EDMs

Electron Density Maps
Eric Martz, April 2010; JSmol January, 2016; More buttons January 2019.

Salmonella flagellin, 1io1, resolution 2.0 Å. The crystallized fragment had 398 residues; 395 residues (56-450) have coordinates. 2.0 Å is the median resolution of entries in the Protein Data Bank.

Coloring by temperature (B factor):

Temperature (B factor):
Local uncertainty:
Disorder in crystal:

Low

High

Lets examine the blue segment 116-125.

Unlike the 1.0 Å map, this 2.0 Å map does not resolve to a sphere for each non-hydrogen atom. Nevertheless, in this low temperature region, it is clear where each atom belongs.

Now let's examine the map for a high-temperature region. This portion of the map is a lot rougher. Some atoms of the model are outside the 1 sigma map. Uncertainty about the positions of atoms is much higher.

Here is a side-by-side comparison.

Zoom: Position your mouse just inside the right edge of Jmol, then drag up and down.
Slide: Hold down Shift, double-click on the molecule, holding down the second click, then drag.

Here is an explanation of how isomesh maps are derived from electron density data.

Technical: The electron density map, in CCP4 format, was obtained from the Uppsala Electron Density Server. Typical maps require more memory than the 100 Mb default allocated to java. Therefore, the Jmol application was started in the OS X terminal with this command:

java -Xmx1024m -jar ~/Downloads/jmol-app/Jmol.jar&

The electron density isomesh was then created with the following script:

load 1io1.pdb.gz;
isosurface s_one color [x800080] within 1.5 {*} "1io1_map.ccp4.gz" mesh nofill;
write 1io1-map-1sigma.jvxl

Loading and creation of the isomesh took several minutes. For ccp4 maps, Jmol defaults to 1 sigma. The ccp4 file was 12 Mb; 2 Mb gzipped. The jvxl (Jmol voxel) file was 412 Kb; 156 Kb gzipped. Saving the isomesh as a jvxl file resulted in ~13-fold reduction in file size, but the jvxl file contains only the 1-sigma isomesh within 1.5 Å of the asymmetric unit. In contrast, the ccp4 map contains the map for any portion of the crystal unit cell, and an isomesh can be generated from the ccp4 file for any specified density cutoff (sigma level). Scripts for displaying the jvxl file can be seen by viewing the source of this page.