A substantial portion of the funding for the development of Chimera comes from a National Center for Research Resources grant (P41 RR-01081) 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 RR-01081).and should cite the primary Chimera reference (see the list of references):The Chimera home page http://www.cgl.ucsf.edu/chimera can also be cited. Please e-mail us the citation of your publication for our records.
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 citations are appropriate when certain features of Chimera are used:
- The solvent-excluded molecular surfaces produced by Chimera are created with the help of the MSMS package from Prof. Michel Sanner. Publications with images of such surfaces should cite:
Sanner, M.F., Olson, A.J., and Spehner, J.C. "Reduced surface: an efficient way to compute molecular surfaces." Biopolymers 38(3):305-320 (1996).
- In Chimera's Multalign Viewer, the sequence-alignment conservation values shown as a histogram may be calculated by the program AL2CO. The Multalign Viewer preferences (Analysis section) control which calculation method is used. Published work using AL2CO conservation values should cite:
Pei, J. and Grishin, N.V. "AL2CO: calculation of positional conservation in a protein sequence alignment." Bioinformatics 17(8):700-712 (2001).
Chimera is the result of the work of many individuals: Conrad Huang, Greg Couch, Eric Pettersen, Thomas Ferrin, Tom Goddard, Elaine Meng, Scooter Morris, Ben Morris, Sam Schreiber, Daniel Greenblatt, David Konerding, Heidi Houtkooper, Teri Klein, Willa Crowell, Norma Belfer, Robin Parsons, and many others.
Chimera incorporates many publicly available software packages. Please read the following list for details.