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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
- Page 57 and 58: Chapter 5Molecular Drawing MethodsE
- Page 59 and 60: When three or more bonds join at on
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- Page 65 and 66: 5.1.19 BeadsA bounding sphere is dr
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- Page 77 and 78: Keyword Arg Descriptionall bool eve
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- Page 81 and 82: Chapter 6Viewing ModesThere are man
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- 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
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- Page 97 and 98: • antialias < on | off >: Turn an
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- Page 113 and 114: 8.3.26 rockRotate the current scene
- Page 115 and 116: 8.3.33 vmdinfo(Tcl) Returns informa
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- Page 119 and 120: In the VMD script library at http:/
- Page 121 and 122: Sourceraster3dmsmsfaqbiocoretachyon
- Page 123 and 124: Table 8.4: Description of Tcl callb
- Page 125 and 126: version (2.2). Thus if you have Pyt
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- Page 131 and 132: ef=AtomSel(’backbone’,frame=0)f
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- Page 137 and 138: 9.5.7 labelPython operations availa
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- 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
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- 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
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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