Using Computers to Study Molecular Structure

Using MacMolecule

The basics

MacMolecule2 and PCMolecule2 are designed for use by students of biology, chemistry and allied fields to learn about the structure of molecules. Molecules have defined structures, determined by the types and numbers of atoms in the molecule, the size of the atoms, the location of the atoms in 3-dimensional space, and the bonding between atoms. Before you begin the DNA Structure Activity, study the MacMolecule Interface pictured below. Notice the MacMolecule icon in the applications menu and the menu bar. Notice the Menus with Select and Format commands. Scroll down past the picture below to learn about the items in the Tool Bar.

The MacMolecule Tool Bar

To choose a tool, click once on its icon in the tool bar. When a tool is active, its icon is grayed out in the tool bar.

Click the Pointer tool on an atom to select it.
Click and drag the Hand tool to rotate a molecule.
Click on the image to Zoom in and Zoom out with the magnifying glass tools.
Click the Eraser tool on an atom to hide it.

These tools allow you to view the molecule in different modes. Starting from left to right, the views are wire-frame, ball and stick, space-filling, ribbon outline, and full ribbon.

These tools are for measuring features of the molecule. They will not be used in this activity.

For more details on how to use this software, an on-line user manual is also available at the Molecular Ventures web site at

The Biology Project
University of Arizona
Modified: May 27, 1997
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All contents copyright © 1997. All rights reserved.