Advanced Visualization for Chemistry

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, to be acquired and understood directly. Visualization enrolls our powerful visual perceptual system to extracting information from our numerical data thus fostering insight.

Unfortunately for many researchers, visualization is something to be used only to prepare beautiful images and movies for presenting 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 supporting tool.

Goal of this course is to re-discover visualization as a discovery 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 research results communication.

Arguments covered

1.       Introduction to scientific visualization: Goal of visualization, the visualization process and the various roles played; the principal scientific visualization techniques; overview of the scientific / information visualization dichotomy.

2.       The importance of knowing your data:  Data types and logical data structure common in chemistry; overview of the most common physical data formats used.

3.       Chemistry representation methods: Usual representation methods: ball-and-stick, scalar volume data, summarizing and abstracting techniques; correspondence between method and representation.

4.       Chemistry visualization techniques: An overview of visualization techniques useful for chemistry data

5.       Getting started with visualization tools: Examples with VMD and STM3; some real life example of tool usage

6.       Tools customization techniques: Why customization needed; example of customization in VMD and STM3

7.       Post processing techniques: Common problems encountered in presenting visualization results; image manipulation techniques; Movie preparation techniques and tools; Putting results on the web


This course is targeted to chemistry, material science, crystallography users that want to gain better insight from their data. For the CSCS chemistry users the course provides also hints on how to effectively use the center scientific services, specifically the ones provided by the center visualization group, to complement the computational en infrastructural ones.


No prerequisite knowledge required, except working experience in computational chemistry.


Two full days