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.
Arguments
- 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
- Postprocessing
- Tools and technique to transform the visualization output into effective communication
Handouts
All the following handouts are in PDF format.
- Introduction
- How chemists work
- Introduction to visualization
- Know your data
- Chemistry representations
- Scientific visualization techniques
- Visualization tools survey
- First day wrapup
- Tools in depth
- Experiences at CSCS
- Tools customization
- Communication issues
- Postprocessing
- Final wrapup
Software
Data conversion
Visualization software
Image manipulation
- The GIMP
- ImageMagick
- Tips and tricks for image manipulation
Movie manipulation
- mencoder
- My experience on video preparation and editing
Examples
- Jmol examples are on its demonstration page.
- Another local simple page that can be downloaded also.
- Virtual Textbox of Organic Chemistry.
- The Online Macromolecular Museum is a truly amazing example of chemistry visualization usage for communication and explanation.
- Jmol scripting tutorial and documentation.
- Other Jmol examples.
Additional readings
I have collected a list of readings that could be useful.