Electron Density: Cloud vs. Isomesh "Map"
Bob Hanson and Eric Martz, April 2010 (Updated to JSmol January 2016)

Here is a piece of an electron density cloud. The cloud is calculated from a protein crystallographic X-ray diffraction experiment. Each point shows the electron density at a position in space. Darker points represent higher densities.

It is clear that the cloud has structure, but it is difficult to see the structure. By hiding lower densities, we can begin to see the structure.


   
Now let's show an isomesh* at 1.0 sigma.The isomesh is easier to see, so let's hide the cloud.Crystallographers fit an atomic model into the isomesh electron density map. The map is the data; the model is an interpretation of the data which has some uncertainty.

To zoom, position your mouse at the right edge of JSmol, then drag up and down.
Due to its very low electron density, hydrogen is usually not seen in electron density maps at protein crystal resolutions.

*An isoline is a line connecting points of equal value. An isomesh is a mesh made of isolines, e.g. connecting points with a value of 1.0 sigma of electron density.

The above example shows 3hyd, a 7-amino acid peptide with an electron density map resolution of 1.0 Ångstrom. Crystals of larger proteins typically have poorer resolutions. The median resolution of entries in the Protein Data Bank is 2.0 Ångstroms. Maps at these resolutions leave greater uncertainty in the atomic positions.

On the next page is shown an electron density map at 2.0 Å, highlighting regions of low and high uncertainty.


Adapted from Bob Hanson's Demo.