Mario Valle Web

Practical Visualization for Chemistry Course

This page collects the supplementary materials and links for the C4 course “Practical introduction to chemistry visualization” held on September 3–4, 2007 at ETH Zürich.

To start, take a look at the course agenda or read the handouts. If you want to learn more about the course, go to the supplementary material page or to the questions raised during the course.

Course description

Visualization provides methods and techniques that help the researcher to see the unseen, to make visible data and information that are too far from our sensitivity, like chemical structures and reactions, so they can be acquired and understood directly. Visualization enrolls our powerful visual perceptual system to extracting information from our numerical data, thus fostering insight.

Unfortunately many researchers see visualization merely as a tool for creating beautiful images and movies in order to present their research results. This is a commending goal, but thinking of visualization simply as a postprocessing discipline greatly limits its capabilities as a research and discovery support tool.

The goal of this course is to re-discover visualization as a research tool, investigating its processes and methods. Specific chemistry visualization tools and methods will be covered as they are used in exploratory visualization, as a support for visual thinking and as the main vehicle for communicating research results.

Course format

  1. The material is split into bite-sized arguments with a practical focus. The goal is not to provide full theoretical explanation of how visualization works, nor to be an in-depth training on a specific tool or argument.
  2. Instead the course will try to transfer usable knowledge, with the intent to catalyze new ideas and convince you to consider visualization as an effective help in your work. But most important, I hope to encourage you to discuss your research needs with the visualization experts.
  3. To this end the teacher will be available in the afternoon to discuss your real work problems, to expand the morning lectures and to work on concrete examples and demos.


Lecture 1: Practical introduction to chemistry visualization [handout]

  • What is visualization? And why is it so effective in the research cycle?
  • A concrete example of visualization process using VMD
  • What makes chemistry visualization different from generic scientific visualization?
  • How to extend visualization tools to couple visualization and analysis (examples from VMD)

Lecture 2: What do we want from our chemistry visualization tools? [handout]

  • How to choose a tool
  • Some available free tools
  • Which hardware do I need?
  • What a chemistry visualization tool usually offers?
  • Data issues

Lecture 3: Standard and unusual chemistry visualization at CSCS [handout]

  • How CSCS supports users’ visualization needs
  • Unusual requests
  • STM4: a platform to implement unusual and advanced visualization requests
  • The rewritten and revamped new Molekel

Lecture 4: Presenting results: images and movies [handout]

  • Visual communication ideas
  • Media you can use
  • Image formats and tools
  • Movie formats and tools
  • Presentations: tips and pitfalls
  • Build a Web presence


All the following handouts are in PDF format.

About the teacher

Ing. Mario Valle works since 2003 in the Data Analysis and Visualization Services of the Swiss National Supercomputing Centre helping the center’s users for their visualization needs, especially in the Chemistry and Molecular Dynamics areas. But the interest for visualization started early, in 1995, when he was with Advanced Visual Systems (AVS) defining and implementing advanced visualization projects for the company customers. Prior to visualization work, ing. Mario Valle was with Digital Equipment (DEC) for eight years working in the software engineering consulting area.

Besides developing concrete visualization projects, ing. Mario Valle teaches various courses on visualization and visual communication, for example at the CINECA Summer Schools in Bologna (Italy).

Ing. Mario Valle holds an Electronic Engineering Degree from Università di Roma “La Sapienza”, is author of various publications and is IEEE Computer Society and American Chemical Society member.