The Greek letter phi is used to indicate angles in biochemistry.
In Foldit, phi and the closely related psi most often refer to the two critical angles of the protein backbone. Phi and psi are graphed in the Rama Map. For a given segment of the protein, phi is the angle between the peptide bond of the previous segment and the alpha carbon, and forms the horizontal x-axis of the Rama map. See Ramachandran Map for more.
Both upper- and lower-case phi typically look like an oval with a vertical stroke through it. The upper-case letter has a closed oval, while the lower-case phi is slightly open. In some fonts, it's easy to confuse lower-case psi with lower-case phi, but phi has a more open "trident" shape.