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Visualizing Molecules in Three Dimensions

Introduction

Visualizing Molecules in Three Dimensions

Although we often see molecules depicted using two-dimensional (2-D) figures, they are in fact three-dimensional (3-D). Many scientific questions can be better understood by seeing and interacting with molecules in three dimensions. There are a number of tools available on the Internet that allow the user to rotate, flip, and otherwise manipulate virtual molecular models of chemicals and macromolecules.

If you would like to explore small molecules in 3-D, download and install Chime on your computer. Chime is a program that is required for viewing molecules from many websites. Once you've installed Chime, you can view molecules you're interested in from one of the molecule libraries listed below. You can also use this program to add pictures of the molecules to display boards for science fair projects. For more advanced uses, such as command line control, you can install RasMol. Some scientific websites are using JMOL, a Java-based viewer, for rendering molecules in 3-D. JMOL and similar tools may replace Chime eventually, but for now, Chime is the program used most for viewing small molecules from websites.

If you would like to view macromolecules in 3-D, download and install Cn3D. This program should be all you need to visualize proteins of interest. For advanced users, investigate Protein Explorer, a RasMol derivative.

Useful Programs and Plug-ins for Molecular Modeling

Other Options

3-D Chemical Libraries

(View using the Chime plug-in)

3-D Macromolecular Structures

(View using the Cn3D plug-in)

Other Resources

This site lists dozens of web resources for 3-D visualization of molecules.