DNA-RNA Structure Tutorials

This tutorial requires Netscape Navigator 2.0 or higher and the Chime plug-in for visualizing PDB structures.

Your window should be as wide as the bar below for optimal viewing.


If everything is working, the following B-DNA molecule should be visible:

You can manipulate the orientation of the molecule and change its display using the mouse.


For the most part, you will not have to manipulate the molecules yourself, instead, you will be guided through the manipulations by using buttons throughout the tutorial.

To see a button in action, try this one: <>.

The buttons manipulate the coloring and orientation of the molecule to correspond to the tutorial text for you. If you change the display yourself, clicking the buttons will usually correct the display. If not, reload the page. On the pages that follow, you will find buttons both in the text and collected in a frame containing all the buttons used in the tutorial.
Below is a table summarizing mouse commands:

Action Windows Macintosh
Rotate about X,Y axis Drag Left Mouse Button Drag Mouse Button
Show Chime's Menu Click Right Mouse Button Hold Down Mouse Button
Zoom In Shift Key-Drag Left Mouse Button Shift Drag Mouse Button
Rotate about Z axis Shift Key-Drag Right Mouse Button Shift & Command Keys-Drag Mouse Button
Translate in X,Y plane Ctrl Key-Drag Right Mouse Button Command Key-Drag Mouse Button
Move Z Slab Plane Ctrl Key-Drag Left Mouse Button Ctrl Key-Drag Mouse Button

Try using some of the mouse commands on the molecule above. First, activate the Chime menu by holding down the mouse button (or clicking the right button). Stop the rotation by slecting "rotation" under the menu and selecting "Stop". Now try rotating the molecule yourself by gragging the mouse around. You can also try some of the options for changing the display listed in the menu if you like.
You will also find links to other parts of the tutorial as underlined text.
Some of the structure files are quite large, depending upon the molecule (up to 100's of Kbytes), so be patient while the pages come up. Once the molecule is loaded, the demonstrations move along as fast as you want.

Available tutorials

Comparison of A, B, and Z DNA

tRNA structure

Nucleotide numbering help
GroupI intron:
Full Structure
P4-P6 domain

Hammerhead Ribozyme:
Pley, et al.
Scott, et al.

Model of an RNase P RNA Tertiary interaction
MATa1/alpha2-DNA Complex

Nucleosome core particle
U1A Protein-RNA structure

Also Check:
Collection of Red-Blue stereograms of many of these molecules You will need Red-Blue 3D glasses to view these.

Please send comments or suggestions to:Jim Nolan
Or see my research web page

Based on the E. coli DNA polymerase III beta subunit tutorial
developed by David Marcey at The Online Macromolecular Museum
of California Lutheran Univerity
Be sure to visit it.
You can also find a directory of moleular tutorial web pages at the World Index of BioMolecular Visualization Resources