Electron Density: Cloud vs. Isomesh "Map"
Bob Hanson and Eric Martz, April 2010
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.

To zoom, position your mouse at the right edge of Jmol, then drag up and down.


*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 a separate page is shown an electron density map at 2.0 Å.

Adapted from Bob Hanson's Demo.