Molecular visualization of tRNA

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.

This is tRNA-Phe, structure determined by S.-H. Kim, PDB ID 6TNA. This is the classic L shape characteristic of all tRNAs. Note the coaxial stacking of the acceptor stem and the TYC stem, and of the anticodon stem and the D stem. Tertiary structure is held together by non-Watson Crick base pairs and specifically bound Mg++ ions. The chain is colored in a gradient from 5' (blue) to 3' (red or greenish depending on color space artifacts).

Small Jmol window..

Here are the scripts that lie beind the buttons, so you can see the syntax to use to make your own versions.

  1. Initial view
  2. Connectivity
  3. Triple pair
  4. Role of Mg++
  5. Spacefill
  6. Default view is done with in-line commands.: jmolButton("select all; wireframe 50; spacefill 50; color cpk; cartoons off; rockets off; backbone off; monitors off; trace off","Default rendering");
  7. Reorient

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