Mario Valle Web

Chemistry Visualization

[ChemViz corner at the CSCS Open Day 2005]

About half of the computing power of CSCS is devoted to Chemistry and Chemistry-related users.

So chemistry visualization is an important research theme for the CSCS Data Analysis and Visualization Group. We support and help chemistry research providing tools, knowledge and training that could enhance researchers' scientific work.

In this section you will find information about STM4, the chemistry visualization toolkit developed for the CSCS users, material from chemistry visualization courses and tutorials, handouts for the ChemViz talks and general resources about visualization applied to chemistry.

STM4 molecular visualization toolkit

The STM4 molecular visualization toolkit is a platform on which new, advanced or unusual visualization techniques can be implemented, extended and tried. For this reason its main goal is not to replace existing tools, or to be a simple-to-use end-user tool like Molekel.

[STM4 Molecular Visualization Toolkit]

STM4, and its predecessor STM3, have a dedicated section of this site. Go there for download instructions, module list and so on. If you are already a STM3 user, you find here the differences with STM4 and changes needed to your applications.

A paper describing STM3 has been published in Zeitschrift für Kristallographie Vol. 220 (2005) Issue 5-6 Pages 585-588 (BibTeX entry) (the PDF is from the publisher: Oldenbourg Wissenschaftsverlag, München).

Courses and tutorials on chemistry visualization

Title Where & When Material
An introduction to the molecular visualization toolkit STM4 ETH Zürich — AVS Workshop (April 9, 2008) commented slides
Practical Visualization for Chemistry Tutorial for the Competence Centre for Computational Chemistry — ETH Zürich (September 3-4, 2007) course pages
Advanced Visualization for Chemistry Swiss National Supercomputing Centre (CSCS) course (March 7-8, 2006) course pages
Beyond Ball-and-Stick – what scientific visualization can do for chemistry users Swiss National Supercomputing Centre (CSCS) tutorial for the CSCS User Day (September 27, 2005) course pages
Chemistry Visualization using the STM3 toolkit Course for the AVS User Meeting held at ETH Zürich(December 7, 2006; April 8, 2005) course pages

Talks about chemistry visualization

Title Where & When Material
Chemistry Visualization Tools in an Integrated Discovery Cycle Talk at the EGEE'07 conference held in Budapest (October 1, 2007)
Beyond Ball-and-Stick – Representation and Perception in Chemistry Visualization Talk at the University of Manchester for the Molecular visualization day (April 20, 2007) talk material
From Tradition to Insight Support – What we can demand from our Chemistry Visualization Tools Talk at the University of Manchester for the Molecular visualization day (April 20, 2007) talk material
Beyond Ball-and-Stick: In search of the perfect visualization tool for Chemistry Talk at SISSA — Trieste (December 11, 2006) talk announcement
Beyond Ball-and-Stick: In search of the perfect visualization tool for Chemistry Talk at CRS4 (Pula, Cagliari) for the EUA4X event: Transport in Polymeric Membranes: Modern Trends in Simulation Methods and Experimental Techniques (October 17, 2006)
Beyond Ball-and-Stick – in search of the perfect visualization tool Talk for the Max-Planck-Institut für Chemische Physik fester Stoffe — Dresden (March 11, 2005) talk material

VMD plugins

Here are plugins developed for VMD to solve our users problems.

  1. The MultiMSMS plugin caches the Solvent Excluded Surface computed by MSMS to speedup animation of a sequence of frames.

The Perfect Tool Project

The name “The Perfect Tool Project” is an ironic name with a double meaning:

  1. Looking at the existing visualization tools with a non-chemist eye, seems that they are far from perceptions and worse, they lags behind the chemistry reliance on graphical representations
  2. It is intended to be an “igniter” for both visualization experts and chemistry researchers to make both fight the status quo and ask for new developments and functionalities

Look at the project page

ChemViz resources

Be patient, the material is not yet ready for public consumption. But, hopefully, will be available shortly. For now here are some pointers:

  • Notes on color usage in chemistry
  • Work in progress about representation in chemistry: a gallery of examples.