Chimera development by the UCSF Resource for Biocomputing, Visualization, and Informatics is funded by the National Institutes of Health. NIH tracks publications that make use of our Resource and its software, and hence your cooperation is appreciated in citing the grant number and reference(s) as described below. Thank you!
Publications include scientific papers, posters, films, videos, exhibits, and artwork. Publications with images or results from Chimera should include an acknowledgement similar to the following:
Molecular graphics and analyses were performed with the UCSF Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).and should cite one or more of the Chimera references, such as:The Chimera home page http://www.cgl.ucsf.edu/chimera can also be cited. In addition: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.
For permission to use images from the Chimera web site, please contact chimera@cgl.ucsf.edu.
- Solvent-excluded molecular surfaces are created with the help of the MSMS package:
Reduced surface: an efficient way to compute molecular surfaces. Sanner MF, Olson AJ, Spehner JC. Biopolymers. 1996 Mar;38(3):305-20.Raytraced images are produced with POV-Ray: [citation information]
Several Chimera tools use published methods or software, and their manual pages provide the appropriate citation information
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Chimera is the work of many individuals:... and many more on related projects (see also Chimera plug-ins on the web and sites with Chimera web data):
- Thomas Ferrin - Principal investigator
- Conrad Huang - Project leader
- Greg Couch - OpenGL graphics, molecule rendering, raytracing, ...
- Eric Pettersen - Structure analysis and superposition, sequence viewer, ...
- Tom Goddard - Volume data display and analysis, molecular assemblies, ...
- Elaine Meng - User's Guide, tutorials, user training, web pages
- Zheng Yang - Modeller interface
- Sam Hertig - MultiDomain Assembler
- Darren Weber, David Mischel - Animation tool
- Victor Muñoz Robles, Jean-Didier Maréchal (The Computational Biotechnological Chemistry Team, Universitat Autònoma de Barcelona; funding from Ministerio de Ciencia e Innovación, Generalitat de Catalunya) - normal mode analysis, molecular dynamics simulation
- Daniel Greenblatt - Collaboratory, movie recorder, bug reporter
- David Konerding - Collaboratory, early version of trajectory viewer
- Greg Pintilie - Segger map segmentation tools
- Wei Zhang - Counterion and solvent addition, morph map
- Therese Lang - Dock Prep ideas
- Sam Schreiber - Intersurf, ...
- Jonathan E. Chen - Protein contact maps
- Ben Morris - Raytracing
- Thomas Margraf - Space Navigator support on Linux
... and undoubtedly others.
- Scooter Morris - Cytoscape plugin structureViz
- Nadezhda Doncheva - Cytoscape plugin RINalyzer
- Structure-Function Linkage Database (SFLD) development team - Chimera web data and sessions in the SFLD
- Ursula Pieper - Chimera web data in ModBase
- Elana Erez, Fabian Glaser - Chimera web data produced by the ConSurf Server
- Forbes Burkowski - Structural bioinformatics course materials and textbook: Computational and Visualization Techniques for Structural Bioinformatics Using Chimera (2014)
- Andrew Jewett - MinRMS
- Cathy Lawson - Protein Data Bank curation
- Suzuki Hirofumi - EM Navigator database images
- Richard Newman - Electron Microscopy Data Bank images
- Ardan Patwardhan - Electron Microscopy Data Bank (EMDB)
- Gabe Lander, Padma Natarajan - VIPERdb image creation scripts
- Heidi Houtkooper - Web page development
- Teri Klein - Scientific collaborations
- Kris Casler, Frank Federico, Robin Parsons, Willa Crowell, Norma Belfer - Administrative support, event planning
Chimera incorporates many publicly available software packages and accesses several web services.