Mario Valle Web

Advanced Visualization for Chemistry Course

This page collects the supplementary materials and links for the CSCS course Advanced Visualization for Chemistry that has been held on March 7–8, 2006.

To start take a look at the course agenda.

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.


How chemists work
Chemists are visual people.
Introduction to visualization
Visualization makes the invisible visible.
Know your data
Raw data should be transformed into information and knowledge to be useful.
Chemistry representations
Traditional structural representation in chemistry.
Scientific visualization techniques
Other data types and the corresponding (scientific) visualization techniques.
Visualization tools survey
A survey of what is available on the free market
Tools in depth
A quick tutorial on VMD and STM4 usage
Experiences at CSCS
My experience with some chemistry visualization projects at CSCS
Tools customization
Why and how a tool should be adapted
Communication issues
Visualization is also communication
Tools and technique to transform the visualization output into effective communication


All the following handouts are in PDF format.

  1. Introduction
  2. How chemists work
  3. Introduction to visualization
  4. Know your data
  5. Chemistry representations
  6. Scientific visualization techniques
  7. Visualization tools survey
  8. First day wrapup
  9. Tools in depth
  10. Experiences at CSCS
  11. Tools customization
  12. Communication issues
  13. Postprocessing
  14. Final wrapup


Data conversion

Visualization software

Image manipulation

Movie manipulation


Additional readings

I have collected a list of readings that could be useful.