As illustrated, the four stages include: (1) gathering all available experimental data and prior information; (2) translating information into representations of assembly components and a scoring function for ranking alternative assembly structures; (3) sampling structural models; and (4) validating the model. In this example, representations of the components of a complex are based on models of its components. Some component representations are coarse-grained by using spherical beads corresponding to multiple amino acid residues, to reflect the lack of information and/or to increase efficiency of structural sampling. The scoring function consists of spatial restraints that are obtained from CX-MS experiments and a cryo-electron tomography density map. The sampling explores both the conformations of the components and/or their configuration, searching for those assembly structures that satisfy the spatial restraints as well as possible. The result is an ensemble of many good-scoring models that satisfy the input data within acceptable thresholds. The sampling is then assessed for convergence, models are clustered, and evaluated by the degree to which they satisfy the input information used to construct them as well as omitted information. The protocol can iterate through the four stages until the models are judged to be satisfactory, most often based on their precision and the degree to which they satisfy the data. Finally, the models and data are deposited into PDB-Dev (https://pdb-dev.wwpdb.org) (Burley et al., 2017; Vallat et al., 2018).