A new platform-independent, integrated, and interactive molecular visualization tool has been developed for teaching and learning molecular structure. This java-based amalgamation of the jmol application and a simple web browser has an overall graphical user interface that is easy to use and intuitive. Initially, it was developed to help undergraduate students learn concepts of protein structure, but it could also be used as a comprehensive molecular visualisation tool for both teaching, and research, in chemistry and biological sciences.
The jAMVLE (pronounced 'jamvil') application was developed by Dave Chandler using version 1.4 of the Java programming language development kit (Java 2 JDK 1.4) (web site ref http://java.sun.com/ ), a Java build tool called Apache Ant (web site: http://ant.apache.org/), and the jmol open source code (ref to web site: http://jmol.sourceforge.net ). Jmol is a Java based application written with free open-source software, and licensed under the GNU Lesser General Public License (web site ref: http://www.gnu.org/licenses/lgpl.html ), that contains Java classes specifically for molecular visualization.
The initial distribution of jAMVLE (version 1.0) was trialed by undergraduate Structural Bioinformatics students in the School of Biomedical Sciences at Curtin University of Technology. A new version (2.0) is now available. To try it out, download the jAMVLE jar file (available in a zip archive) and follow the instructions in the Readme file (on Windows PCs or Mac OSX, simply double-click on the jar file if you have a Java Virtual Machine installed).
Download the pre-compiled jAMVLE jar file - a sample tutorial on carboxypeptidase A is included
Download the jAMVLE source code and build files
The updated version of jAMVLE has a number of improvements, including a browser 'back' button and the ability to reset the 'Home Page' for the application.
Figure 1 - The initial startup screen.
Figure 2 - A view of insulin
Figure 3 - alpha cobratoxin
Figure 4 - The pdb file can be displayed in the browser window
Figure 5 - The beta barrel of green flourescent protein (1ema.pdb)
Contact the developer Dave Chandler if you experience any technical difficulties or to report bugs/errors.
Contact Dr. S.Bottomley@curtin.edu.au for comments and suggestions regarding the overall program design.
