Try Exercises 1, 2 and 3 below to check your mastery of these basic features of JSmol. Zoom in or out using the mouse wheel, or by holding down the Shift key while dragging the cursor vertically in the window. Rotate the molecule simply by clicking anywhere in the window and dragging the cursor. In the "ball & stick" view it is easy to see the geometrical arrangement of the bonds around each atom. 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 this view atoms are represented as small spheres, and bonds are shown as cylinders connecting the spheres. 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. If it still does not appear, check that JavaScript is enabled in your browser. If the molecule is not visible, try reloading the page. The JSmol applet should be visible below left, and a molecule should be displayed. JSmol is compatible with all modern browsers (Internet Explorer must be version 9 or later) on almost all computers, tablets and smart phones. To check your JSmol skills, try the exercises that are suggested at several points below. Read the notes below and practice manipulating the molecule in the JSmol window. Moreover, measurements such as bond lengths and bond angles can easily be obtained. JSmol can also be used to view other chemically important objects, such as orbitals, in the same interactive way. These features are very helpful for visualising the three-dimensional shapes of molecules, and understanding shapes is crucial to understanding some properties of substances. 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. 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. JSmol is one of the key "applets" used in ChemInteractive. This page provides help on using the JSmol 3D viewer. Measure geometric properties of molecules displayed in JSmol. Rotate, scale and change the appearance of molecules in JSmol. On completing the exercises you should be able to: Viewing Structures Using JSmol Learning Outcomes
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