Background

Electron density maps are the direct results of X-ray crystallography, and the atomic model is the interpretation of the map. So if we want to check the uncertainties of one published model, it's a must to examine the correspondence bwtween its density map and itself.

Methods

For me, density of one crystal structure can be accessed through two ways.

One is to check it online, using PDB, and the others is to use software coot.

Online Tool

1. Go to the Summary page of one pdb, such as https://www.rcsb.org/structure/3ehv
2. Go to the subpage 3D View, such as https://www.rcsb.org/3d-view/3EHV
3. In the right part, you can find a button Density. Click it, then the button Enable
4. Click one residue, and the density map will show.

Local software

Notes

References

Basic information File format