Cryo-EM atomic model refinement using CryoNet.Refine v1

This protocol describes the installation and use of CryoNet.Refine for density-guided refinement of atomic models against cryo-electron microscopy maps. It covers software setup, preparation of an aligned starting model and density map, execution of refinement, and inspection and validation of the resulting model. A human CNT3 example demonstrates the workflow and produces a refined mmCIF model for comparison with the starting structure. Users can then apply the same procedure to their own aligned model–map pairs.