Submitted by Marion Cass / Carleton College on Thu, 03/13/2014 - 22:31
My Notes


    Every day when I teach Inorganic Chemistry (and in most of my problem sets and take home exams) I create Web pages to show 3D images of selected molecules to my students.  I am a visual learner and I find the structures beautiful and informative.

    In the past few months, you likely have found that web sites scripted with Jmol scripts calling a Jmol applet (which is a Java applet) are blocked. 

    The following short document walks you through how see Jmol images and animations that are currently blocked as security risks when calling a Jmol applet to load.  Ultimately, many of us have and/or will begin creating web pages with molecular images using JSmol, HTML5 or other solutions to avoid this problem, however there are many great web sites out there scripted in Jmol that are now blocked, including our interface to WebMO at Carleton.  The block is imposed on web pages that call a Java applet due to security breaches that occurred through Java in 2013.  Java has since been updated (Java 7 version 51) to address those issues, however in the meantime, the sites are still blocked and labeled as a security risk by the browsers.  Of course this will be an ever-moving target; browsers will update, Jmol has already updated and will continue to do so, Java will update, security breaches will occur, and all these computer-assisted tools will continue to evolve.  The document I have attached titled “Viewing_Jmol_Images_that_call_a_Java_applet3-14-14” describes two methods (that work as of 3-14-14) to override the security block; either by accepting a higher security risk overall or exempting sites from the security block.  Hope this helps anyone who is interested.  Please feel free to edit this document to fit your needs for your courses.



Learning Goals

To learn about molecular structure, symmetry and molecular motiions by viewing images of molecules in 3D.

The more specific goal of this LO is to allow us to view the numerous web sites that are already scripted in Jmol and are currenlty blocked.

Time Required
10 minutes to test one site
Creative Commons License
Amanda Reig / Ursinus College

THANK YOU!  I was fighting with Java for the last few weeks and was very disappointed I could not share my favorite sites for viewing solid state structures with my class.  Our IT people were of no help, so this is huge.  Also, I was able to get Chrome to work by adjusting the settings in Java site by site.

Thu, 04/03/2014 - 23:09 Permalink