CryoEM maps are full of potential

•Maps derived by X-ray crystallography display electron density, whereas maps derived by electron microscopy display Coulomb potential.•Negatively charged oxygen can result in attenuated positive potentials and even regions of negative density or ‘holes’ in Coulomb potential maps.•Biological molecules are exquisitely sensitive to damage from electron irradiation, especially the carboxylates of acidic amino acids.•A challenge in the interpretation of Coulomb potential maps is distinguishing the relative contributions from the charged states of oxygen atoms versus radiation damage.•High-resolution Coulomb potential maps can reveal information lacking in electron density maps, including protein and ion charged states, bond visualization and the presence of hydrogen atoms. Electron microscopy is based on elastic scattering due to Coulomb forces between the incident electrons and the sample; thus, electron scattering is dependent on the charge distribution in the sample. Unlike atomic scattering factors for X-rays, electron scattering factors for some atoms are strongly dependent on scattering angle, and the scattering factor for ionic oxygen is negative at low scattering angle. This phenomenon can result in a significant negative contribution to Coulomb potential maps by oxygen and can result in deviations in the positions of positive map features from atomic centers. An important factor that can also complicate the interpretation of cryoEM maps is the exquisite sensitivity of macromolecules to damage from electron irradiation, especially the carboxylates of acidic amino acids. Ideally, when compared with electron density maps derived by X-ray crystallography, Coulomb potential maps can provide additional details about the electrostatic environment and charge state of atoms. Enhancements in model building, refinement and computational simulation will be required to realize the full potential of EM-derived maps to reveal deeper insight into the electronic structure and functional properties of macromolecular complexes and their interactions with binding partners, ligands, cofactors, and drugs.