PyMOL User's Guide written by Warren L. DeLano, Ph.D. with assistance from Sarina Bromberg, Ph.D. Copyright © 2004 DeLano Scientific LLC All Rights Reserved. Table of Contents Copyright Notice and Usage Terms..................................................................................................................1 Copyright Notice......................................................................................................................................1 Terms of Usage for the PyMOL User's Manual......................................................................................1 Trademarks..............................................................................................................................................1 Preface..................................................................................................................................................................2 Why PyMOL?..........................................................................................................................................2 Words of Caution.....................................................................................................................................2 Strengths..................................................................................................................................................3 Weaknesses..............................................................................................................................................3 Introduction.........................................................................................................................................................4 Welcome to PyMOL!...............................................................................................................................4 Is PyMOL Free Software?.......................................................................................................................4 Yes, but..............................................................................................................................................4 The DeLano Scientific Mission...............................................................................................................4 Installation...........................................................................................................................................................6 Windows..................................................................................................................................................6 Recommendations.............................................................................................................................6 Minimal System Requirements.........................................................................................................6 Python−Free Installation...................................................................................................................6 Python−Dependent Installation.........................................................................................................6 MacOS X.................................................................................................................................................6 Recommendations.............................................................................................................................7 Minimial Requirements.....................................................................................................................7 If you use Fink...................................................................................................................................7 If you do not use Fink........................................................................................................................7 Linux and Unix........................................................................................................................................8 System Requirements........................................................................................................................8 Dependency−Free Approaches.........................................................................................................8 Dependency−Based Approaches.......................................................................................................9 Getting Started with Mouse Controls.............................................................................................................10 Launching..............................................................................................................................................10 Using the Mouse..............................................................................................................................10 Using a Command Line...................................................................................................................10 PyMOL's Windows................................................................................................................................11 The Viewer Window.......................................................................................................................11 The External GUI Window.............................................................................................................12 Loading PDB Files.................................................................................................................................13 Manipulating the View..........................................................................................................................13 Basic Mouse Control.......................................................................................................................13 Virtual Trackball Rotation...............................................................................................................14 Moving Clipping Planes..................................................................................................................16 Changing the Origin of Rotation.....................................................................................................16 Getting Comfortable........................................................................................................................17 i Table of Contents Getting Started with Commands.....................................................................................................................18 Recording Your Work (Optional)..........................................................................................................18 Loading Data..........................................................................................................................................18 Manipulating Objects.............................................................................................................................19 Atom Selections..............................................................................................................................19 Coloring Objects and Selections.....................................................................................................21 Turning Objects and Selections On and Off...................................................................................22 Changing Your Point of View..............................................................................................................23 Saving Your Work.................................................................................................................................23 Scripts and Log Files.......................................................................................................................24 png Files..........................................................................................................................................24 Session Files....................................................................................................................................25 Command−Line Shortcuts.....................................................................................................................25 Command Completion using TAB..................................................................................................26 Filename Completion using TAB....................................................................................................26 Automatic Inferences......................................................................................................................26 Other Typed Commands and Help.......................................................................................................27 Command Syntax and Atom Selections..........................................................................................................28 Syntax....................................................................................................................................................28 Selection−expressions.....................................................................................................................28 Named Atom Selections..................................................................................................................29 Single−word Selectors.....................................................................................................................31 Property