Learning Outcomes On completing the exercises you should be able to:
•	Rotate, scale and change the appearance of molecules in JSmol.
•	Measure geometric properties of molecules displayed in JSmol.

This page provides help on using the JSmol 3D viewer.  JSmol is one of the key "applets" used in ChemInteractive.   Much of the analysis of structures that users draw is carried out by JSmol, but that work is carried out behind the scenes, invisible to the user.   However, JSmol is also very useful as a learning tool because it allows the user to rotate and scale structures, and to display them in several different styles.   These features are very helpful for visualising the three-dimensional shapes of molecules, and understanding shapes is crucial to understanding some properties of substances.   JSmol can also be used to view other chemically important objects, such as orbitals, in the same interactive way.   Moreover, measurements such as bond lengths and bond angles can easily be obtained.

 

How To Use This Page:   Read the notes below and practice manipulating the molecule in the JSmol window.   To check your JSmol skills, try the exercises that are suggested at several points below.

JSmol is compatible with all modern browsers (Internet Explorer must be version 9 or later) on almost all computers, tablets and smart phones.   The JSmol applet should be visible below left, and a molecule should be displayed.   If the molecule is not visible, try reloading the page.   If it still does not appear, check that JavaScript is enabled in your browser.

The Basics:   As you can see in the JSmol window, the default view of the molecule, the amino acid cysteine in this case, is a "ball and stick" representation.   In this view atoms are represented as small spheres, and bonds are shown as cylinders connecting the spheres.   Note that all atoms, including all hydrogens are shown, and the elements can be identified by a colour coding scheme that is very commonly used: C is black, H is white, O is red, N is blue, S is yellow, etc.   In the "ball & stick" view it is easy to see the geometrical arrangement of the bonds around each atom.   Rotate the molecule simply by clicking anywhere in the window and dragging the cursor.   Zoom in or out using the mouse wheel, or by holding down the Shift key while dragging the cursor vertically in the window.   Try Exercises 1, 2 and 3 below to check your mastery of these basic features of JSmol.

Other display styles:   You can change the representation of the structure using the menu which pops up if you right click in the JSmol window.   For example, on the pop-up menu choose   Style…Atoms…100% van der Waals   to get a "space filling" representation.   The space filling representation is more "realistic" in that it represents the molecule as a set of overlapping spheres.   Experiment with other settings in the Atoms and Bonds submenus.
Various representations of the "surface" of the molecule can be accessed from the Surfaces submenu.   Selecting Surfaces…Molecular Electrostatic Potential   from the pop-up menu gives a particularly useful representation in which the molecular surafce is coloured according to charge.   The most electron-rich (negatively charged) areas are coloured red, and the most electron-poor (positively charged) are coloured blue, with shades of yellow and green in between.   Try this now and then try Exercise 4.

Measurements:   Bond lengths and bond angles can be measured using JSmol, but bear in mind that these measurements are pnly as accurate as the data used to generate the model of the molecule.   Select   Measurements…Click for distance measurement   from the pop-up menu, and then click at the centres of any two atoms to display the distance between them.   Bond angles can be displayed in a similar way.   Experiment with this feature and then try Exercise 5.

JSmol has many other powerful capabilities, such as the display of orbitals and molecular vibrations (provided that the relevant data are available for the molecule).   Take a look at the companion site Molevision to see some of these features in action.

Choose an Exercise: Exercise 1 Exercise 2 Exercise 3 Exercise 4 Exercise 5
	A     B     C     D	JSmol 3D structure viewer