Primary reference:UCSF Chimera--a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct;25(13):1605-12.Additional papers on features and methodology:
Enhancing UCSF Chimera through web services. Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W478-84.UCSF Chimera, MODELLER, and IMP: An integrated modeling system. Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE. J Struct Biol. 2012 Sep;179(3):269-78.Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. Pintilie GD, Zhang J, Goddard TD, Chiu W, Gossard DC. J Struct Biol. 2010 Jun;170(3):427-38.structureViz: linking Cytoscape and UCSF Chimera. Morris JH, Huang CC, Babbitt PC, Ferrin TE. Bioinformatics. 2007 Sep 1;23(17):2345-7.Visualizing density maps with UCSF Chimera. Goddard TD, Huang CC, Ferrin TE. J Struct Biol. 2007 Jan;157(1):281-7.Tools for integrated sequence-structure analysis with UCSF Chimera. Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. BMC Bioinformatics. 2006 Jul 12;7:339. PMID: 16836757Nucleic acid visualization with UCSF Chimera. Couch GS, Hendrix DK, Ferrin TE. Nucleic Acids Res. 2006 Feb 14;34(4):e29.Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. Goddard TD, Huang CC, Ferrin TE. Structure. 2005 Mar;13(3):473-82.