VMD User’s Guide Version 1.9.4a48 October 13, 2020 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 behavior of VMD. VMD development is supported by the National Institutes of Health grant numbers NIH P41- GM104601. 1http://www.ks.uiuc.edu/ Contents 1 Introduction 11 1.1 Contactingtheauthors. ....... 12 1.2 RegisteringVMD.................................. 12 1.3 CitationReference ............................... ...... 12 1.4 Acknowledgments................................. ..... 13 1.5 Copyright and Disclaimer Notices . .......... 13 1.6 For information on our other software . .......... 15 2 Hardware and Software Requirements 17 2.1 Basic Hardware and Software Requirements . ........... 17 2.2 Multi-core CPUs and GPU Acceleration . ......... 17 2.3 Parallel Computing on Clusters and Supercomputers . .............. 18 3 Tutorials 19 3.1 RapidIntroductiontoVMD. ...... 19 3.2 Viewing a molecule: Myoglobin . ........ 19 3.3 RenderinganImage ................................ 21 3.4 AQuickAnimation................................. 21 3.5 An Introduction to Atom Selection . ......... 22 3.6 ComparingTwoStructures . ...... 22 3.7 SomeNiceRepresenations . ....... 23 3.8 Savingyourwork.................................. 24 3.9 Tracking Script Command Versions of the GUI Actions . ............ 24 4 Loading A Molecule 26 4.1 Notes on common molecular file formats . ......... 26 4.2 Whathappenswhenafileisloaded? . ....... 27 4.3 Babelinterface .................................. ..... 27 4.4 Raster3Dfileformat ............................... ..... 28 5 User Interface Components 29 5.1 UsingtheMouseintheGraphicsWindow . ........ 29 5.1.1 MouseModes ................................... 29 5.1.2 PickModes ..................................... 30 5.1.3 HotKeys ...................................... 32 5.2 Using the Spaceball in the Graphics Window . .......... 33 5.2.1 SpaceballDriver ............................... 33 2 5.3 Using the Joystick in the Graphics Window . .......... 35 5.4 Description of each VMD window . ....... 36 5.4.1 MainWindow.................................... 36 5.4.2 Main Window Molecule List browser . ...... 36 5.4.3 Main Window Animation Controls . ..... 38 5.4.4 Molecule File Browser Window . ..... 39 5.4.5 MouseMenu .................................... 40 5.4.6 Display Menu and Display Settings Window . ........ 42 5.4.7 GraphicsWindow ................................ 45 5.4.8 LabelsWindow.................................. 49 5.4.9 ColorWindow ................................... 51 5.4.10 MaterialWindow............................... 53 5.4.11 RenderWindow ................................. 54 5.4.12 ToolWindow ................................... 54 5.4.13 IMD Connect Simulation Window . ..... 57 5.4.14 SequenceWindow ............................... 59 5.4.15 RamaPlot..................................... 61 6 Molecular Drawing Methods 63 6.1 Renderingmethods................................ ..... 63 6.1.1 Lines......................................... 64 6.1.2 Bonds ........................................ 64 6.1.3 DynamicBonds .................................. 65 6.1.4 HBonds ....................................... 65 6.1.5 Points ........................................ 65 6.1.6 VDW ........................................ 66 6.1.7 CPK......................................... 66 6.1.8 Licorice ...................................... 66 6.1.9 Polyhedra..................................... 66 6.1.10 Trace ........................................ 67 6.1.11 Tube......................................... 67 6.1.12 Ribbons...................................... 67 6.1.13 NewRibbons ................................... 68 6.1.14 Cartoon...................................... 68 6.1.15 NewCartoon ................................... 69 6.1.16 PaperChain................................... 69 6.1.17 Twister ...................................... 69 6.1.18 QuickSurf.................................... 69 6.1.19 Surf ......................................... 70 6.1.20 MSMS........................................ 71 6.1.21 NanoShaper................................... 71 6.1.22 VolumeSlice.................................. 72 6.1.23 Isosurface ................................... 72 6.1.24 FieldLines................................... 73 6.1.25 Orbital ...................................... 73 6.1.26 Beads ........................................ 73 6.1.27 Dotted....................................... 73 3 6.1.28 Solvent ...................................... 74 6.2 ColoringMethods................................. ..... 74 6.2.1 Colorcategories ............................... 75 6.2.2 ColoringMethods ............................... 75 6.2.3 Coloring by color categories . ....... 76 6.2.4 Colorscale .................................... 77 6.2.5 Materials ..................................... 77 6.3 SelectionMethods ................................ ..... 79 6.3.1 Definition of Keywords and Functions . ....... 80 6.3.2 BooleanKeywords ............................... 81 6.3.3 ShortCircuiting ............................... 81 6.3.4 QuotingwithSingleQuotes . ..... 81 6.3.5 Double Quotes and Regular Expressions . ........ 82 6.3.6 Comparisonselections . ..... 83 6.3.7 ComparisonOperators. 83 6.3.8 Otherselections ............................... 84 7 Viewing Modes 90 7.1 Perspective/Orthographic views . ........... 90 7.2 MonoscopicModes ................................. 90 7.3 StereoscopicModes............................... ...... 90 7.3.1 Quad-bufferedStereo. 91 7.3.2 Side-By-Side and Cross-Eyed Stereo . ........ 91 7.3.3 HDTVSide-by-sideStereo. ..... 92 7.3.4 CheckerboardStereo . 92 7.3.5 Column Interleaved Stereo . ...... 92 7.3.6 RowInterleavedStereo . 92 7.3.7 AnaglyphStereo ................................ 92 7.3.8 StereoParameters .............................. 93 8 Scene Export and Rendering 94 8.1 ScreenCaptureUsingSnapshot . ........ 94 8.2 HigherQualityRendering . ....... 94 8.3 Caveats ......................................... 95 8.4 OneStepPrinting ................................. 96 8.5 MakingStereoImages .............................. ..... 96 8.6 MakingaMovie.................................... 97 9 Tcl Text Interface 99 9.1 Usingtextcommands ............................... 99 9.2 Tcl/Tk.......................................... 100 9.3 TclTextCommands ................................. 100 9.3.1 animate ....................................... 100 9.3.2 atomselect.................................... 102 9.3.3 axes .........................................105 9.3.4 color......................................... 105 9.3.5 colorinfo..................................... 106 4 9.3.6 display....................................... 107 9.3.7 draw.........................................109 9.3.8 exit .........................................110 9.3.9 graphics...................................... 110 9.3.10 gettimestep .................................. 112 9.3.11 help ......................................... 112 9.3.12 imd .........................................112 9.3.13 label........................................ 113 9.3.14 light ........................................ 114 9.3.15 logfile ....................................... 115 9.3.16 material..................................... 115 9.3.17 mdffi.........................................116 9.3.18 measure...................................... 116 9.3.19 menu ........................................126 9.3.20 mol .........................................127 9.3.21 molecule..................................... 130 9.3.22 molinfo ...................................... 130 9.3.23 mouse ........................................ 132 9.3.24 parallel ..................................... 133 9.3.25 play ......................................... 134 9.3.26 quit ......................................... 134 9.3.27 render....................................... 134 9.3.28 rock ......................................... 135 9.3.29 rotate ....................................... 135 9.3.30 scale........................................ 135 9.3.31 stage........................................ 136 9.3.32 tool ......................................... 136 9.3.33 translate.................................... 136 9.3.34 user ......................................... 137 9.3.35 vmdinfo...................................... 137 9.3.36 volmap ....................................... 137 9.3.37 voltool...................................... 143 9.3.38 wait ......................................... 145 9.3.39 sleep........................................ 145 9.4 Tclcallbacks .................................... 145 10 Python Text Interface 148 10.1 Using the Python interpreter within VMD . ...........148 10.2 PythonmoduleswithinVMD . 148 10.3 AtomselectionsinPython. ........149 10.3.1 Thebuilt-inatomseltype . 149 10.3.2 TheAtomSelclass(DEPRECATED). 152 10.3.3 An atom selection example . 154 10.3.4 Changing the selection and the frame . ........155 10.3.5 Combining atom selections