Chemistry software

JMol applet molecule viewer

This is for web authors. Have a look at Jmol where you can find information about the JMol applet viewer. With this you can publish chemical structures in your web pages and it usually works just fine (including support for RasMol/Chime scripts) provided your viewers have fast access to the internet. For an example of Jmol in action try this VSEPR tutorial.

Chemis3D, Molecular Viewer Applet

I picked this up on ChemNet. To quote:

"Chemis3D 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 (about 30Kb) running well on any Java-enabled browser and requiring no specialized plug-in nor professional applications."

The means that web site publishers have a small java application to use in addition to the rather larger JMol.

Chemis3D claims to support Brookhaven Protein DataBank (*.pdb), MSC XMol files (*.xyz), and MDL molfiles (*.mol). The user can choose how to display the molecule (wire, balls and sticks etc.), and can read off bond lengths, angles, and torsion angles.

Interacting with molecules on the WWW

There are many chemical web pages that display chemical structures within the web page itself. You, the viewer can then rotate the molecule on screen, read off bond lengths and angles, and do other useful things. To do this, a free piece of software known as a plug-in is required.

There are at least two plugins available for you to use. In practice you will probably need both since they have different abilities and chemistry web site authors often cater for one rather than the other. Both are available for Macintoshes as well as PCs and bother are free.

The first available is known as Chime. On a Mac you have to use a NetScape browser in Classic mode while on a PC either NetScape or Internet Explorer is OK. The features available for Chime under MacOS and Windows differ unfortunately.

The second available is known as the Chem3D Net Plugin. On Macs and PCs either NetScape or Internet Explorer is OK.

Remember, some of what Chime can do, the Chem3D Net Plugin can not, and vice versa, so I suggest you get both (they are free). Many pages in WebElements benefit from these plugins, so get them and give them a try.

Note: links updated December 2009. The Chem3D Net Plugin seem to be available no longer.

WebElements: the periodic table on the WWW [http://www.webelements.com/]

Copyright 1993-2011 Mark Winter [The University of Sheffield and WebElements Ltd, UK]. All rights reserved.