Jmol Tutorial Help
How to get the most out of molecular structure tutorials in Jmol.
A resource provided with the Jmol Tutorial-Authoring Template (JTAT)
available from the
Top Five 3D Molecular Visualization Technologies
at MolviZ.Org

Jmol tutorials work well in:

Can't see the molecule?

Please see this separate document.

Select Color, then Background, then click on a color. This will change the background color only until you

Use Select to select the portion of the molecule whose colors you wish to change. The number of atoms selected is shown in parentheses, on the menu, after the word Select.

After making a selection, use Color on the menu to apply a plain color, or a color scheme. These colors will remain only until you

  1. If spinning is on, turn it off by clicking Toggle Spinning below the molecule.
  2. Click on the blank black (or white) background near the molecule, in order to focus Jmol. (This is necessary on Macs, but you can skip it on Windows.)
  3. Simply touch (don't click) on an atom with the mouse. Hold the mouse still over the atom without moving it, which is called "hovering". After a short delay, a yellow message will appear near the mouse pointer (see snapshot at right) with an atom identification report. Clicking on an atom suppresses the hover report -- to see the report, simply move the mouse away and then back over the atom of interest.

The hover report may not work in Safari under Mac OSX 10.3 (Panther), but it does work under Mac OSX 10.4 (Tiger) and 10.5 (Leopard), and all versions of Windows. On Macs with 10.3, click on the atom and an identification report will appear in the status line at the very bottom left of the browser window.

The sequence number in the hover report (17 in the above snapshot) is that assigned by the authors of the molecular model (PDB file) you are viewing. It may or may not agree with the numbering in a different model of the same molecule, or with other published reports.

To measure the distance between two atoms, double click on the first atom. Now, as you touch other atoms, the distances will be shown on a red line connecting the atoms. Double click on a second atom to fix the distance report.

If you wish to cancel without fixing a distance report, simply move the mouse outside of the Jmol rectangle. If you wish to remove one already fixed report, double click on each of those two atoms again. If you wish to remove all distance reports, click the View button to refresh the molecular view.

You may also measure angles and dihedral angles by double-clicking on three or four atoms, respectively.

If you wish to explore the molecules in this tutorial on your own, you can do so with the links that display them in FirstGlance in Jmol, the easiest tool for general exploration of 3D macromolecular structures. These links are in the How To section at the bottom of each control panel in the tutorial.

You may also go directly to to initiate exploration of any available molecule of your choosing.

The Jmol Menu provides access to a wide range of Jmol's capabilities. The menu is good for exploring what Jmol can do, or for making a small number of changes to the molecular view. However, it is too cumbersome for extensive, self-guided exploration, which can be done much more easily in FirstGlance in Jmol (previous section, above).

Jmol's Console is where you can enter typed commands to change the molecular view while using a tutorial. For those who have learned some of Jmol's command language, this is more efficient than using Jmol's menu. The Console can be opened from Jmol's menu.