A crystal structure is a model built to explain experimental data. Looking at the electron density around a residue or a ligand shows how well the data supports that part of the model. This matters before you rely on a structure for modeling or design.
For an X-ray structure, 3decision shows two maps:
The difference map has positive and negative peaks. 3decision colors them as most crystallography programs do, for example Coot:
A green peak next to a red one often means that a group is in the wrong place, for example a ligand flipped or modeled with the wrong substituent. The Assess structural quality use case shows an example.
Small peaks are common in flexible parts of a protein, at the surface and in the solvent. Strong peaks around a ligand or an active site are worth a closer look.
A map is a grid of density values. The 3D viewer draws a surface where the density equals the contour level (the Iso Value).
Typical starting levels are 1σ for the 2mFo-DFc map, and +3σ and −3σ for the difference map. These are the 3decision defaults. Lowering the level shows weaker density, but also more noise.
A cryo-EM map is the reconstructed density of the whole sample. There is no difference map. The right contour level depends on the map, so EMDB stores a level recommended by the authors.