vmd-tutorial.Bioinfo.2009

University of Illinois at Urbana-ChampaignBeckman Institute for Advanced Science and TechnologyTheoretical and Computational Biophysics GroupVMD Molecular GraphicsJordi CohenVMD Developer: John StoneMarcos SotomayorElizabeth VillaMay 2003.A web version, in color, is available athttp://www.ks.uiuc.edu/Training/SumSchool03/Tutorials/vmdCONTENTS 2Contents1 Basics of VMD 41.1 Loading a Molecule . . . . . . . . . . . . . . . . . . . . . . . . . . 41.2 Displaying the Protein . . . . . . . . . . . . . . . . . . . . . . . . 51.3 Exploring Di!erent Drawing Styles . . . . . . . . . . . . . . . . . 61.4 Di!erent Coloring Methods . . . . . . . . . . . . . . . 81.5 Exploring Di!erent Selections . . . . . . . . . . . . . . . . . . . . 81.6 Multiple Representations. . . . . . . . . . . . . . . . . . . . . . . 101.7 Sequence Extension. . . . . . . . . . . . . . . . . . . . . . . . . . 111.8 Saving your Work . . . . . . . . . . . . . . . . . . . . . . . . . . 122 Multiple Molecules and Scripting 142.1 Loading Multiple Molecules . . . . . . . . . . . . . . . . . . . . . 142.2 Using the Main Window . . . . . . . . . . . . . . . . . . . . . . . 152.3 Tcl Scripting Basics and TkCon. . . . . . . . . . . . . . . . . . . 162.4 The atomselect Command . . . . . . . . . . . . . . . . . . . . . 172.5 Aligning Two Molecules . . . . . . . . . . . . . . . . . . . . . . . 202.6 Using Color to Display the Deviation . . . . . . . . . . . . . . . . 223 Trajectories, Macros and ...