Jmol Tutorial Help How to get the most out of molecular structure tutorials in Jmol. Can't see the molecule? Troubleshooting. Powerpoint® Slides: Presenting Molecular Views from Jmol Different Background Color Different Color Scheme Identifying Atoms, Residues, Chains Measuring Distances or Angles FirstGlance in Jmol Advanced Uses: Jmol Console | 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:

- Windows (Vista, XP, ME, 2000) in Internet Explorer or Mozilla Firefox. We recommend installing all high priority Windows Updates. Some Windows systems may need installation or updating of java. Simply go to java.com and follow instructions for the free java download and installation.
- Mac OS X (10.3, 10.4, 10.5) in Safari or Mozilla Firefox. Safari works better with Jmol. We recommend installing all Apple Software Updates (Open System Preferences, then Software Update). Importantly, these updates keep java up to date.
- linux in Mozilla Firefox. Java is required, and installing a current version of java is recommended.
- Other browsers, such as Opera, Camino, Konqueror, etc. may not display Jmol tutorials well, or at all.

Can't see the molecule?

- No molecule at the outset. This is common with Windows systems because they are often supplied without java. Java is required by the Jmol applet, as well as many other websites and applications. Java is free, and its installation in Windows is quick and easy. Simply go to java.com and follow instructions for the free java download and installation.
- Molecule stops appearing after seeing many molecular views. The Java startup message may remain indefinitely, or you may see a blank white Jmol. Sometimes this happens in a long tutorial with many molecular views, or after complex molecular views with surfaces or orbitals.
  Try reloading the page, or better yet, try holding down the Shift key while clicking your browser's reload.
  If reloading doesn't work, or if the molecule fails to appear soon after a reload, simply quit your browser and then start a new session. Make sure you close all browser windows (on Windows) or quit (on Macs) to stop the browser application. This also stops java and clears its memory, which is the underlying problem.

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 firstglance.jmol.org 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.