In the mid to late 1990's the pair of programs, RasMol and Chime, saw wide-spread acceptance as tools for viewing and sharing information about the three dimensional structures of molecules. The two applcations produce similar images and share a common scripting language, but complement each other in their use; RasMol is standalone program, while Chime is a browser plugin that allows RasMol like, 3-dimensional, interative models to be displayed from inside web pages. The development of both these programs has languished over the past several years, so we will also take a look at some open source alternatives that have appeared in the past couple of years. On of these is PyMOL, which, like RasMol, is a standalone application, and is currently seeing wide-spread use for its ability to produce high quality images for publications. We will also look at Jmol, which is a Java applet that is emerging as a functional replacement for both RasMol and Chime. Jmol produces images that are similar to those produced by RasMol and Chime and it's scripting language evolved from the RasMol/Chime scripting language. It is currently going through a rapid phase of development, with new features being added almost daily.
Try out RasMol by viewing a model of the artificial sweetener aspartame (Nutrasweet)
For this to work on your browser at home, you must have RasMol installed on your computer, and you must set up your browswer to launch RasMol when it encounters the MIME type "chemical/x-ras". This is done in Netscape Navigator by selecting "Edit>Preference...>Navigator>Applications", and set files with MIME type "chemical/x-ras" and the suffix ".ras" to be handled by the application "RasMol". Alternatively, you can manually open the "aspartame.ras" file that is downloaded with the applcation RasMol.
Download your own copy of RasMol
One of the best ways to learn how to use RasMol is read the RasMol manual from front to back (or top to bottom).
The manual will open in its own window; it is contained on a single web page so can be easily printed to be read offline. Return to this window when you wish to continue.
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PyMOL, like RasMol, is a standalone molecular graphics application. It can be used to produce high-quality, publication quality graphics and animations. The Introduction page contains an example of an image created with PyMOL. PyMOl is an Open-Source project directed by Warren DeLano of Delano Scientific. There is a license fee for those using PyMOL in their work, but the fee is waived for students and those using PyMOL in their teaching.
A copy of PyMOL can be downloaded from the PyMOL site. It is available for platforms running under Windows, Linux, Mac OS X, and Unix operating systems.
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Chime is a browser-based, molecular visualization application, which was written by researchers at MDL Information Systems. The images it produces look very similar to those of RasMol and many of the menu-based commands that are available in RasMol are also available in Chime through pop-up menus. What Chime lacks, however, is RasMol's command line, which is used to type in commands that are not found in the menus. Chime does, however, understand RasMol commands, which can be sent to it by using embedded buttons. This makes Chime a very valuable tool for developing web-based tutorials and images.
Download your own copy of Chime
The Chime plug-in works best with the legacy Netscape 4.x browsers. On the Macintosh platform it can only be used under Classic (Mac OS 9). It also does not work reliably with the Microsoft Internet Explorer browser. The Chime installation application places the Chime plug-in your browser's "Plug-ins" folder and configures the browser to handle the MIME types and suffix mapping for the various input files that Chime accepts. The important ones for our discussions are the files with the suffix ".pdb" and the MIME type "chemical/x-pdb", and files with the suffix ".spt" and MIME type "application/x-spt".
Try out a Chime based tutorial on oxygen binding the oxygen-binding muscle protein myoglobin. (You will need to be using a Chime enabled browser.)
Try out a Chime based molecular modeling kit for low molecular weigh biological molecules. (You will need to be using a Chime enabled browser.)
To learn more about Chime
Visit MDL's Chime support site.
The site will open in its own window so that you can continue using this site and the Chime Support site same time.
Work through the Chime Tutorials and Demonstrations.
The site will open in its own window so that you can continue using this site and the Chime Tutorials and Demonstrations site same time.
MDL Information Systems has stopped supporting Chime development, so the number of systems out there that are capable of using Chime are diminishing rapidly. With the emergence of Jmol (see below) as a viable alternative for both RasMol and Chime, Chime's star if fading fast.
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Jmol is an Open-Source molecular modeling application that is written in Java. It comes in two forms: a Java applet, which like Chime, is used to display interactive models from web sites; and a Java application, which like RasMol, is used as a standalone program. Because it is written in Java, it does not require any special browser plug-in like Chime does. Instead of residing on the client machine, the Jmol applet resides on the server and is downloaded to the client when needed. Another characteristic that distinguishes Jmol from Chime is access to a command line that can be used to manipulate the models from a web site. Jmol uses a command language that is similar in many ways to that used by RasMol and Chime, but the scripting language is fast evolving to include many new features that are lacking in RasMol and Chime. It also produces are also similar to RasMol and Chime. An example of a Jmol model can be found on the Introduction page.
To learn more about Jmol
Visit the Jmol website.
The site will open in its own window so that you can continue using this site and the Jmol Support site same time. It contains a variety of resources to help you get started with Jmol.