VMD User's Guide

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atch mode, 173beta values, 164BioCoRE, 13bondsadd or remove, 24determining, 21label, 44resolution, 58unusual, 21cachemode, 38callbacksPython, 132Tcl, 118, 123center of mass, 159CHARMMfiles, 20, 34chemical2vmd, 177clipping planes, 38user defined, 108coloraccess definitions, 95assignment, 18background, 46category, 46, 66, 67, 95, 170command, 66, 94, 120form, 18, 45, 66, 67id, 39, 66in user-defined graphics, 99index, 95map, 46material properties, 99, 100names, 66, 95properties, 95Python module, 134redefinition, 46, 169revert to default, 169scale, 46, 68, 94, 168changing, 46set minmax, 110, 141color map, 66colorinfocommand, 95, 120coloringby category, 67by color scale, 68by property, 170methods, 15, 39, 57, 65–67, 108, 170Command line options, 171contact residues, 76copyright, 11Coulomb potentialvolumetric data, 116culling, 97debugcommand, 120densityvolumetric data, 115depth cue, 97depth cueing, 37displaycommand, 96, 120device, 172form, 36Python module, 134update, 96, 156, 169distancevolumetric data, 115distance between atoms, 18drawcommand, 97drawingmethod, 15, 39drawn, 31electrostaticsvolumetric data, 116environment variables, 173DISPLAY, 173MSMSSERVER, 63SURF BIN, 63TCL LIBRARY, 176VMD EXCL GL EXTENSIONS, 175VMDBABELBIN, 21, 173VMDCAVEMEM, 174VMDCUSTOMIZESTARTUP, 173VMDDIR, 173VMDFILECHOOSER, 173VMDFORCECONSOLETTY, 174VMDFORCECPUCOUNT, 174VMDFREEVRMEM, 174VMDGDISPLAY, 174VMDGLSLVERBOSE, 174180
VMDHTMLVIEWER, 174VMDIMAGEVIEWER, 174VMDIMMERSADESKFLIP, 175VMDMSECDELAYHACK, 175VMDMSMSUSEFILE, 175VMDPREFERSTEREO, 175VMDSCRDIST, 175VMDSCRHEIGHT, 175VMDSCRPOS, 175VMDSCRSIZE, 175VMDSHEARSTEREO, 175VMDSIMPLEGRAPHICS, 175VMDSPACEBALLPORT, 27VMDTMPDIR, 173VMDVMDMACENABLEEEXTENSIONS,175VMDWIREGL, 175example scriptsPythoncallbacks, 132Tclcustomized startup file example, 176exitcommand, 120eye separation, 83, 96fileload, 14file typesinput, 20, 34output, 31filesoutput, 16read, 91reading, 14, 16, 20, 33, 34, 108startup, 26, 173, 176writing, 31, 91fitRMSD, 166focal length, 83, 96formanimate, 16, 32color, 18, 45, 66, 67display, 36files, 14graphics, 15, 17, 39hot keys, 28label, 43main, 30, 32material, 46molecule file browser, 33mouse, 34RamaPlot, 55render, 16, 47sequence, 52sim, 51tool, 48forms, 106framedelete, 32, 91duplicate, 90write, 91frames, 31frames per second indicator, 37geometric center, 158gettimestepcommand, 100, 120gopythoncommand, 124graphicscommand, 98delete, 100form, 39loading, 98primitives, 98Python module, 135replace, 100user-defined, 97Gromacsfiles, 20, 34gyration, radius of, 162help, 30command, 100, 120topics, 121highlight, 53hot keys, 26, 114animation control, 29customizing, 26menu control, 28mouse control, 27rotation and scaling, 28hydrogen bonds, 59, 104181
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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
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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
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} {$
Page 171 and 172: Chapter 12Customizing VMD SessionsT
Page 173 and 174: • -nt : Do not display the VMD ti
Page 175 and 176: • VMDIMMERSADESKFLIP : Enable a s
Page 177 and 178: axes location lowerleftstage locati
Page 179: Index.mailcap, 177.vmdrc, 26, 89, 1
Page 183 and 184: move, 35atom, 35fragment, 35highlig
Page 185 and 186: short circuit logic, 72, 75sleepcom
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