Primary reference:Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E. "UCSF Chimera - A Visualization System for Exploratory Research and Analysis." J. Comput. Chem. 25(13):1605-1612 (2004).Additional papers on features and methodology:
Morris, J.H., Huang, C.C., Babbitt, P.C., and Ferrin, T.E. "structureViz: Linking Cytoscape and UCSF Chimera." Bioinformatics 23(17):2345-2347 (2007).Goddard, T.D., Huang, C.C., and Ferrin, T.E. "Visualizing density maps with UCSF Chimera." J. Struct. Biol. 157(1):281-287 (2007).Meng, E.C., Pettersen, E.F., Couch, G.S., Huang, C.C., and Ferrin, T.E. "Tools for integrated sequence-structure analysis with UCSF Chimera." BMC Bioinformatics 7(1):339 (2006).Couch, G.S., Hendrix, D.K., and Ferrin, T.E. "Nucleic acid visualization with UCSF Chimera." Nucleic Acids Res. 34(4):e29 (2006).Goddard, T.D., Huang, C.C., and Ferrin, T.E. "Software extensions to UCSF Chimera for interactive visualization of large molecular assemblies." Structure 13(3):473-482 (2005).