Course supplementary material

Lecture 1: Practical introduction to chemistry visualization: General on visualization, Visual perception, Gestalt laws, General visualization examples, Exploratory data analysis, ChemViz tools survey, Extending VMD
Lecture 2: What do we want from our chemistry visualization tools?: Free tools, Tutorials, New rendering methods, Representation methods, Chemistry data formats, Format conversion, Data management issues
Lecture 3: Standard and unusual chemistry visualization at CSCS: Visualization at CSCS, STM4, Molekel
Lecture 4: Presenting results: images and movies: Tufte, Confound with visualization, Chemistry humor, Image manipulation, Movie manipulation, Presentations, Web presence
General: Readings, Blog, Visualization examples

Visual perception

Exploratory Experimentation: Goethe, Land, and Color Theory, Neil Ribe and Friedrich Steinle — Physics Today July 2002 p. 43-49
Usually the researcher uses the experiment to prove or disprove some theory. This is the usual theory oriented experimentation. Instead the exploratory experimentation defining characteristic is the systematic and extensive variation of experimental conditions to discover which of them influence or are necessary to the phenomena under study.
In the IST/SEMATECH e-Handbook of Statistical Methods there is a chapter on Exploratory Data Analysis
There is a nice article on C&EN, titled Molecules That Could Be, about the study of stable, but imaginary molecules.
Look at this really unusual paper by Seth Roberts: Self-experimentation as a source of new ideas: Then examples about sleep, mood, and weight. It is about a form of Exploratory Data Analysis using visualization.
A serious, statistically oriented exploratory data analisys for complex models (plus discussion and re-discussion).

VMD plugin and script library
Extending VMD: Tcl Text Interface, Python Text Interface, Molecular Analysis support
The MultiMSMS VMD plugin caches the Solvent Excluded Surface computed by MSMS to speedup animation of a sequence of frames.
Tcl tutorial and more Tcl resources

An introduction to scientific data management
Sander B. Nabuurs, Chris A. E. M. Spronk, Geerten W. Vuister, Gert Vriend: Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors. Seems there are major problems in structures deposed in the Protein Data Bank
C&EN reports on a study of structure quality that highlight how crystal structures in 'hotter' journals tend to have more errors

STM4 main site
The list of current STM4 modules
STM4 download
The original STM3 paper: M. Valle, STM3: a chemistry visualization platform,
Zeitschrift für Kristallographie, vol. 220, no. 5-6, pp. 585-588, 2005
A user level AVS/Express course
A (marketing) brochure on AVS/Express

Junk Charts
Articles from the Vol.33 No.3 August 1999 SIGGRAPH newsletter; especially the article by Alan Davies Bad Graphs, Good Lessons on the "creative" usage of charts by corporation annual reports
Misleading Visualizations by Henrik Ingo. “The Post-Enron world with its tough requirements on reliable financial reports has left US accountants and CEOs without choice. They will now have to tell us the truth and nothing but the truth about their companies financial status. Or do they?” A story about pictures that lie…
THE ANCIENT CHINESE ART OF CHI-TING. Jim Blinn explain why computer graphic must cheat (chi-ting) sometimes. Unfortunately this paper disappeared from the net, but can be find in the web archives.
How to display data badly, Howard Wainer, The American Statistician 1983. Especially interesting is the online Wainer lesson

Life after Death with Powerpoint A funny Powerpoint-based video by comedian Don McMillan, who attempts to give some good advice on using the PowerPoint tool properly.
A series of tutorials and suggestion to use powerpoint for teaching.
Now that I know PowerPoint, how can I use it to TEACH? [available also as a Flash presentation]

A simple flowchart to start setting-up your web presence. It is also an organized entry point into the list of tools I tried for my web pages.
Other useful pointers about setting up a web presence.
Teaching Organic Chemistry with Blogs and Wikis

Here are, with a minimal justification, some references useful for the course.

A. Globus, E. Raible: 14 Ways to Say Nothing with Scientific Visualization
Rules for effective visualization explained in a humorous way
R. Sayle: PDB: Cruft to Content
Perception of Molecular Connectivity from 3D Coordinates