VMD User’s Guide Version 1.9.3 November 27, 2016 NIH Biomedical Research Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group1 Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign 405 N. Mathews Urbana, IL 61801 http://www.ks.uiuc.edu/Research/vmd/ Description The VMD User’s Guide describes how to run and use the molecular visualization and analysis program VMD. This guide documents the user interfaces displaying and grapically manipulating molecules, and describes how to use the scripting interfaces for analysis and to customize the be- havior of VMD. VMD development is supported by the National Institutes of Health grant numbers NIH 9P41GM104601 and 5R01GM098243-02. 1http://www.ks.uiuc.edu/ Contents 1 Introduction 10 1.1 Contactingtheauthors. ....... 11 1.2 RegisteringVMD.................................. 11 1.3 CitationReference ............................... ...... 11 1.4 Acknowledgments................................. ..... 12 1.5 Copyright and Disclaimer Notices . .......... 12 1.6 For information on our other software . .......... 14 2 Hardware and Software Requirements 16 2.1 Basic Hardware and Software Requirements . ........... 16 2.2 Multi-core CPUs and GPU Acceleration . ......... 16 2.3 Parallel Computing on Clusters and Supercomputers . .............. 17 3 Tutorials 18 3.1 RapidIntroductiontoVMD. ...... 18 3.2 Viewing a molecule: Myoglobin . ........ 18 3.3 RenderinganImage ................................ 20 3.4 AQuickAnimation................................. 20 3.5 An Introduction to Atom Selection . ......... 21 3.6 ComparingTwoStructures . ...... 21 3.7 SomeNiceRepresenations . ....... 22 3.8 Savingyourwork.................................. 23 3.9 Tracking Script Command Versions of the GUI Actions . ............ 23 4 Loading A Molecule 25 4.1 Notes on common molecular file formats . ......... 25 4.2 Whathappenswhenafileisloaded? . ....... 26 4.3 Babelinterface .................................. ..... 26 4.4 Raster3Dfileformat ............................... ..... 27 5 User Interface Components 28 5.1 UsingtheMouseintheGraphicsWindow . ........ 28 5.1.1 MouseModes ................................... 28 5.1.2 PickModes ..................................... 29 5.1.3 HotKeys ...................................... 31 5.2 Using the Spaceball in the Graphics Window . .......... 32 5.2.1 SpaceballDriver ............................... 32 2 5.3 Using the Joystick in the Graphics Window . .......... 34 5.4 Description of each VMD window . ....... 35 5.4.1 MainWindow.................................... 35 5.4.2 Main Window Molecule List browser . ...... 35 5.4.3 Main Window Animation Controls . ..... 37 5.4.4 Molecule File Browser Window . ..... 38 5.4.5 MouseMenu .................................... 39 5.4.6 Display Menu and Display Settings Window . ........ 41 5.4.7 GraphicsWindow ................................ 44 5.4.8 LabelsWindow.................................. 48 5.4.9 ColorWindow ................................... 50 5.4.10 MaterialWindow............................... 52 5.4.11 RenderWindow ................................. 53 5.4.12 ToolWindow ................................... 53 5.4.13 IMD Connect Simulation Window . ..... 56 5.4.14 SequenceWindow ............................... 58 5.4.15 RamaPlot..................................... 60 6 Molecular Drawing Methods 62 6.1 Renderingmethods................................ ..... 62 6.1.1 Lines......................................... 63 6.1.2 Bonds ........................................ 63 6.1.3 DynamicBonds .................................. 64 6.1.4 HBonds ....................................... 64 6.1.5 Points ........................................ 64 6.1.6 VDW ........................................ 65 6.1.7 CPK......................................... 65 6.1.8 Licorice ...................................... 65 6.1.9 Polyhedra..................................... 65 6.1.10 Trace ........................................ 66 6.1.11 Tube......................................... 66 6.1.12 Ribbons...................................... 66 6.1.13 NewRibbons ................................... 67 6.1.14 Cartoon...................................... 67 6.1.15 NewCartoon ................................... 68 6.1.16 PaperChain................................... 68 6.1.17 Twister ...................................... 68 6.1.18 QuickSurf.................................... 68 6.1.19 Surf ......................................... 69 6.1.20 MSMS........................................ 70 6.1.21 VolumeSlice.................................. 70 6.1.22 Isosurface ................................... 71 6.1.23 FieldLines................................... 71 6.1.24 Orbital ...................................... 72 6.1.25 Beads ........................................ 72 6.1.26 Dotted....................................... 72 6.1.27 Solvent ...................................... 72 3 6.2 ColoringMethods................................. ..... 73 6.2.1 Colorcategories ............................... 73 6.2.2 ColoringMethods ............................... 73 6.2.3 Coloring by color categories . ....... 73 6.2.4 Colorscale .................................... 74 6.2.5 Materials ..................................... 75 6.3 SelectionMethods ................................ ..... 77 6.3.1 Definition of Keywords and Functions . ....... 79 6.3.2 BooleanKeywords ............................... 80 6.3.3 ShortCircuiting ............................... 80 6.3.4 QuotingwithSingleQuotes . ..... 80 6.3.5 Double Quotes and Regular Expressions . ........ 81 6.3.6 Comparisonselections . ..... 82 6.3.7 ComparisonOperators. 82 6.3.8 Otherselections ............................... 83 7 Viewing Modes 89 7.1 Perspective/Orthographic views . ........... 89 7.2 MonoscopicModes ................................. 89 7.3 StereoscopicModes............................... ...... 89 7.3.1 Quad-bufferedStereo. 90 7.3.2 Side-By-Side and Cross-Eyed Stereo . ........ 90 7.3.3 HDTVSide-by-sideStereo. ..... 91 7.3.4 CheckerboardStereo . 91 7.3.5 Column Interleaved Stereo . ...... 91 7.3.6 RowInterleavedStereo . 91 7.3.7 AnaglyphStereo ................................ 91 7.3.8 StereoParameters .............................. 92 8 Scene Export and Rendering 93 8.1 ScreenCaptureUsingSnapshot . ........ 93 8.2 HigherQualityRendering . ....... 93 8.3 Caveats ......................................... 94 8.4 OneStepPrinting ................................. 95 8.5 MakingStereoImages .............................. ..... 95 8.6 MakingaMovie.................................... 96 9 Tcl Text Interface 98 9.1 Usingtextcommands ............................... 98 9.2 Tcl/Tk.......................................... 99 9.3 TclTextCommands ................................. 99 9.3.1 animate ....................................... 99 9.3.2 atomselect.................................... 101 9.3.3 axes .........................................104 9.3.4 color......................................... 104 9.3.5 colorinfo..................................... 105 9.3.6 display....................................... 106 4 9.3.7 draw.........................................108 9.3.8 exit .........................................109 9.3.9 graphics...................................... 109 9.3.10 gettimestep .................................. 111 9.3.11 help ......................................... 111 9.3.12 imd .........................................111 9.3.13 label........................................ 112 9.3.14 light ........................................ 113 9.3.15 logfile ....................................... 114 9.3.16 material..................................... 114 9.3.17 mdffi.........................................115 9.3.18 measure...................................... 115 9.3.19 menu ........................................123 9.3.20 mol .........................................123 9.3.21 molecule..................................... 127 9.3.22 molinfo ...................................... 127 9.3.23 mouse ........................................ 129 9.3.24 parallel ..................................... 129 9.3.25 play ......................................... 130 9.3.26 quit ......................................... 130 9.3.27 render....................................... 130 9.3.28 rock ......................................... 131 9.3.29 rotate ....................................... 132 9.3.30 scale........................................ 132 9.3.31 stage........................................ 132 9.3.32 tool ......................................... 132 9.3.33 translate.................................... 133 9.3.34 user ......................................... 133 9.3.35 vmdinfo...................................... 133 9.3.36 volmap ....................................... 134 9.3.37 wait ......................................... 139 9.3.38 sleep........................................ 139 9.4 Tclcallbacks .................................... 140 10 Python Text Interface 142 10.1 Using the Python interpreter within VMD . ...........142 10.2 PythonmoduleswithinVMD . 142 10.3 AtomselectionsinPython. ........143 10.3.1 Thebuilt-inatomseltype . 143 10.3.2 TheAtomSelclass(DEPRECATED). 143 10.3.3 An atom selection example . 145 10.3.4 Changing the selection and the frame . ........146 10.3.5 Combining atom selections . 147 10.3.6 RMSexample................................... 148 10.4 Pythoncallbacks ...............................