The Virtual Museum of Minerals and Molecules v.3 is a web-based focal point and resource for 3-D visualizations of molecules and minerals. Visualizations in VMMM version 3 utilize the JSmol applet in a web browser without plug-ins, which allows them to be interactively zoomed and rotated so they can be viewed from all angles, much as with a real molecule. They can also be programmed with highlighting features that allow identification of specific atoms, structural sub-components, and mineralogical planes.
The 3-D visualizations are incorporated into stand-alone HTML (WWW) instructional modules that combine text, graphics, molecular formulae, highlighting features, electron micrographs, and other appropriate instructional aids and materials.
Availability and Distribution
These modules are offered free for instructional use. Interested individuals may view them with any modern web browser. Although the visualizations are research-quality, they can be readily transmitted across the internet due to their small size: most modules are less than 10 kB in size, though the JSmol applet itself is ~2MB in size. All necessary software is free and is downloaded into browser cache and automatically updated as new versions become available.
The VMMM first went live in 1997 using the Chime plug-in for molecular visualization on the leading browsers of the time, Netscape, Internet Explorer and Safari. With the decline in support for the Chime plug-in, the VMMM in 2005 switched to Jmol as the visualization engine, after a year or more assisting Michael (‘Miguel’) Howard with Jmol’s development with respect to particularly ionic radii, bonding rules and polyhedral models. Jmol enjoyed a long run but ultimately suffered from the security risks attendant to the Java browser plug-in, support for which has been slowly written out of modern browsers.
Hopefully this VMMM incarnation will, like its two predecessors, last 10 years. Ten years in computer-years, like dog-years, is a lifetime!
We plan to continuously develop visualizations and instructional modules of the most important molecules and minerals in soil and environmental sciences, taken broadly. We will also gladly consider collecting modules on related topics from other individuals.
The permanent URL for the Virtual Museum is: http://virtual-museum.soils.wisc.edu
Dr. Phillip Barak, Professor, Dept of Soil Science, University of Wisconsin-Madison, firstname.lastname@example.org
Dr. Edward Nater, Professor, Dept of Soil, Water and Climate, University of Minnesota, Twin Cities, email@example.com
The VMMM may be referenced as Barak, P, and EA Nater. 1997-201x. The Virtual Museum of Minerals and Molecules. online resource. http://virtual-museum.soils.wisc.edu.
This work is described in: Barak, P., and E.A. Nater. 2005. “The Virtual Museum of Minerals and Molecules: Molecular visualization in a virtual hands-on museum”. J. Nat. Resour. Life Sci. Educ. 34:67-71. [html]
We have many people to thank over the years. VMMM v3 particularly is grateful to Al Nemec and Jason Pursian from CALS IT at the UW-Madison and to Mr Yishai Barak, who diligently transferred the contents of VMMM v2 into the templates for VMMM v3. VMMM v2 was grateful to Dr Cythnia Stiles as collaborator for her suggestions and direction and to Alyssa Stafford and Jim Lyne for transferring the contents of VMMM v1 into the XML templates for v2. The VMMM v1 values our collaborators, Drs. Ann Hill Duin and Janice Bettinger, and contributors, Dr. Rachid Bouabid and Jennie Swanson, who helped create many of the original materials.
The VMMM was funded twice by the USDA Higher Education Challenge grant, in 1998 and 2004, and received internal development grants from both the Univ of Wisconsin-Madison and Univ of Minnesota, Twin Cities in the early years.