VMD User's Guide

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• Tcl and Python scripting languagesVMD uses the freely available Python and Tcl scripting languages for processing text commands.These popular languages which contain variables, loops, subroutines, and much more.VMD also uses the Tk Toolkit - a simple user interface toolkit that interfaces with Tcl.• Easy to extendVMD is written in C and C++ and employs object-oriented design. VMD implements aplugin interface for extending its file format support and for general purpose extensions infunctionality.• Support for multimodal input and various display systemsA number of different visual display and control systems are supported in addition to the usualmonitor, keyboard, and mouse. The VRPN library is used to get position and orientationinformation from a wide variety of spatial input devices, including magnetic trackers, haptic(force feedback) devices, Spaceballs, etc. VMD works with WireGL and Chromium on tileddisplay walls, and immersive VR environments via compiled-in CAVE and FreeVR support.1.1 Contacting the authorsThe current developer of VMD is John E. Stone. The list of individuals that made signficantcontributions to this version of VMD in the form of patches, bug fixes, and completely new pluginsincludes Anton Arkhipov, Michael Bach, Jordi Cohen, Markus Dittrich, John Eargle, PeterFreddolino, Luis Gracia, Justin Gullingsrud, Konrad Hinsen, Axel Kohlmeyer, John Mongan, JimPhillips, Jan Saam, Alexander Spaar, Marcos Sotomayor, and Kirby Vandivort.We are very interested in and grateful for any user comments and reports of program bugs orinaccuracies. If you have any suggestions, bug reports, or general comments about VMD, pleasesend them to us at vmd@ks.uiuc.edu.1.2 Registering VMDVMD is made available free of charge for all interested end-users of the software (but please see theCopyright and Disclaimer notices). Please check the current VMD license agreement for details.Registration is part of our software download procedure. Once you’ve filled out the forms on theVMD download area and have read and agreed to the license, you are finished with the registrationprocess.1.3 Citation ReferenceThe authors request that any published work or images created using VMD include the followingreference:Humphrey, W., Dalke, A. and Schulten, K., “VMD - Visual Molecular Dynamics” J. Molec.Graphics 1996, 14.1, 33-38.VMD has been developed by the Theoretical and Computational Biophysics Group at theUniversity of Illinois and the Beckman Institute. This work is supported by grants from the NationalInstitutes of Health (grant number PHS 5 P41 RR05969-04), the National Science Foundation (grantnumber BIR-9423827 EQ), and the Roy J. Carver Charitable Trust.10
1.4 AcknowledgmentsThe authors would particularly like to thank those individuals who have contributed suggestions andimprovements, particularly those contributing new features. Special thanks go to Anton Arkhipov,Andrew Dalke, Michael Bach, Alexander Balaeff, Ilya Balabin, Eamon Caddigan, Jordi Cohen,Markus Dittrich, John Eargle, Peter Freddolino, Todd Furlong, Luis Gracia, Paul Grayson, JustinGullingsrud, Konrad Hinsen, Barry Isralewitz, Sergei Izrailev, Axel Kohlmeyer, John Mongan, JimPhillips, Jan Saam, Alexander Spaar, Charles Schwieters, Marcos Sotomayor, John E. Stone, andKirby Vandivort. The entire VMD user community now benefits from your contributions.The authors would like to thank individuals who have indirectly helped with development bymaking suggestions, pushing for new features, and trying out buggy code. Thanks go to AlekseiAksimentiev, Daniel Barsky, Axel Berg, Tom Bishop, Robert Brunner, Ivo Hofacker, Mu Gao,James Gumbart, Xiche Hu, Tim Isgro, Dorina Kosztin, Ioan Kosztin, Joe Landman, Ilya Logunov,Clare Macrae, Amy Shih, Lukasz Salwinski, Stephen Searle, Charles Schwieters, Ari Shinozaki,Svilen Tzonev, Emad Tajkhorshid, Michael Tiemann, Elizabeth Villa, Raymond de Vries, SimonWarfield Willy Wriggers, Dong Xu, and Feng Zhou.Many external libraries and packages are used in VMD, and the program would not be as capablewithout them. The authors of VMDwish to thank the authors of FLTK; the authors of Tcl and Tk;the authors of Python; the authors of VRPN; Jon Leech for uniform point distributions; AmitabhVarshney for SURF; Dmitrij Frishman for developing STRIDE; Jack Lund for the url get perlscript; Brad Grantham for the ACTC triangle consolidation library; John E. Stone for the Tachyonray tracer and Spaceball drivers; and Ethan Merrit for one of the ribbon drawing algorithms.1.5 Copyright and Disclaimer NoticesVMD is Copyright c○ 1995-2007 Theoretical and Computational Biophysics Group and theBoard of Trustees of the University of IllinoisPortions of this code are copyright c○ 1997-1998 Andrew Dalke.The terms for using, copying, modifying, and distributing VMD are specified by the VMDLicense. The license agreement is distributed with VMD in the file LICENSE. If for any reasonyou do not have this file in your distribution, it can be downloaded from:http://www.ks.uiuc.edu/Research/vmd/current/LICENSE.htmlSome of the code and executables used by VMD have their own usage restrictions:• ACTCACTC, the triangle consolidation library used in some versions of VMD, is Copyright (C)2000, Brad Grantham and Applied Conjecture, all rights reserved.Redistribution and use in source and binary forms, with or without modification, are permittedprovided that the following conditions are met:1. Redistributions of source code must retain the above copyright notice, this list of conditionsand the following disclaimer.2. Redistributions in binary form must reproduce the above copyright notice, this list of conditionsand the following disclaimer in the documentation and/or other materials providedwith the distribution.11
Page 1 and 2: VMD User’s GuideVersion 1.8.6Apri
Page 3 and 4: 4.4.4 Molecule File Browser Form .
Page 5 and 6: 8.3.20 molecule . . . . . . . . . .
Page 7 and 8: List of Figures2.1 Sample VMD sessi
Page 9: Chapter 1IntroductionVMD is a molec
Page 13 and 14: • TachyonThe Tachyon multiprocess
Page 15 and 16: Figure 2.1: Sample VMD session disp
Page 17 and 18: 2.5 An Introduction to Atom Selecti
Page 19 and 20: selection: protein and (name CA or
Page 21 and 22: no coordinate information. It must
Page 23 and 24: Chapter 4User Interface ComponentsV
Page 25 and 26: • Center (hot key ’c’)This mo
Page 27 and 28: Hot Key Command Purposer, R mouse m
Page 29 and 30: Hot Key Command Purpose+,f,F animat
Page 31 and 32: information. Atoms shows the number
Page 33 and 34: Animation SpeedThe rate of playback
Page 35 and 36: can change the view of the scene, e
Page 37 and 38: • Perspective - The view of the s
Page 39 and 40: 4/3 SCRHEIGHTi.e. 8.0YViewer’sEye
Page 41 and 42: Hiding a rep. To hide a rep, double
Page 43 and 44: Periodic TabThe Periodic tab contro
Page 45 and 46: • Name - the name of the atom as
Page 47 and 48: Figure 4.10: The Material Formslide
Page 49 and 50: force-feedback (haptic) devices suc
Page 51 and 52: the simulated spring is connected t
Page 53 and 54: Figure 4.13: The Sequence formmolec
Page 55 and 56: • Selections by chain: When there
Page 57 and 58: Chapter 5Molecular Drawing MethodsE
Page 59 and 60: When three or more bonds join at on
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segment pieces are colored accordin
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• Representation Method - The sur
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5.1.19 BeadsA bounding sphere is dr
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those names to color the atoms. Mol
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Figure 5.1: RGB color scale: the th
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esname ALA to CYS TYRselects atoms
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esname ’A 1’More importantly, r
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the numeric sense) or greater than
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Keyword Arg Descriptionall bool eve
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FunctionDescriptionsqr(x) square of
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Chapter 6Viewing ModesThere are man
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sci-fi and horror movie showings. T
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Name Description Default Render Com
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• Dotted spheres are not drawn wi
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Chapter 8Tcl Text InterfaceThe Tcl
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• speed n: Set animation speed to
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last frame. If the frame is a speci
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- BWG - Blue to white to green.- Bl
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• antialias < on | off >: Turn an
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• cylinder {x1 y1 z1} {x2 y2 z2}
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• kill: Disconnect from the simul
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- ambient- specular- diffuse- shini
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the area contributions are coming f
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8.3.19 molLoad, modify, or delete a
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• modselect rep number molecule n
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• index n: Returns the id of the
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8.3.26 rockRotate the current scene
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8.3.33 vmdinfo(Tcl) Returns informa
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• -minmax {{ x min y min z min }
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In the VMD script library at http:/
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Sourceraster3dmsmsfaqbiocoretachyon
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Table 8.4: Description of Tcl callb
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version (2.2). Thus if you have Pyt
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• align(ref=None, move=None, fram
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esid5.frame()50>>> resid5.frame(22)
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ef=AtomSel(’backbone’,frame=0)f
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functions (e.g., listall()) overlap
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• update ui():• update on():Upd
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9.5.7 labelPython operations availa
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• add volumetric(molid, name, ori
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• set colorupdate(molid, rep, ono
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9.6 High-level Python InterfaceVMD
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9.6.2 MoleculeRepThe MoleculeRep cl
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Chapter 10Vectors and MatricesTcl d
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• veccross v1 v2 - Returns the ve
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• transaxis amount [deg|rad|pi]
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-axiszamount [rad|deg|pi] - Adds a
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Chapter 11Molecular Analysis11.1 Us
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vmd> set sel [atomselect top "water
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The decimal in ”1.0” is importa
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# get the sidechain atoms (CB and o
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Applying this to the alanin.pdb coo
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have the same number of atoms, then
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set transformation_matrix [measure
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}display update offfor {set i 0} {$
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Chapter 12Customizing VMD SessionsT
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• -nt : Do not display the VMD ti
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• VMDIMMERSADESKFLIP : Enable a s
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axes location lowerleftstage locati
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Index.mailcap, 177.vmdrc, 26, 89, 1
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VMDHTMLVIEWER, 174VMDIMAGEVIEWER, 1
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move, 35atom, 35fragment, 35highlig
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short circuit logic, 72, 75sleepcom
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