Molecular visualization of idealized A-form RNA

This set of web pages 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. Currently the page runs Jmol 11.4.5.

Here is the color coding scheme used in many of the scripts:

Major groove -- red
Minor groove -- yellow 		Watson-Crick H-bonding face -- blue
major groove and WC face -- purple
major groove and WC face -- green 		backbone -- white, with orange P atoms
other atoms -- brown. Sugar protons not shown.
imino protons -- pink

The buttons below the Jmol window are generally intended to be clicked in order. There are some glitches if you show/hide waters. For more sophisticated commands, bring up a console window with a right-click/control click in the Jmol window.

The list on the right takes you to each of the other Jmol pages in the DNA/RNA tutorial.If your screen is large enough, use the "big" pages.

Go to small ideal B-DNA

Go to big ideal B-DNA

Go to small real B-DNA

Go to big real B-DNA

Go to small ideal A-RNA

Go to big ideal A-RNA

This is real A-RNA from an NMR structure by the Butcher lab (1SYZ). Note the extrahelical base in the stem and the loop closing the top. The "animate" button loops through different structures that are all comsistent with the NMR data, illustrating either flexibility of the molecule or limitations of the method.

Go to big real A-RNA
DNA/RNA tutorial home. Teaching resources. J. Kahn home page.