A substantial portion of the funding for the development of Chimera comes from a National Center for Research Resources grant (P41 RR001081) from the National Institutes of Health. NIH carefully tracks publications that make use of NCRR Resource Centers, 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 images were produced using the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIH P41 RR001081).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:
- 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, molecular assemblies, ...
- Elaine Meng - User's Guide, tutorials, user training, web pages
- Daniel Greenblatt - Collaboratory, movie recorder, bug reporter
- David Konerding - Collaboratory, early version of trajectory viewer
- Greg Pintilie - Segger map segmentation tools
- Wei Zhang - Amber tools, morph map
- Therese Lang - Dock Prep ideas
- Sam Schreiber - Intersurf, ...
- Ben Morris - Raytracing
- Thomas Margraf - Space Navigator support on Linux
... and undoubtedly others.
- Scooter Morris - Cytoscape plugin structureViz
- Shoshana Brown, Scott Pegg - Chimera Web data in the Structure-Function Linkage Database
- Ursula Pieper - Chimera Web data in ModBase
- Elana Erez, Fabian Glaser - Chimera Web data produced by the ConSurf Server
- Wolfgang Skala - PscViewer for viewing sequence and structure alignments
- Mark Moll - ViewMatch for viewing 3D motif search results from LabelHash
- Steve Ludtke - Volume colorizer, EMANimator
- Randy Heiland - MutDB viewer
- Charles Moad - NLOPredict
- Matthew Baker - AIRS toolkit
- Sean Mooney - SBlest interface, catalytic site prediction
- Forbes Burkowski - Structural bioinformatics course materials
- Serge Gorelsky - AOMix molecular orbital attribute viewer
- Karin Gross, Christoph Best - TomoPlane tomography viewer
- Ranyee Chiang - Structure Superposition Database interface
- Andrew Jewett - MinRMS
- Cathy Lawson - Protein Databank curation, EM Databank search
- Suzuki Hirofumi - EM Navigator database images
- Richard Newman - EM Databank images
- Gabe Lander, Padma Natarajan - VIPERdb image creation scripts
- Heidi Houtkooper - Web page development
- Teri Klein - Scientific collaborations
- Frank Federico, Robin Parsons, Willa Crowell, Norma Belfer - Administrative support, event planning
Chimera incorporates many publicly available software packages and accesses several Web services.