VMD User's Guide

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First Wordanimateatomselectaxescolorcolorinfodisplayexit, quitgettimestephelpimdlabellightlogfilematerialmeasuremenumolecule or molmolinfomouseplayrenderrockrotatescalestagetooltranslateuservmdinfovolmapwaitsleepDescriptionPlay/Pause/Rewind a molecular trajectory.Create atom selection objects for analysis.Position a set of XYZ axes on the screen.Change the color assigned to molecules, or edit the colormap.(Tcl) Obtain color properties for various objectsChange various aspects of the graphical display window.Quit VMD.Retrieve a timestep as a binary Tcl array (use for plugins)Display an on-line help file with an HTML viewer.Control the connection to a remote simulation.Turn on/off labels for atoms, bonds, angles, dihedral angles, or springs.Control the light sources used to illuminate graphical objects.Turn on/off logging a VMD session to a file or the console.Create new material definitions and modify their settings.Measure properties of moleculear structures.Control or query the on-screen GUI menu forms.Load, modify, or delete a molecule.Get information about a molecule or loaded file.Change the current state (mode) of the mouse.Start executing text commands from a specified file.Output the currently displayed image (scene) to a file.Rotate the current scene continually at a specified rate.Rotate the current scene around a given axis by a certain angle.Scale the current scene up or down.Position a checkerboard stage on the screen.Initialize and control external spatial tracking devices.Translate the objects in the current scene.Add new keyboard commands.(Tcl) Get information about this version of VMDCreate volumetric data based on molecular informationWait a number of seconds before reading another command. Animation continues.Sleep a number of seconds before reading another command. Animation is frozen.Table 8.1: Summary of core text commands in VMD.120
Sourceraster3dmsmsfaqbiocoretachyonbabelhomepagequickhelpradiancemaillistscriptsnamdvrmlrayshadepovraypluginspythonsoftwaretcluserguideAssociated URLhttp://www.bmsc.washington.edu/raster3d/http://www.scripps.edu/pub/olson-web/people/sanner/html/msms home.htmlhttp://www.ks.uiuc.edu/Research/vmd/allversions/vmd faq.htmlhttp://www.ks.uiuc.edu/Research/biocore/http://jedi.ks.uiuc.edu/~johns/raytracer/http://www.eyesopen.com/babel/http://www.ks.uiuc.edu/Research/vmd/http://www.ks.uiuc.edu/Research/vmd/vmd help.htmlhttp://radsite.lbl.gov/radiance/HOME.htmlhttp://www.ks.uiuc.edu/Research/vmd/mailing list/http://www.ks.uiuc.edu/Research/vmd/script library/http://www.ks.uiuc.edu/Research/namd/http://www.web3d.org/http://www-graphics.stanford.edu/~cek/rayshade/rayshade.htmlhttp://www.povray.org/http://www.ks.uiuc.edu/Research/vmd/plugins/http://www.python.org/http://www.ks.uiuc.edu/Research/vmd/allversions/related programs.htmlhttp://www.tcl.tk/http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.1/ug/ug.htmlTable 8.2: On-line Help Sources121
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VMD User’s GuideVersion 1.8.6Apri
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4.4.4 Molecule File Browser Form .
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8.3.20 molecule . . . . . . . . . .
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List of Figures2.1 Sample VMD sessi
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Chapter 1IntroductionVMD is a molec
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1.4 AcknowledgmentsThe authors woul
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• TachyonThe Tachyon multiprocess
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Figure 2.1: Sample VMD session disp
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2.5 An Introduction to Atom Selecti
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selection: protein and (name CA or
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no coordinate information. It must
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Chapter 4User Interface ComponentsV
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• Center (hot key ’c’)This mo
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Hot Key Command Purposer, R mouse m
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Hot Key Command Purpose+,f,F animat
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information. Atoms shows the number
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Animation SpeedThe rate of playback
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can change the view of the scene, e
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• Perspective - The view of the s
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4/3 SCRHEIGHTi.e. 8.0YViewer’sEye
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Hiding a rep. To hide a rep, double
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Periodic TabThe Periodic tab contro
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• Name - the name of the atom as
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Figure 4.10: The Material Formslide
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force-feedback (haptic) devices suc
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the simulated spring is connected t
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Figure 4.13: The Sequence formmolec
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• Selections by chain: When there
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Chapter 5Molecular Drawing MethodsE
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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
Page 69 and 70: Figure 5.1: RGB color scale: the th
Page 71 and 72: esname ALA to CYS TYRselects atoms
Page 73 and 74: esname ’A 1’More importantly, r
Page 75 and 76: the numeric sense) or greater than
Page 77 and 78: Keyword Arg Descriptionall bool eve
Page 79 and 80: FunctionDescriptionsqr(x) square of
Page 81 and 82: Chapter 6Viewing ModesThere are man
Page 83 and 84: sci-fi and horror movie showings. T
Page 85 and 86: Name Description Default Render Com
Page 87 and 88: • Dotted spheres are not drawn wi
Page 89 and 90: Chapter 8Tcl Text InterfaceThe Tcl
Page 91 and 92: • speed n: Set animation speed to
Page 93 and 94: last frame. If the frame is a speci
Page 95 and 96: - BWG - Blue to white to green.- Bl
Page 97 and 98: • antialias < on | off >: Turn an
Page 99 and 100: • cylinder {x1 y1 z1} {x2 y2 z2}
Page 101 and 102: • kill: Disconnect from the simul
Page 103 and 104: - ambient- specular- diffuse- shini
Page 105 and 106: the area contributions are coming f
Page 107 and 108: 8.3.19 molLoad, modify, or delete a
Page 109 and 110: • modselect rep number molecule n
Page 111 and 112: • index n: Returns the id of the
Page 113 and 114: 8.3.26 rockRotate the current scene
Page 115 and 116: 8.3.33 vmdinfo(Tcl) Returns informa
Page 117 and 118: • -minmax {{ x min y min z min }
Page 119: In the VMD script library at http:/
Page 123 and 124: Table 8.4: Description of Tcl callb
Page 125 and 126: version (2.2). Thus if you have Pyt
Page 127 and 128: • align(ref=None, move=None, fram
Page 129 and 130: esid5.frame()50>>> resid5.frame(22)
Page 131 and 132: ef=AtomSel(’backbone’,frame=0)f
Page 133 and 134: functions (e.g., listall()) overlap
Page 135 and 136: • update ui():• update on():Upd
Page 137 and 138: 9.5.7 labelPython operations availa
Page 139 and 140: • add volumetric(molid, name, ori
Page 141 and 142: • set colorupdate(molid, rep, ono
Page 143 and 144: 9.6 High-level Python InterfaceVMD
Page 145 and 146: 9.6.2 MoleculeRepThe MoleculeRep cl
Page 147 and 148: Chapter 10Vectors and MatricesTcl d
Page 149 and 150: • veccross v1 v2 - Returns the ve
Page 151 and 152: • transaxis amount [deg|rad|pi]
Page 153 and 154: -axiszamount [rad|deg|pi] - Adds a
Page 155 and 156: Chapter 11Molecular Analysis11.1 Us
Page 157 and 158: vmd> set sel [atomselect top "water
Page 159 and 160: The decimal in ”1.0” is importa
Page 161 and 162: # get the sidechain atoms (CB and o
Page 163 and 164: Applying this to the alanin.pdb coo
Page 165 and 166: have the same number of atoms, then
Page 167 and 168: set transformation_matrix [measure
Page 169 and 170: }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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