An Introduction to Molecular Visualization：分子可视化导论.ppt

August 13, 2007 Introduction to Molecular Visualization CSB 2007, UCSD An Introduction to Molecular Visualization John “Scooter” Morris, Ph.D. Conrad Huang, Ph.D. University of California, San Francisco Introductions Who we are Conrad Huang: RBVI Director of Software Development 25+ years of experience in Molecular Visualization John “Scooter” Morris: RBVI Executive Director 19 years in pharmaceutical industry (Genentech) 3 years at RBVI Introductions Who are you? Biologists? Chemists? Bioinformaticists? Computer Scientists? Other Computational Sciences? Other? Materials Handouts CD Chimera installers Examples data files Agenda Molecular Visualization Available Tools Scenarios of use Using UCSF Chimera Extending Chimera Molecular Visualization Data sources Representations Manipulations Analysis Modeling Definitions visualization: Function: noun 1 : formation of mental visual images 2 : the act or process of interpreting in visual terms or of putting into visible form modeling (model): Function: verb transitive verb 1 : to plan or form after a pattern : SHAPE 3 b : to produce a representation or simulation of using a computer to model a problem 4 : to construct or fashion in imitation of a particular model modeled its constitution on that of the United States intransitive verb 1 : to design or imitate forms : make a pattern enjoys modeling in clay Data sources Structural determination Xray Crystallography NMR EM/Cryo EM Models (ab initio, homology) Volumetric data EM/Cryo EM Electron density Light microscopy Non-structural data sources Sequence data Pathway data Interaction data Expression data Data sources Structure repositories Protein Databank: / Nucleic Acid Database (NDB): / Structural Classification of Proteins (SCOP): http://scop.mrc-lmb.cam.ac.uk/scop/ ModBase: / Cambridge Structural Database (CSD): http://www.ccdc.cam.ac.uk/products/csd/ VIPER EM Database: /emdb/ EM Database: http://www.ebi.ac.uk/msd-srv/emsearch/index.html Uppsala Elec