Modelling structures in cryo-EM maps

•Approaches to the structure determination and modelling of macromolecular assemblies depend on the resolution of their cryo-EM map.•Insights into structure dynamics can be obtained starting from both atomic structures and cryo-EM maps.•Integrative modelling approaches are key for characterising structures and functions of assemblies at mid-to-low resolution.•Experimental and computational methods for model validation are key for successful and reproducible modelling attempts.