Jmol Tutorial Help
How to get the most out of molecular structure tutorials in Jmol.
available from the
Top Five 3D Molecular Visualization Technologies
Jmol tutorials work well in:
System Preferences, then
Software Update). Importantly, these updates keep java up to date.
Can't see the molecule?
Please see this separate document.
Background, then click on a color.
This will change the background color only until you
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
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
Toggle Spinningbelow the molecule.
The hover report may not work in Safari under Mac OSX 10.3
it does work under Mac OSX 10.4 (
Tiger) and 10.5 (
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
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.