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_ N_How to view structures at home or in school?
 Table of Contents
  Introductory Comments
 What is Molecular Modeling?
  Why is Molecular Modeling Important?
 What do some common molecules look like?
 Where's the Math?
 Carbon 3 Ways
  Carbon Compounds
 Water and Ice
 Water and Ice pt.II
  How to view structures in class or at home
  MathMol Library of Structures.
 Tutorial 1: 1-Dimension, 2-Dimensions, 3-Dimensions...
 Tutorial2: The Geometry of 2 Dimensions..
 Tutorial3: The Geometry of 3- Dimensions
 Tutorial4: The Geometry of Molecules.
 Appendix1: Scientific Notation
  Appendix 2: Mass
  Appendix3: Volume
  Appendix4: Density

Although designed for University level research, the following software packages are ideal to supplement high school and advanced middle school chemistry lessons. The software can also be used as a tool for student science projects.

These are all 'free software programs', although many require registration.


Chime is a plug-in program that allows you to view molecules in 3-D via Netscape or Explorer browsers. Although Chime is free you will have to register to download the version from MDL.

RasMol (Recommended for K-12 Applications)

RasMol is a molecular graphics program developed at the University of Edinburgh. The software is intended for the visualization of proteins, nucleic acids and small molecules. The program has the ability to read in PDB as well as several other formats. For more information on RasMol visit the RasMol Home Page.

SwissPDB Viewer

Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.


ArgusLab contains: An interactive 3D molecule builder that allows the user to build and manipulate complex structures; and, a rich suite of computational methods, both quantum mechanical and molecular mechanical, for calculating ground and excited states properties. The program is free for academic use


Mage requires the use of Kinemage files. There are presently available a large number of these files for both education and research purposes (see the Kinemage Home Page for more information. ) You can now run Kinemages on your home page using a Java enabled Mage. Because of the large number of Kinemage files available to the public this makes for an interesting teacher tool.


eChem is a simplified and learner-centered design version of professional visualizing tools. It allows students to build and manipulate three-dimensional models of molecules with a visualizer module. It also allows students to compare computationally predicted properties of the molecule with properties they observe in the laboratory

JME Molecular Editor

JME Molecular Editor is a Java applet which allows to draw / edit molecules and reactions (including generation of substructure queries) and to depict molecules directly within an HTML page. Editor can generate SMILES or MDL mol file of created structures. You can download a copy at the JME Site.

Viewer Applet Chemis 3D

Chemis3D, Molecular viewer is a Java Applet which renders virtual 3D molecular models within a Web document. It is specially designed for open interactive molecular visualization on the Internet or via an intranet. Chemis3D is a small applet (~30Ko) running well on any Java-enabled browser and requiring no specialized plug-in nor professional applications.


The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L).


YASARA is a molecular-graphics, -modeling and -simulation package for Linux and Windows.YASARA is powered by PVL (Portable Vector Language), a new development framework . PVL allows you to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard PCs. The initial level stage can be downloaded free.

Questions or Comments?