Molecular visualization of real B-form DNA

This web page uses the open-source Java Applet program Jmol, a proposed platform-independent replacement for Chime and Rasmol, neither of which is available in an OS X native version. You will need a relatively recent Java Virtual Machine to use it.

The buttons below are generally intended to be clicked in order, with some glitches if you show and hide waters. Use the console for more sophisticated commands.

This page shows a view generated in Pymol similar to the final rendering below, emphasizing the spine of hydration/sodium.

This is real B-DNA from Loren Williams group, PDB ID 355D. Note that it is not perfect B-form: groove widths vary, base pairs roll and tilt, there are several buckled or propellor-twisted base pairs. The "NMR" view doesn't work, because as an X-ray structure this has no hydrogens.

Go to big real B-DNA

Go to small real B-DNA

Go to big ideal B-DNA

Go to small ideal B-DNA

Go to big ideal A-RNA

Go to small ideal A-RNA
DNA/RNA tutorial home. Teaching resources. J. Kahn home page.