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PyMOL: How Pursuit of an Open-Source Molecular Modeling Environment Can Promote Understanding of Molecular Systems.

Warren L. DeLano, Ph.D.
DeLano Scientific LLC San Carlos, California, USA

The PyMOL Experiment tests the hypothesis that significant progress in understanding of molecular systems will result from widespread dissemination and adoption of Open-Source software in the biological and chemical sciences. Because PyMOL has no restrictions on usage, extension, and redistribution, it can serve as a ubiquitous tool for researching, communicating, and teaching about structure and molecular interactions. The program has been designed to fill a variety of roles, from performing specialized research tasks, to preparing illustrations and animations, to providing general purpose, web-based molecular visualization for distributed audiences. As the PyMOL project begins its fifth year of existence, it can now be used by developers to explore a wide variety of scientific topics relating to the structure, function, and evolution of proteins. However, the package still needs substantial improvements in the areas of documentation and usability in order to be accessible to novices and to scientists who are not yet comfortable writing programs.