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In this and the associated article 'BioBlender: A Software for IntuitiveRepresentation of Surface Properties of Biomolecules', (Andrei et al) wepresent BioBlender as a complete instrument for the elaboration of motion(here) and the visualization (Andrei et al) of proteins and othermacromolecules, using instruments of computer graphics. A vast number ofprotein (if not most) exert their function through some extent of motion.Despite recent advances in higly performant methods, it is very difficult toobtain direct information on conformational changes of molecules. However,several systems exist that can shed some light on the variability ofconformations of a single peptide chain; among them, NMR methods providecollections of a number of static 'shots' of a moving protein. Starting fromthis data, and assuming that if a protein exists in more than 1 conformation itmust be able to transit between the different states, we have elaborated asystem that makes ample use of the computational power of 3D computer graphicstechnology. Considering information of all (heavy) atoms, we use animation andgame engine of Blender to obtain transition states. The model we chose toelaborate our system is Calmodulin, a protein favorite among structural anddynamic studies due to its (relative) simplicity of structure and smalldimension. Using Calmodulin we show a procedure that enables the building of a'navigation map' of NMR models, that can help in the identification ofmovements. In the process, a number of intermediate conformations is generated,all of which respond to strict bio-physical and bio-chemical criteria. TheBioBlender system is available for download from the websitewww.bioblender.net, together with examples, tutorial and other useful material.

BioBlender: Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine