Fig. 3. Multiple alternative coordinates and multiple alternative identities.

A unique and distinctive feature of MSL is the ability of storing multiple alternative coordinates in an Atom, and multiple alternative amino acid identities in a Position. Panels a and b illustrate a case in which a Phe side chain has three alternative conformations, one of which active (green), two inactive (gray). The internal redirection of a pointer switches the active conformation of the side chain's atoms from 0 to 1, changing rotamer. Panels c and d show a case in which a Position contains two alternative residues or amino acid identities. The redirection of a pointer switches the active amino acid identity from Phe to Lys. These two features – multiple coordinates and multiple identities – can be combined, and a Position can load multiple amino acid types in multiple conformations, a feature that greatly eases the development of protein design code.