To explore the electron density of the structure 233D (a short piece of DNA containing some sulfur-modified sugars), choose one of the two scenes below (either the entire molecule, or just a base pair. The latter will load faster and is less confusing, so maybe start with the base pair).
The following is the command to fetch the electron density from the pdbe.org database and display it around the selected atoms:
isosurface s_one sigma 1.0 color blue within 1.5 {selected} "http://www.ebi.ac.uk/pdbe/coordinates/files/233d.ccp4" mesh nofil
Electron density
Click on the following buttons to display electron density at different contour levels. One sigma means to show the area (within the chicken wire) that has values higher than one standard deviation over the mean. The higher the sigma, the less density you see (but you get to see the highest peaks in the density).
The peaks are mostly around the phosphorous atoms. P has about twice as many electrons as C, N and O, so it is expected to have roughly twice the electron density (and, even more roughly, twice the maximum electron density at the center of the atom).
At 3 sigma, you begin to see other parts of the structure when it is highly ordered. You also see the sulfur atoms, which are also third row elements.
This is a good contour level for modelling. You can see evidence for most of the atoms, but the level of noise is not that bad.
If you don't see your model at 1 sigma, you probably should not put in those atoms. At this level, you see a lot of solvent molecules and a lot of noise.
