Electron Density: Cloud vs. Isomesh "Map"
Bob Hanson and Eric Martz, April 2010 (Updated to JSmol January 2016)
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 JSmol, then drag up and down.
hydrogen is usually not seen
in electron density maps at protein crystal resolutions.
is a line connecting points of equal value. An
is a mesh made of isolines, e.g. connecting points with a value of 1.0 sigma of electron density.
The above example shows
, a 7-amino acid peptide with an electron density map
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.
Bob Hanson's Demo