UCSF Chimera—A visualization system for exploratory research and analysis

Journal of Computational Chemistry - Tập 25 Số 13 - Trang 1605-1612 - 2004
Eric F. Pettersen1, Thomas D. Goddard2, Conrad C. Huang2, Gregory S. Couch2, Daniel M. Greenblatt2, Elaine C. Meng2, Thomas E. Ferrin2
1Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94143-2240, USA.
2Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94143‐2240

Tóm tắt

AbstractThe design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real‐world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1605–1612, 2004

Từ khóa


Tài liệu tham khảo

10.1126/science.7455704

Huang C. C., 1996, Pac Symp Biocomput, 1, 724

10.1016/0263-7855(88)80054-7

10.1093/nar/28.1.235

10.1016/0263-7855(95)00003-O

10.1016/S0263-7855(98)80030-1

10.1016/0263-7855(91)80016-S

10.1016/S0065-3233(08)60520-3

Python;http://www.python.org/.

IDLE (Interactive DeveLopment Environment);http://www.python.org/idle/.

Tkinter;http://www.python.org/topics/tkinter/.

Tix (Tk Interface eXtension);http://tixlibrary.sourceforge.net/.

Pmw (Python megawidgets);http://pmw.sourceforge.net/.

10.1002/(SICI)1097-0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y

OpenGL;http://www.opengl.org/.

10.1038/26694

10.1128/JVI.76.18.9533-9536.2002

10.1093/nar/gkg500

10.1093/nar/30.1.264

10.1016/S0022-2836(05)80134-2

10.1093/bib/3.3.265

10.1093/nar/gkg127

10.1023/A:1011115820450

10.1126/science.257.5073.1078

10.1007/BF00134183

Case D. A.;Pearlman D. A.;Caldwell J. W.;Cheatham T. E. I.;Wang J.;Ross W. S.;Simmerling C.;Darden T.;Merz K. M.;Stanton R. V.;Cheng A.;Vincent J. J.;Crowley M.;Tsui V.;Gohlke H.;Radmer R.;Duan Y.;Pitera J.;Massova I.;Seibel G. L.;Singh U. C.;Weiner P.;Kollman P. A.AMBER;http://amber.scripps.edu/.

van Gunsteren W. F.;Berendsen H. J. C.GROMOS;www.igc.ethz.ch/gromos/.

10.1006/jcph.1999.6201

10.1107/S0907444994003112

Jones T. A.;Kjeldgaard M.The O protein crystallographic package;http://www.imsb.au.dk/∼mok/o/.

10.1107/S0907444998003254

10.1002/(SICI)1097-0134(19990401)35:1<25::AID-PROT3>3.0.CO;2-V

10.1006/jsbi.1996.0030

10.1126/science.7761829

10.1002/prot.340110407

10.1006/jsbi.1996.0010

10.1109/38.56302

Network Common Data Form; Unidata Program Center Boulder CO;http://www.unidata.ucar.edu/packages/netcdf/.

Extensible Markup Language;http://www.xml.org/.

10.1109/4236.656066

Common Object Request Broker Architecture;http://www.corba.org/.

Banatao D. R., 2001, Pac Symp Biocomput, 6, 240

10.1002/pro.5560040404

10.1093/nar/gkh095

10.1107/S0907444902005851

10.1038/nsb1094-717

10.1096/fasebj.9.5.7896002

10.1289/ehp.919311

10.1038/nsb1001-868

10.1006/jmbi.2001.4633

10.1038/373167a0

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Journal of Computational Chemistry

Tập 25 Số 13

1605-1612

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