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This book emphasizes computer programs that analyze protein structural data with program output generating data files and visual feedback in the form of a molecular display. The theoretical part of the text considers both the mathematical models related to molecular structure and the computational strategies that work with these models to derive results. The practical part of the text presents UCSF Chimera as a "workbench" that provides a Python programming environment and the ability to see program output in the molecular display. The accompanying CD-ROM includes Python code, color figures, and session files for Chimera.