Electron density maps: Difference between revisions

Fo-Fc is a "difference map". It shows where the experimental density and the atomic model disagree<ref name="silvaggi" />. If the atomic model fitted the experimental density perfectly (and there were no experimental noise), the difference map would have no densities. Typically, it has '''{{Font color|red|negative densities}}''' (atoms in the model where there is no electron density, isomesh conventionally colored '''{{Font color|red|red}}''') and '''{{Font color|blue|positive densities}}''' (electron density where there is no atom in the model, isomesh typically colored '''{{Font color|blue|blue}}''' or '''{{Font color|green|green}}'''). The isomesh typically represents the boundaries at ±3 sigma, namely, regions with a substantial level of disagreement. Because ±3 sigma is a relative measure, there will always be features in the Fo-Fc Difference Map. When the atomic model contains glaring mistakes, these peaks will correspond to real features. When the atomic model agrees optimally with the electron density, these peaks will mostly correspond to experimental noise.