggling easier. Or to make helices and sheets so you can apply the Tweak tools where you want them. The game itself seems to not care how you decide to "paint over" these secondary structures, and you can always press CTRL+"E" on the keyboard to restore them all back to the default.
Proteins will often arrive with no secondary structure at all; the game wants you to apply your own choices. It's useful to build helices and/or sheets for rotation at places you think it might help, but you certainly don't have to do so.
The "Primary Structure" (there's a secondary, so there must be a primary, right?) is the sequence of amino acids that composes the protein.
Fold.it's blog described Structure Mode as follows, in a post dated June 9, 2008. (The post has since expired from the front page, but it can still be accessed):
- Structure Mode: when you switch to structure mode, you can change the type of structures the protein is made up, between helices, sheets, and loops. This will have an effect on rebuilding; you can make new helices or sheets, or try to find better loops! Left click and drag to paint existing structures across the backbone. You can also select directly with the ctrl/right-click pie menu.
Structure mode can also be entered by pressing "2" on the main keyboard. It is one of two current modes in the game, the other being Pull Mode.