Organic Chemistry at Penn State: Jmol Help

Jmol applets can be a lot of fun, but you need to learn a little about their operation and menus to take the full advantage of the molecular information they contain. Jmol is Java-based program that is completely and safely executed on your computer, independently of the operating system, as long as you have Java installed and your browser is Java-script enabled. You may learn much more about the applet and even download your own (desktop) version at Jmol website or Jmol wiki pages.

Here are two Jmol applets for illustration purposes. One represent a small molecule (8 atoms), while the other shows a relatively large protein-DNA complex (1762 atoms) .

propenal (acrolein)

Protein - DNA complex (1D66)

Here you can play with a molecule of a simple conjugated aldehyde. The file contains structural data, vibrational data, and some details of electronic structure. For now you just want to get comfortable with the applet. Follow instructions on this page to get a flavor of what can be visualized.

What you see here is an X-ray crystal structure of a complex between GAL4 (yeast transcriptional activator) with 17-base pair DNA sequence. It is a synthetic construct that illustrated protein-DNA interactions and gives us an opportunity to explore Jmol display capabilities for large bio-molecules.

Basic Operations

Start with some basic mouse manipulations. After some practice open the menu and stop the spinning (Spin -> Off). Then, practice some measurements. Approximately, how many times is the protein-DNA complex longer than acrolein?

	left mouse button	middle mice button (when available)	right mouse button
rotate around X, Y
rotate around Z	hold Shift and		hold Shift and
zoom	hold Shift and
	or use mouse wheel
move along X, Y (translate)	double click, hold down on the second click, and	double-click, hold down on the second click and	Ctrl and
	you may click on a molecule or anywhere with the applet
restore and center	hold Shift and double click	double click
	you must click with the applet but away from the molecule
open menu	Ctrl and click		click
	= press and drag in any direction	= press and drag horizontally	= press and drag vertically

measurements	atom id	hover over the atom ( a tooltip will show identification)
	select starting atom	double click	as a pointer is moved a red rubberband extends from the origin until the pointer hovers over another atom at which point a provisional distance measurement is displayed
	second atom	double click	the measurement line is set and the distance is shown
		single click	the provisional angle measurement is displayed with second rubberband when the pointer hovers over another (third) atom
	third atom	double click	the angle measurement is set and displayed
		single click	the provisional dihedral angle (torsional angle) measurement is displayed with another rubberband when the pointer hovers over another (fourth) atom
	fourth atom	single or double click	the dihedral angle measurement is set

Menu Options:

Menu (see above) provides many other option for visualizing molecular information. Information available depends on the file being served to the applet and may vary from just basic geometry to sophisticated aspects of electronic structures. In most cases the choices are self-explanatory. We summarize here the options that may be of particular interest to students of organic chemistry. Not all option are always available (it depends on what we offer in the file) and on rare occasions we may remove the menu altogether for simplicity. Do not be afraid to try on your own. If you get "lost" just reload the page.

Main	1^osub-level	1^osub-level	Comments
Style	Schemes	CPK Spacefill	various molecular representations, especially applicable to organic molecules; explore on the structure of acrolein (on the left)
		Ball and Stick
		Sticks
		Wireframe
	Structures	Backbone	various molecular representations, especially applicable to large bimolecules such as proteins or nucleic acids; explore these options on the complex on the right
		Cartoon
		Cartoon Rockets
		Ribbons
		Rockets
		Strands
		Trace
model			shows number of "models" included in the file; usually these are different models of the same molecule, showing different properties In the example of acrolein we have 19 models, (1.1) show electronic structure details such as molecular orbitals or electrostatic potential map (check them under surfaces) and 18 others (1.2-1.9) showing molecular vibrations (select one or more for fun).
Console			opens Java console for scripting (see Jmol website for details) For acrolein, make sure that model 1.1 is selected (model menu). Open console and type in the lower frame one of the following (without quotation marks) and then press enter (or press "Run" button): "set showMultipleBonds on", "set showMultipleBonds off", "mo homo", "mo lumo", "mo lumo (-1)" "mo next"
Show			opens Java console and shows menu-requested details
Surfaces	Van der Waals		shows "true" volumes of molecules
	Molecular Electrostatic Potentials		shows electrostatic potential mapped on the van der Waals surface
	Molecular Orbitals		shows MOs (if available in the file)