VMD User's Guide

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the variable remains, and the amount of rotation, in radians, is returned. This is used by thosefunctions which need a rotation. The valid values are: a number, followed by one of rad, radian,or radians for a value in radians, the word pi to give the rotation in factors of pi, or one of deg,degree, ordegrees for a value in degrees. If no units are given, the value is assumed to be indegrees.Examples:vmd > set a "180 deg north"180 deg northvmd > find_rotation_value a3.14159vmd > set anorthvmd > set a "1 pi to eat"1 pi to eatvmd > find_rotation_value a3.14159vmd > set ato eatvmd > set a 4545vmd > find_rotation_value a0.785398vmd > expr $M_PI * 3.0 / 2.04.71239vmd > set a "4.71238 radians"4.71238 radiansvmd > find_rotation_value a4.71238154
Chapter 11Molecular Analysis11.1 Using the molinfo commandThis section covers how to extract information about molecules and atoms using the <strong>VMD</strong> textcommand molinfo.Examples:Two functions, one to save the current view position, the other to restore it. The position ofthe axis is not changed by these operations.proc save_viewpoint {} {global viewpointsif [info exists viewpoints] {unset viewpoints}# get the current matriciesforeach mol [molinfo list] {set viewpoints($mol) [molinfo $mol get {center_matrix rotate_matrix scale_matrix global_matrix}]}}proc restore_viewpoint {} {global viewpointsforeach mol [molinfo list] {puts "Trying $mol"if [info exists viewpoints($mol)] {molinfo $mol set {center_matrix rotate_matrix scale_matrixglobal_matrix} $viewpoints($mol)}}}Cycle through the list of displayed molecules, turning each one on one at a time. At the end,return the display flags to their original state.# save the current display stateforeach mol [molinfo list] {set disp($mol) [molinfo $mol get drawn]155
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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
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 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
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: -axiszamount [rad|deg|pi] - Adds a
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 and 180: Index.mailcap, 177.vmdrc, 26, 89, 1
Page 181 and 182: VMDHTMLVIEWER, 174VMDIMAGEVIEWER, 1
Page 183 and 184: move, 35atom, 35fragment, 35highlig
Page 185 and 186: short circuit logic, 72, 75sleepcom
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