VRML Converters

VRML Converter for Chemical Structures

We have implemented a WWW-accessible service which accepts chemical structures in more than 40 established 2D and 3D chemistry exchange formats and produces a VRML scene according to user-specified visualization parameters [2]. If the exchange formats do not contain 3D coordinates, they will be computed automatically. The application allows the interactive change of display style and measurement of atom distances and angles by clicking on the atoms. These are pure client-side functionalities implemented by automaticlly generated, embedded scripts. It is also possible to label atoms with atom properties such as atomic number, atom symbol, polarizability or sigma-charge.

A further feature of the application is the visualization of multi-frame files. These chemical exchange formats contain several 3D datasets of one molecular ensemble in different time steps. These files can be used to save molecular movements as they occur in reaction paths or molecular dynamics. Our application saves these movements as trajectories and displays them as animated 3D scenes.

VRML Converter for Biological Macromolecules

Biological macromolecules, like proteins or nucleic acids (e.g. DNS) involve several 100 to several 10000 atoms. This fact leads to problems for the visualization of such molecules. Single bonds and atoms cannot displayed anymore as separate graphical objects, because the interactive rendering of the resulting 3D scene would be impossible on low-budget computers. On the other side, scientists are often not interested in the display of macromolecules which includes all the atomar detail information. Too much information down to the level of single atoms leads to an overloaded scene, which makes it very difficult to recognize important elements like secondary structures. So, specific display styles for secondary structure elements have emerged. The visualization of these molecules requires special methods to obtain a high rendering quality while maintaining responsiveness. We have developed an optimizing VRML converter for biological macromolecules to their common display styles. It allows a flexible representation of selected groups and atoms. This option makes it possible to add detailed atomic information into the scene only where it is useful and required.