Supporting Information for: Mechanisms of Size Control and Polymorphism in Viral Capsid Assembly

Bond vector construction. Our models are derived from the T=1 and T=3 crystal structures of BMV capsids by associating each twofold or quasi-twofold symmetry axis (the dimer interfaces) with the center of a spherical subunit. We then draw a ‘bond’ at each interface between neighboring subunits, resulting in Fig. 1a. We construct the subunit geometries such that each subunit has a ‘bond-vector’ pointing from its center toward each of its interfaces, which are indexed as listed in Table 1. At the same time, we construct a table of interfaces, Table 1b, that specifies for each interface a pair of primary bond vectors, α and β, and a pair of secondary bond vectors, γ and δ. The primary bond vectors designate the interface on each subunit across which the favorable bond is formed. The secondary bond vectors, also one from each subunit, are used to define a dihedral angle. This interaction enforces directional specificity in the plane perpendicular to the primary pair, thereby creating a bond that resists torsion. During the simulation, we store the orientation of each subunit as a vector in a hybrid reference frame where the origin is the center of the subunit but the orientation is with respect to the global coordinate system. When the subunit experiences a torque, all its bond-vectors rotate rigidly – i.e. the bond vectors have no internal degrees of freedom that could change their relative orientations.