Secondary structure is assigned to every accepted conformation in order to maintain a structural propensity list, which is needed to determine each residue's conformational bias. Secondary structure assignments are based solely on backbone torsion angles. For this purpose, φ, ψ space is partitioned into 144 bins, each represented by a two-letter code as show here.

We refer to these bins as mesostates and to the two-letter codes as mesostate codes. To assign secondary structure, φ, ψ-values for each residue are mapped onto the corresponding mesostate code. In turn, the mesostate codes are mapped into a secondary structure class: H (helix), E (strand) P (PII), T (turn) or C (coil). Definitions for the different secondary structures are explained here.

Note on ψ in the LINUS code:

The Z-matrix description of the protein makes it more efficient to describe ψ as the angle

N(i) - CA(i) - C(i) - O(i)

instead of

N(i) - CA(i) - C(i) - N(i+1)

Consequently the internal "psi" in LINUS working code is off by 180 deg. to the standard definition of ψ. However, all ψ values reported are corrected.