I believe that you can press Q and it will center your protein.
Please re-open this feedback tracker if that does not work.

I tried Q and all it did was close Foldit. The Help says "Mouse on a segment: Focus on segment: Q" but I cannot put my mouse on the segment and press Q because I cannot see any of my segments.

I thought about my problem some more this morning and realized that the protein had folded behind the camera instead of off the bottom of the screen (I had not learned about zoom yet). That is why I could not get it back by moving the protein up or down.

What would help would be for the "Reset Puzzle" to reset the location of the puzzle and camera angle to the original location and angle as when the puzzle is first started. Another option would be is for the View Options menu's "Default view options" or some other option to reset the puzzle location and camera angle to the original location and angle as when the puzzle is first started.

I hate losing this puzzle because I was not done playing with it yet.

I found the solution on http://foldit.wikia.com/wiki/Shortcut_Keys.

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If your protein gets "lost" somewhere off the screen, this will recenter the protein on your screen.