foldit dev comment: we strongly discourage doing this procedure as this protocol will not guarantee that your high-scoring structure will be reported to the servers thus defeating the key purpose of playing this game.
The steps to play Foldit offline under Windows follow.
You will need a software firewall like Sygate Personal to accomplish the goal. It can be accomplished using the default Windows firewall but it's a bit less elegant, at least for me.
Once Sygate Personal or a similar firewall is installed and operating: (note that this example uses Sygate since that's what I use and I have no details on other products to that end.)
1. Open foldit
2. Once the main foldit menu is shown (after logging into the game the "normal way"), use Sygate to block internet traffic to and from the foldit site. This will not impinge on your game play or your competition score, except that you will need to re-load foldit and unblock it from communication to upload your score following offline play.
In Sygate, the process is pretty staightforward:
a) open the Sygate console by clicking on the symbol in your tray (bottom right side of the window)
b) in the lower portion of the console, under the heading of "running applications", locate the foldit.exe.
c) Right click the icon and choose "Block"
3. When you are done playing offline, make sure to re-enable internet communications between the program and the foldit website so that your score can update on reload of the application as follows:
a) open the Sygate console by clicking on the symbol in your tray (bottom right side of the window)
b) in the lower portion of the console, under the heading of "running applications", locate the foldit.exe.
c) Right click the icon and choose "Allow"
Since you're already logged in as <username> to the game, your work is already assigned to you.