Silberberg/Chemistry: The Molecular Nature of Matter and Change

Online Learning Center (Student) - Visual Chemistry

Chapter 1

Learning to Use the Chime Viewer

The Chime Viewer is a free application that allows you to view and manipulate images of molecules. There are many sources of molecular images on the WWW that are designed for use with Chime. These first questions are designed to introduce you to some of the basic features of the Chime Viewer. Some links and instructions are given separately (Chime.doc). You must install the Chime 2 viewer on your computer to do these questions.

1. Find a molecule from one of the sites on the WWW. For example, go to http://www.sci.ouc.bc.ca/chem/molecule/molecule.html (site 1), select "amines" under the categories of compounds, from this list select "alanine". This is one of the amino acids, the building blocks of proteins. You should now have a Chime image on the screen.

Learn how to do the following. There are many more options than are explored here, but quite a few are designed for viewing biological macromolecules and will not concern us for most of the questions.

a. Rotate the molecule about the x and y axes, the axes in the plane of the screen.

b. Rotate the molecule about the z axis, the axis perpendicular to the screen.

c. Make the molecule larger and smaller (zoom).

d. Change the molecule to display it different ways using the "Display" command from the menu. Wireframe, stick, ball and stick, and Spacefill/Van der Waals Radii options are available. Rotate each version. What are the differences and what are the advantages of each type of view?

e. Find out what the atoms are by clicking on each one and looking at the bottom of the display. The name includes more than just the symbol.

f. See the two dimensional version of the molecule as it would be drawn on paper by choosing "2D Rendering". This also labels all of the atoms. Note that the 2D view changes as the orientation of the molecule changes. Try to orient it so it is easy to read. Return to the 3D version by choosing "3D Rendering" from the menu.

g. Turn on "Rotation" from the menu to set the model constantly rotating. Select it again to turn it off (this is called "toggling"). The speed of the rotation depends on the complexity of the model, the type of display, and the speed of your computer.

h. Under options "Display Hydrogens" can be toggled on or off. Usually hydrogens are displayed for small molecules, but they can clutter to the display of large biological molecules.

i. Under "Color" on the menu, a single color display may be produced with "Monochrome" and the standard colors with "CPK". This can make some atoms, especially those that are dark colors and difficult to see against the black background, more visible. The actual color displayed can be controlled with the menu item "Select" and "Change Color To".

j. There are some more features that accompany the views other than "wireframe". To see these best change the display to "Spacefill/Van der Waals Radii", start rotation, and then from the Menu choose "Select" and "Specular" or "Shadows" or both. This is a test of the speed of your computer, the rotation slows considerably when "Shadows" are turned on.

k. The are several ways that the mouse can be used besides the default use of identifying atoms. From the menu choose "Select/Mouse Click Action" and then "Distance". Click on two atoms and the distance between them appears at the bottom of the screen. Alternatively, pick "Toggle Distance Monitor" instead of "Distance" and a dotted line will appear between the two atoms selected and it will be labeled with the distance. Use the browser to reload the page in order to remove all of the distance monitor lines. Click on a pair of atoms a second time to remove a single distance monitor line.

l. Another option is "Labels" which turns on atomic labels for atoms other than C and H. Some of these are difficult to see. This is also a toggle.

m. Also under "Options "is "Slab mode" this allows a plane to be cut through the molecule, showing only the part of the molecule "behind" the screen. Turn your molecule so that its longest dimension is along the z axis, in and out of the screen, then select slab mode and move the molecule forward and back by pressing the "ctrl" key, the left mouse button, and dragging the mouse up and down. This effect is most clear in "spacefill" or "ball and stick" mode.

n. The menu item "Mouse/Open Mouse Control Help Page" shows the mouse functions.

o. Save the file on your computer using the "File/Save Molecule As" command and giving your own name to the molecule.

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