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.

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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 modelled in the wrong place -- in red.