Exploiting the full potential of cryo-EM maps

The Coulomb potential maps generated by electron microscopy (EM) experiments contain not only information about the position but also about the charge state of the atom. This feature of EM maps allows the identification of specific ions and the protonation state of amino acid side chains in the sample. Here, we summarize qualitative observations of charges in EM maps, discuss the difficulties in interpreting the charge in Coulomb potential maps with respect to distinguishing it from radiation damage, and outline considerations to implement the correct charge in fitting algorithms.