Closely packed myosin filaments are an example of a disordered biological array responsible for the contraction of muscle. X-ray fiber diffraction data is used to study these biomolecular assemblies but the inherent disorder in muscle makes interpretation of the diffraction data difficult. Limited knowledge of the precise nature of the myosin lattice disorder and its effects on X-ray diffraction data is currently limiting advances in studies on muscle structure and function. This thesis covers theoretical and computational efforts to incorporate the myosin lattice disorder in X-ray diffraction analysis. An automated image analysis program is developed to rapidly and accurately quantitate the disorder from electron micrographs of muscle cross-sections. The observed disorder is modelled as an antiferromagnetic Ising model and the model verified using Monte Carlo simulations. Theory and methods are developed for efficient calculation of cylindrically averaged X-ray diffraction from two-dimensional lattices that incorporate this disorder.