Biological models bring the molecular world of cells into view, enabling experts and the public to explore and understand biological discoveries. Building mesoscale models requires organizing many molecular components into spatial arrangements that can be revised as evidence and interpretations develop. We present MesoCraft, a browser-based tool for structural biologists centered on interactive procedural modeling. User-defined rules generate collections of molecular instances, while a geometry-node editor and visual feedback support authoring and revision of their spatial relationships. Beyond model construction, MesoCraft integrates exploration and communication, enabling researchers to inspect molecular organization and create guided animations that highlight key spatial relationships. By connecting modeling, exploration, and explanation in a unified workflow, MesoCraft allows insights gained during exploration and communication to inform iterative model refinement, supporting the development of mesoscale models into visual narratives of cellular organization. A demonstrative deployment of the tool is available at https://mesocraft.kaust.edu.sa/.

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