AbstractCells function through dynamic interactions between macromolecules. Detailed characterization of the dynamics of large biomolecular systems is often not feasible by individual biophysical methods. In such cases, it may be possible to compute useful models by integrating multiple sources of information. We have previously developed an integrative method to model dynamic processes by computing biomolecular heterogeneity at fixed time points, then generating static integrative structural modes for each of these heterogeneity models, and finally connecting these static models to produce a scored trajectory model that depicts the process. Here, we demonstrate how to compute, score, and assess these integrative spatiotemporal models using our open‐source Integrative Modeling Platform (IMP) program (https://integrativemodeling.org/).