Molecular Visualization on Netscape

3D Molecules on the Internet
Adenosine - A nucleotide in DNA. Click on it
if you have the Chime plug-in installed.

Download Chime the Netscape Plug-In

MDL Chemscape Chime is the work horse for 3D molecular visualizing on Netscape. It works simultaneously with Netscape so that you may view molecules as you browse the internet. This Netscape plug-in is provided free for individuals or educational institutions at this site. Download it for a MacIntosh or Windows at Free Chime for All Users.

First examine the versions available at Free Chime for All Users to see what is appropriate for your machine. Then click to download, and on a PC, direct the file (ch20w32.exe) into your Programs folder.
Turn off Netscape and find the file in the Programs folder of your hard drive.
Install the plug-in software by double clicking on the file. An automatic install shield will take you through the quick installation.
Restart Netscape and test Chime with their example pages which include 3D samples (or try clicking on the ATP molecule above.).

Chime Images are Interactive

Right click on the image below and hold down to display a menu of options. Try several of them - start with Display, Ball & Stick..
Zoom on the image by holding down the shift key as you click and drag across the screen.
Right click and select File, and then Save Image As in order to save a copy onto your disk or hard drive.

Chime Images can be Embedded into Web pages
You can view images for the sake of demonstration that others have embedded into their own web pages, or view images you download as independent files. However what is perhaps most exciting is that you can embed these images yourself into tutorials you create or projects that students create.
This page has been authored with the free web-page editor Netscape Composer. However I only know how to embed these images with html tags. For example the image above uses the following source code: <embed ALIGN="CENTER" SRC="water.pdb" WIDTH="200" HEIGHT="150"></ul> In this code there are 3 things to notice.

embed src="file.name" - allows you to embed a file that requires the support of a plug-in such as chime or quicktime or shockwave.
align="center" - obviously designates that the image be aligned in the center of the page.
width="200" height="150" - allows you to designate the size of the image displayed.

The 3D Molecules Project was my first foray into this media. I plan to refine these ideas this year. I provided my students with an example template which they simply modified by replacing the text and images of their selected 3D molecules. Students found and downloaded their molecules from the sites linked below. Feel free to examine these student samples. Use the following steps to practice modifying the template.

Save a chime.pdb file to the disk provided from one of the resources listed below.
Use the application Notepad or like program to open the file "ProjectTemplate1.html" from the disk provided.
Find a line which includes the tag "embed src=filename.pdb".
Replace the original filename with that of the molecule file you just saved.
Save the modified text file and then open it in your Netscape browser to see your molecule displayed in place of the original.

Searching for Molecular Structures

Small Molecules

New York University has a beautiful Library of 3D Molecular Images organized and accessible in different formats. The format we use is PDB. Adenosine above was downloaded from here.

Molecules from Chemistry at Okanagan University College is a well organized collection of molecular Chime files that is worth trying. This site apparently requires Netscape 3.0, otherwise it crashes my computer.

The Smell Database is a well organized collection of stimulating molecules for the olfactory glands. You may not recognize the names but further examination reveals relevant information.

The Flavornet contains compilations of aroma compounds sorted by their chromatographic and sensory properties. To qualify for the Flavornet an odorant must have been detected in a natural product or real environment by some form of quantitative method. Benzaldehyde below is the flavor of almonds - represented 2 dimensionally here.

benzaldehyde, the flavor of almonds

Jamaica has an interesting resource which includes some startling inorganic and organic molecules.

Klotho appears to be a private collection of Chime files of interesting and esoteric molecules. You might very well find what you're looking for here.

Biomolecules is a collection of important molecules ranging from small to large that have been collected for quick demonstrations in biology classes.

Large Molecules

Molecules R Us is a utility program created by the National Institute of Health (NIH) that allows easy searching of the Protein Data Base at Brookhaven National Laboratories according to key words. Type in the name of a protein or enzyme and this will produce a list of related structures to access. The file tag .pdb refers to this database of molecular structures.

PDB At A Glance is a useful tool for finding polypeptides of interest. The entire Protein Data Base collection is organized by category here.

Valence Shell Electron Pair Repulsion Theory

VSEPR Tutorial appears to be an excellent tool in teaching students the basics of molecular geometry. It includes quizzes to test student knowledge.

The VSEPR at Lebanon site is a good place to refer to in order to understand the basic types of Molecular Shapes. The examples are clear and offer the opportunity for 3D viewing with Chime.

The VSEPR at Purdue site is another good place to refer to in order to understand the basic types of Molecular Shapes. The examples are clear and offer the opportunity for 3D viewing with Chime.

Additional Resources

Index of Biomolecular Tutorials by Eric Martz includes resources from around the world. I recommend examing the tutorials for Protein Secondary Structure by McClure, plus Hemoglobin and DNA resources by Martz.

Eric Martz has collected Chime Resources at the University of Massachusetts. These include how to create your own tutorials.

Molecular Models for Biochemistry has a some beautiful pieces showing how sugar is broken down in the Glycolysis pathway and also the TCA cycle. This may be useful in Advanced Biology.

The Macromolecular Tutorials are also located at California Lutheran University. It is a fascinating collection including interactive lessons in biochemical mechanisms. I recommend examining the enzyme mechanism of Topoisomerase which can unwind DNA.

A fragment of DNA polymerase. Click on it to see a tutorial of how it works.

The University of Massachusetts has the original program Rasmol. The chime plug-in that works with Netscape is a simplified derivative of Rasmol. Rasmol is a stand alone program which allows viewing and manipulation of 3D molecules in the PDB format. There are even some movies and tutorials that can be found at this site which use Rasmol. You are encouraged to visit the RasMol Home Page

RasMol/Chime Movie Scripts/Animated Tutorials is a fascinating resource. It demonstrates how Chime can be a useful learning tool for the biological and chemical fields.

The ChemFinder is a valuable research tool for looking up information about a particular compound. Besides the basic physical properties, this service may provide a 2 dimensional image as well as links to more information about the particular molecule.

ChemDrawNet plug-in is an alternative 3D structure viewer free from Cambridge Software. It may allow you to view even more structures - in particular those found in the ChemFinder above.

Isis/Draw allows you to draw organic molecules easily, accurately and provides the potential to convert 2D drawings into 3D, rotatable images. Isis/Draw: Download