What is electron density map?

In X-ray crystallography, a representation that resembles a geological survey map of planes drawn through a crystal. It shows contours of equal electron density surrounding the individual atoms: steeper around heavier atoms; more shallow around lighter atoms.

How do you find electron density?

Free Electron Density in a Metal will have free electron density n = x10^ /m3. will have a number of atoms per unit volume n’ = x10^ /m3. The number of atoms per unit volume multiplied by the number of free electrons per atom should agree with the free electron density above.

What is electron density surface?

The electron density tells us the relative amount of negative charge that is located at each point. Each point on the solid surface holds 10 times as much negative charge as each point on the mesh surface.

How are electron density maps generated?

Crystallography Produces Electron Density Maps An X-ray crystallographic experiment produces an electron density map for the average unit cell of the protein crystal. The amino acid (or nucleotide) sequence of the crystallized polymer(s) is known in advance.

What are the contours of the electron density distribution?

A contour map of the electron density distribution (or the molecular charge distribution) for H2in a plane containing the nuclei. Also shown is a profile of the density distribution along the internuclear axis. The internuclear separation is 1.4 au. The values of the contours increase in magnitude from the outermost one inwards towards the nuclei.

How to read an electron density map in CCP4?

Loading a Map or MTZ FileThe Contour Display ObjectMap SlicesCustomising the Map DisplayMap drawing style preferencesSee also the tutorialon electron density maps. Loading a Map or MTZ File An electron density map can be read from a CCP4 map file or an MTZ experimental data file.

How can I clip an electron density map?

The electron density can also be clipped to show only the density within a given distance of a selected set of atoms. The Clip..sub-menu lists all of the model display objects for models associated with the map and if you choose one of these then the map will be clipped to the atoms in that display object. An example of map clipping is shown below.

Can a electron density map be read from a MTZ file?

Loading a Map or MTZ File An electron density map can be read from a CCP4 map file or an MTZ experimental data file. Loading an MTZ file is slower as the map needs to be calculated but there is an option to recalculate the map with a different grid spacing which can be useful in creating the optimum image.