Show the electron density of a public X-ray structure when you want to check how well the model, for example a ligand, fits the experimental data.
Prerequisites: the structure is open in the Workspace. It is a public X-ray structure.
- In the Collections panel, open the ⋮ menu of the structure and select Fetch electron density.
- In the dialog Fetch electron density maps from RCSB, keep 2mFo-DFc map selected. To also see the difference map, select mFo-DFc map.
- Click Fetch.
Result: after a few seconds the maps appear in the 3D viewer and in the State Tree, under Density Maps. The 2mFo-DFc map is blue at 1σ. The difference map is green at +3σ and red at −3σ.
- Compare several structures: superpose them first (see How to superpose structures in the Workspace), then repeat the steps for each structure. Each map moves with its structure and is listed separately in the State Tree. Give each map its own color to tell them apart.
- Change the contour level or the color: see How to change the contour level or color of a map.
- Hide or remove a map: in the State Tree, click the eye icon of the map, or open its ⋮ menu and select Remove element.