Molecular Visualization Day - talks

Stefano Leoni, Max-Planck Institute for Chemical Physics of Solids
Thinking with the Eyes: Productive Visualization in Natural Sciences

Real life examples of visualizations from his own research. A lot of images were done with my STM4, but he added an interesting creative touch. Notable highlights:

• Illuminated streamlines to show atom movements
• Translucent polyhedra to draw attention to the important parts of the scene
• Busy ball-and-stick structure where, due to the crossing of bonds, the formation of a phase transition seed was highligthed

Matt Cooper, Department of Science and Technology (ITN), University of Linköping
Evaluating the Effectiveness of Haptics for Biomolecular Education

Interesting study on the effectiveness of haptic interfaces for a protein docking problem. He made a distinction between been used to an interface method and having help from the interface. At the end the conclusion was thatreally haptic does not help much for understanding of data. Another consideration worth noting is that the haptic force feedback device needed was not a simple 3D one, but a 6D one (position plus rotations). That means higher cost and computation requirements.

He also defined visualization as a process with an image at the end. Later someone corrected the definition to: visualization is a process with an image in the middle. Quite true, also if compared to the James Watson discovery loop I show in my talks.

I envy the T-shirt Matt was wearing: the capsicine structural formula on the front and hot peppers on the back!

Jens Thomas, Computational Chemistry Group, Daresbury Laboratory
CCP1GUI Visualization System

A GUI for the Gamess-UK computational code. Besides the usual structure viewer, it featured an interesting Grid interface for the computational code. The idea was to create and unified, simple interface for computationale chemists so they have a single entry point for all their works. Interesting. The code is written in Python and is available.

Ganga Periyasamy, School of Chemistry, University of Manchester
Visualization to understand magnetically induced currents in transition metal complexes

This talk was interesting because visualization were disappointing...

She spoke on her research about the electronic currents in various compounds. The computations were done with Matlab that produced the 2D contour charts (1 a.u. below, on the molecule plane and 1 a.u. above). Due to the scarcity of points, Matlab produced horrible artefacts instead of smooth contours of the modulus of the vector currents).

This problem has been already solved (see the work of Daniel Sebastiani here at CSCS), but in my opinion the interest of this talk derived from a study of the problems a non-specialized tool could create for visualization.