- University of Hamburg - Faculty of Biology - Biocenter Klein Flottbek
How to use the Chime scripts in this project
From atomic coordinates to interactive graphics: a virtual molecular modelling kit
Life may be described as a set of biochemical reactions involving substances as small as hydrogen ions up to the size of giant macromolecules. Life sciences try to explain all aspects of living nature from simple metabolic steps in microorganisms up to the generation of conscience in higher organisms. The description may be rather abstract like a chemical formula defining reactands and products with an exact mass balance. However, to gain some understanding of the mechanisms involved it is helpful to "see" the molecules at work, on an atomic scale. Work has the meaning of interactions of the electron clouds of atoms involved in chemical reactions. To "see" requires the elucidation of the structures of molecules and to find a way to display the spatial configurations or even movements accompanying the "work".
Atomic coordinates of (in July 1999) 10.000 macromolecules are available from the Protein Data Bank, other databanks hold the structures of small molecules or nucleic acids and their complexes, so many facets of biochemistry and molecular biology may be made visible. Computer programs were developed to generate high quality images of molecular structures. For the average enthusiast owning a wintel PC there is a program set allowing the interactive exploration of molecules using publicly accessible atomic data sets. The program Chime enables the generation of movies for viewing by a web browser. The spectator may step through the movies at his own pace or be guided by the author of the underlying script. In the following some conventions for the display of structures are described which ease the understanding of the molecules.
Small molecules displayed with Chime