The carbon atoms on the DNA are colored yellow to distinguish them from the protein. Red=oxygen, blue=nitrogen, for both protein and DNA.

How to zoom:Shift+left mouse.
How to identify an atom:Just hover over the atom. You will see something like [Arg]10:A O #69. This means you were hovering over the oxygen of arginine at postion 10 in the chain. The "A" refers to one chain, #69 is just a file postion, you can ignore that.
How to measure a distance:Right click the mouse when over the Jmol window. This brings up a menu, select "Measurement" and "Double click..". Now double click on one atom and then the atom you want to measure the distance to.