Molecular Visualization Day - my talks

Beyond Ball-and-Stick – Representation and Perception in Chemistry Visualization

The morning talk was about:

• Representational conformism in chemistry visualization software
• How a good representation could enhance understanding
• How all the chemistry representations are metaphorical
• How standard representation could limit insight
• All this with examples of strange, new representations and how standard representations could be chosend with different criterias.

From Tradition to Insight Support – What we can demand from our Chemistry Visualization Tools

The final talk was on tools. I presented my tools survey that covers:

• Usability problem with visualization tools
• Divorce between the chemists' mental process and what a tool offers.
• And how visualization tool are mostly used for presentation and not for discovery

Ideas and questions from the audience:

1. As an example I cite Photoshop as one example of perfect tools in its field. Someone said that it is considered perfect because it is the bestseller of its category. Chicken and egg problem... anyway, the best seller draw the path and must stay in the top. That means it is forced to be perfect every time more in my opinion.
2. Is there any universal data file format? Yes! It is called CML (Chemystry Markup Language) but unfortunately no one care about it.
3. Why instead of doing more, the tools try to do less? That means, why the tools does not try to be built around components? Good suggestion. One example is OpenBabel. It tries to create a component devoted to data file input/output and nothing more. Good idea, but has shortcomings.
4. Visualization for the disabled. In UK if a blind person asks to take a visualization course you are forced to take him. I never had this kind of problem, but nonetheless it is something worth thinking about. For example studying auralization or considering broadly visualization as perceptualization.
5. How do you show something that is missing? (from the Stefano Leoni talk). For example it is difficult to show a vacancy or where water transforms into vapor.
6. An image is worth 10.000 words, but should be the right 10.000 words!

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.

Manchester Molecular Visualization Day

Last April 20 the University of Manchester organized a Molecular Visualization Day to advertise what visualization could do to help chemistry researchers.

I was the star of the show with two talks (here are the abstracts and slides). I tried to cover my research on chemistry representations and visualization tools. The questions were stimulating (and the hospitality splendid too!).

Next posts I will cover ideas from the other speakers and comments and ideas from my own talks.

STM4 released!

At last I have released the new varsion of my chemistry visualization environment STM3. It is obviously called STM4.

If you already know STM4, take a look to the new STM4 pages.

If you do not know what STM3 is look at its pages. Briefly STM3 does not want to sobstitute any existing chemistry visualization tools, but istead provides an environment in which to implement unusual and advanced visualization techniques as requested by my users.

STM4 is built on top of the commercial visualization development environment AVS/Express. This is good (it saves me from developing everything needed, it provides visualization techniques not normally available in a chemistry visualization tool) and bad (you need to buy a license).

Currently STM4 has been tested and compiled under:

• Linux Suse 10.x
• Windows XP
• Mac OSX 10.4
• Linux Red Hat Enterprise Linux AS release 4 (64 bits)
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