VMMM ionic column

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The Virtual Museum of Minerals and Molecules™

The Virtual Museum of Minerals and Molecules™ is a web-based focal point and resource for 3-D visualizations of molecules and minerals designed for instructional use. Please see the Fair Use guidelines.

Go to the Displays!

or read About the Virtual Museum of Minerals and Molecules™.

Organized by The Minerals & Molecules Project

Curators: Phillip Barak, Ed Nater, & Cindy Stiles

News: 17 Jan 2014 Update! We now know that the VMMM (and other Java-enabled sites w/o signed applets) can be made to run by the user whitelisting the VMMM server in the Security tab of the Java Control Panel. The url to whitelist is http://virtual-museum.soils.wisc.edu/ . If, when updating Java, you hit 'Restore defaults (recommended)', this setting is wiped clean and would need to be reset. This whitelisting operation is obviously only a temporary solution since it obliges changes at the user end, one user at a time, instead of a change at the server end. Our early efforts converting to signed Java applets were not successful. The future of Jmol is in javascript and html5, with no Java at all, and we will move in that direction as time and resources permit, but not very fast since currently there are no development funds.
8 Jan 2014 New Java Security Update Jeopardizes VMMM Operability! ! As our visitors undoubtedly know, Java has been beset by security woes for a couple of years and its multiplatform functionality has been impaired by the Apple decision not to run Java on the iPad. Our visitors also will have noticed that the later Java updates require three clicks through security questions before the molecules are displayed. The word from Oracle is that the next Java 7 update, v51 due in Jan 2014, will require that Java applications such as Jmol be 'signed' by an trusted, authorizing agent. The latest version of Jmol, v. 14.x, is available in a signed format but the VMMM currently runs an earlier Jmol version. The VMMM could be updated to the current Jmol version to use the signed app and, once updated, could be tweaked to use JSmol, a Java-free JavaScript version that runs on almost all devices, including mobile. Alas, our proposal to the USDA-HEC to fund the update of the VMMM to JavaScript, HTML5 and CSS was declined (rather firmly). As a consequence, with no staff or funds at our disposal for this project, once the new Java release is made we will drop Jmol v14 into place instead of the older version, and hope for the best. If it works, and by that we mean that the scores of scripts underneath the shell continue to work as intended, we may turn off the Java altogether in favor of the JavaScript version. If it fails, we will consider our options carefully, but those options may include writing the obituary for the VMMM, 1998-(2014?). We will under no circumstances recommend that visitors run an outdated version of Java or run Java in an unsafe manner by turning off security measures. Keep your fingers crossed and we will keep you posted.
15 Aug 2005 VMMM with Jmol is here!!
In the past 10 months, the entire Virtual Museum has been transferred into XML files for standardization of format and then has been recast using XLST as Jmol implementations instead of Chime. This should make these displays workable in Firefox, Explorer, and Safari (...and to Chime, we bid a fond farewell, with our thanks for years of service.) Also in that time, we have worked closely with Jmol developers to add polyhedral representation to the package, which adds considerably to the conceptualization of the crystal structures in the VMMM. Please let us know what you think and help us find the many bits-and-pieces that no doubt still aren't quite right. (e-mail:Phillip Barak)
15 Jul 2005:
'The Virtual Museum of Minerals and Molecules: Molecular Visualization in a Virtual Hands-On Museum' by Phillip Barak and Edward A. Nater, was published in J. Nat. Resour. Life Sci. Educ. 34:67–71 (2005). Available on-line at www.jnrlse.org and in print format at year's end.
10 May 2005: Upcoming at the ASA/CSSA/SSSA annual meeting in Salt Lake City: "The New and Improved 'Virtual Museum of Minerals and Molecules', with Jmol", P. Barak, C.A. Stiles, E.A. Nater, and Michael 'Miguel' Howard, scheduled for Tuesday,  8 Nov 2005, at 3:15 PM.
26 Oct 2004: The VMMM is 'Site of the Week' at American Scientist On-Line! This online publication of Sigma Xi, a well-respected scientific research society, wrote:
Educators who despair of describing the three-dimensional structure of a mineral or organic molecule will rejoice to find this "virtual museum," in which anyone can pick up a plastocyanin protein and turn it over like a giant Tinkertoy model.
Created by soil scientists Phillip Barak of the University of Wisconsin and Ed Nater of the University of Minnesota, the gallery includes samples of everything from a simple graphite crystal to an enormous example of soil organic matter. These "displays" are gathered into standalone instructional modules that the site offers freely to educators...
In addition to the images themselves, each "display" includes a summary description of the mineral or molecule shown, as well as references for further study. Together they make a tremendously useful site for students, educators and anyone seeking a more intuitive understanding of the molecular world.

Old (Nov 2003) News:We, the curators, note with pleasure that on 8 October 2003, The Royal Swedish Academy of Sciences announced award of the 2003 Nobel Prize in Chemistry to Roderick MacKinnon "for structural and mechanistic studies of ion channels", specifically the potassium channel, and Peter Agre, "for the discovery of water channels", specifically aquaporin. In both cases, the VMMM posted 3D displays of these transmembrane proteins within several months of original publication (1998 and 2000, respectively) and have since disseminated these interactive structure/function models to many thousands of visitors--quite a testimonial to the virtues of web-based publication in keeping materials current.
Older (Sept 2003) News: We note with pleasure having the Virtual Museum recognized by the Editors of Scientific American as one of the top 50 Websites of 2003 from the (follow sciam.com link on logo at left).

We enjoy receiving the occasional e-mail message now and again...
- - -The Curators

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Sources and Links

As with most relatively complex projects, we are greatly indebted to others. Some of the data sources and tools we have used can be reached via these links.

This page is part of the Virtual Museum of Minerals and Molecules™.
©All rights reserved to the Minerals & Molecules Project.
For further information about the Jmol applet, see the Jmol Source and Reference Page.
Original release: 20 May 1998; Last modified: 7 Nov 2014.