Difference density map

In protein crystallography, a difference density map shows the spatial distribution of the difference between the measured electron density of the crystal and the electron density explained by the current model.

Conventionally, they are displayed as isosurfaces with positive density -- electron density where there's nothing in the model, usually corresponding to some constituent of the crystal that hasn't been modelled, for example a ligand or a crystallisation adjutant -- in green, and negative density -- parts of the model not backed up by electron density, indicating either that an atom has been disordered by radiation damage or that it is in the wrong place -- in red.