Introduction

JMV is a Java Molecular Viewer written in Java and Java3D. It can be used to load data files to display molecules in common molecular representations and color styles. Users can load files from a URL, from a local file, or from the RCSB databank. Users can also load PDB files when using BioCoRE. JMV also provides display and lighting options, and support for stereoscopic viewing. Java technology gives JMV platform independence, and allows it to run within a web browser or as a standalone application. It also uses Java Beans, making it modular and customizable, so developers can choose which components they wish to add. Since it can be used in webpages, it is i deal for applications such as electronic textbooks, to replace static images with an interactive tool. Online information on JMV is available at: http://www.ks.uiuc.edu/Development/jmv/.

List of key JMV features:

• General molecular visualization
  JMV has the ability to read PDB files, and view the molecules in common representations and color schemes.

• Applications
  JMV can be run as an applet, as a standalone application, or within another application.

• VRML files
  JMV can also read in VRML version 2.0 files. This makes it possible to view molecular representations JMV cannot draw on its own, such as Cartoon, if the right VRML file can be found. It also allows JMV to draw non-molecular data.

• Saving and loading states
  Once you start JMV and load a molecule, and get it into a representation, color, and orientation that you like, you can then save that state so that you can see that same view later, or so others can see the same view. You also have the option of saving a jpeg of the JMV screen.

• Interaction with BioCoRE
  BioCoRE, the Biological Collaborative Research Environment, uses JMV. From within BioCoRE, you can view PDB files, and save states and pictures to its own filesystem.