Pedagogy for Molecular Visualization

Provided for the NSF-Supported Workshops by Eric Martz, PD.

If you are reading a paper version of this document, it is also available at
Software, molecules, and visualization help is at the RasMol Classic Main Page,

Caveat: I have little experience using molecular visualization in my own teaching, especially with student-active learning. I'm a novice to this pedagogy. I offer the following ideas only as a starting place for discussion. Be creative! I plan to expand this document with what I learn from you, the participants in these workshops.

General Principles

Visualizing 3D structures of molecules is a great help in understanding the structural basis of function.

3D structure is most easily grasped when the molecule is moved by slow rotation. Rotation eliminates the need for stereo views in most cases. Don't forget to move your molecules early and often! You have probably become intimately familiar with the 3D structure of the molecule you are showing, but your students haven't. Forgetting to move the structure often enough is a common pedagogic mistake.

Simple visualization methods with RasMol can be very effective. You don't need to do any programming to teach structure effectively. I expect few if any participants in these workshops to write RasMol "movie" scripts or Chime web pages -- these can be excellent but are by no means necessary.

Each segment of your molecular visualization presentation should answer a question. The question and the answer should be explicitly stated.

Illustrating Lectures (linear presentations)

Very easy - no scripts. Just open the PDB file for your molecule and show it. Good preparation is important to plan the views to show, and to know how to get them up quickly. If you want to emphasize RasMol's interactive qualities to your students, this is a good method. If you just want to show the best views quickly without dwelling on the RasMol software, the next method is better.

Easy - RasMol-saved scripts. Before class, explore your molecule. When you get a great view, use RasMol's save script filename command. In lecture, use the script filename command to bring up the desired view immediately. Then you can rotate manually, and change the view interactively if you wish. (See Note 1 for how to run your script automatically, in the correct sequence.)

Challenging - RasMol-saved scripts in Chime. Put your scripted views into a Chime presentation which can be viewed in Netscape, either for projection in lecture, or for individual review by students later from your class web site. See Note 2 for examples and help. You don't need an Internet connection to show Chime web pages in Netscape as long as you have copies of the Chime HTML files, scripts and PDB files on the local hard disk.


Student-Active Hands-On Approaches (nonlinear)

All of the approaches listed above can be adapted to student-active, self-paced, hands-on learning in a computer lab, or on the student's privately owned computer at home or in the dorm. There are no licensing issues: RasMol and Chime are free for all users; Netscape is free for academic users.

With any of the approaches below, it works well to hand out, on paper, a series of questions for students to answer. This gives a focus to their exploration. Examples of such questions are provided with my Chime presentations on antibody ( and MHC A general set of questions applicable to any molecule is also available (

No scripts. RasMol's user interface draws one into exploration very effectively. Having students explore molecules (perhaps molecules of their choice) with RasMol is ideal. Examples of the kinds of questions you can ask about any molecule are at

RasMol-saved scripts. These could be provided so that students can start with a predefined view, then explore on their own. This approach may be best when time limits the ability of the students to get familiar with RasMol menus and commands.

Chime-delivered RasMol-saved scripts. Same as above but the students don't have to learn how to use RasMol. Chime installation is very easy (Mac users see Note 3), and then you just do the viewing in Netscape. You don't need an Internet connection to show Chime web pages in Netscape as long as you have copies of the Chime HTML files, scripts and PDB files on the local hard disk.

Manually programmed Chime tutorials. Considerable programming effort is needed (see Note 4). One example of what can be done is a nonlinear tutorial on DNA ( I use nonlinear to mean that there is no beginning nor end, and no particular sequence of views. The student has to make choices frequently or nothing happens -- there is no 'continue' button. This should make it difficult to tune out and learn nothing. (Contrast this with a linear presentation with a continue button, such as the one on protein secondary structure, surely a much less effective learning tool when operated by a student alone.) This tutorial is intended to supplement a class and textbook, not to stand alone. Its labels and help are intentionally short to challenge the student to figure out what they are seeing. Eventually, I hope to add questions which pop up randomly every few mouse clicks.

This sort of Chime presentation facilitates exploration of specific features. Note, however, that all the pedagogic virtues I listed above beginning with the word nonlinear apply equally to having students load PDB files and explore them with RasMol, which requires no programming.

Other examples of extensively programmed Chime tutorials can be found via the world index (see Note 2). For the most part the ones presently available have a linear structure.

Assign students to create their own presentations. If you can spend a large enough portion of your course, the students will learn the most this way. And they can use what they have learned to visualize (or present) molecules they encounter after your course is over.



Note 1. You can easily put your automatically generated scripts into a master script sequence. Suppose you used RasMol to save script files named s1.spt, s2.spt, s3.spt. Use wordpad/simple-text to create a plain text file named master.spt containing:
script "s1.spt"
script "s2.spt"
script "s3.spt"

Be sure to save master.spt into the folder which already contains the relevant PDB file (and on Macs, the RasMol application).

To play back the sequence, use the command script master.spt. The first image will appear -- rotate it, and optionally zoom it etc. When you are finished manipulating the first view, press the space bar to release the pause and run the next script. The second view will appear automatically, and so forth.

Of course you must have all the necessary PDB files in the same folder as the scripts (and on Macs, the RasMol application). Note that this method is suitable only if all the desired manipulations of the script-generated views can be done from the mouse/menus -- you can't type a command while master.spt is running.

In Windows, you can start the master script automatically. Copy the RasMol icon to make a separate icon, and give it the name of this presentation. Change its working folder to the one containing the relevant scripts and PDB files (Win95: Right-click on icon, Properties, Shortcut, Start in; Win 3.1: click icon, File, Properties, Working Directory). Create in the working folder a file named rasmol.ini containing the single command line script master (or whatever you named your master script file). Now, double clicking on the icon will open RasMol and run your script sequence automatically, without typing any commands in the command line window. If there is a way to do this on Macintosh, I don't know it.

Note 2. RasMol-saved scripts delivered by Chime. A good example of a Chime presentation made largely from RasMol-saved scripts is the one on hemoglobin ( Instructions for creating your own presentations in this format are provided ( You can download a template so you won't have to do any programming. Examples created by students in a graduate class may be viewed at ( See the World Index of Animated Tutorials for other examples (

Note 3. Installation of Chime 1.0 on the Macintosh is tricky at one point, whereas installation in Windows is totally automatic. Get Chime from Now Quit from Netscape. Discard the hqx file after the Installer is unpacked to your desktop. Run the Installer. When it asks you to Select Folder, you must specify the correct folder! Use Finder to find the folder containing your Netscape application. This folder should contain a folder named plug-ins. In Chime's Select Folder dialog, you want the Netscape Navigator folder at the top, with plug-ins higlighted in the list, then push the Select button. The Installation Location should now show "in the folder 'plug-ins'". Only when this is the case, click the Install button. Chime's installer will announce success regardless of whether you put Chime in the correct folder. Restart Netscape, and use the pulldown menu Help, About Plug-ins. If Chemscape Chime is not listed, then it was installed in the wrong folder. That would mean you have several copies or versions of Netscape in various places. Figure out which is the active one and rerun the Chime Installer.

Note 4. Resources to help in writing Chime web sites from scratch (not using the above template, and creating the chemical scripts by hand) are at A simple example, which explains how to create similar web pages, is at For reasons given at, Chime is ultimately superior to RasMol for presenting such "movies". However, it usually works best to program the basic views into a RasMol script, and then incorporate that script into a Chime web site as a later step. Sophisticated examples of what can be done with manually written scripts are the presentations on protein secondary structure (, and on DNA ( Extensive information about writing scripts manually is available for RasMol ( and for Chime (

Feedback to Eric Martz.