FirstGlance in Jmol automatically alerts users to five kinds of covalent protein crosslinks, such as isopeptide bonds. It can also show the electron density maps, the best way to decide whether such bonds are real.
FirstGlance in Jmol: firstglance.jmol.org (This will always be the most recent version from the fastest server. If you google "firstglance" you may get obsolete versions or slower servers.)
Evaluating Protein Crosslinks: proteopedia.org/w/FirstGlance/Evaluating_Protein_Crosslinks (A tutorial with interactive molecules and examples of thioester, His-Tyr, and Lys-Cys NOS crosslinks.)
Introduction to Electron Density Maps: proteopedia.org/w/Electron_density_maps
Tutorials on the structures and functions of the CoViD-19 spike protein, DNA, hemoglobin, antibody, major histocompatibility proteins, collagen, lipid bilayers, the lac repressor, how the drug Tamiflu interacts with influenza virus, the Ramachandran principle vs. Phi and Psi angles in polypeptide protein chains, and much more: MolviZ.Org