VMD User's Guide

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Examples:vmd > vecsub 6 3.22.8vmd > vecsub {10 9.8 7} {0.1 0 -0.1}9.9 9.8 7.1vmd > vecsub {1 2 3 4 5} {6 7 8 9 10}-5 -5 -5 -5 -5• (C++) vecsum v – Returns the sum of the elements in vExamples:vmd > vecsum { 1 2 3 }6.0• (C++) vecmean v – Returns the mean of the elements in vExamples:vmd > vecmean { 1 2 3 }2.0• (C++) vecstddev v – Returns the standard deviation of the elements in vExamples:vmd > vecstddev { 1 2 3 4 5 6 7 8 9 10 }2.87228131294• (C++) vecscale cv–• (C++) vecscale vc– Returns the vector of the scalar value c applied to each term of vExamples:vmd > vecscale .2 {1 2 3}0.2 0.4 0.6vmd > vecscale {-5 4 -3 2} -210 -8 6 -4vmd > vecscale -2 3-6• vecdot v1 v2 – Returns the scalar dot product of the two vectorsExamples:vmd > vecdot {1 -2 3} {4 5 6}12vmd > vecdot {3 4} {3 4}25vmd > vecdot {1 2 3 4 5} {5 4 3 2 1}35vmd > vecdot 3 -2-6148
• veccross v1 v2 – Returns the vector cross product of the two vectors.Examples:vmd > veccross {1 0 0} {0 1 0}0 0 1vmd > veccross {2 2 2} {-1 0 0}0 -2 2• veclength v – Returns the scalar length of v (‖v‖)Examples:vmd> veclength 55.0vmd > veclength {5 12}13.0vmd > veclength {3 4 12}13.0vmd > veclength {1 -2 3 -4}5.47723• veclength2 v – Returns the square of the scalar length of v (‖v‖ 2 )Examples:vmd > veclength2 525vmd > veclength2 {5 12}169vmd > veclength2 {3 4 12}169vmd > veclength2 {1 -2 3 -4}30• vecnorm v – Returns the vector of length 1 directed along vExamples:vmd > vecnorm -10-1.0vmd > vecnorm {1 1 }0.707109 0.707109vmd > vecnorm {2 -3 1}0.534522 -0.801783 0.267261vmd > vecnorm {2 2 -2 2 -2 -2}0.408248 0.408248 -0.408248 0.408248 -0.408248 -0.408248• vecdist v1 v2 – Returns the distance between the two vectors (‖v 2 − v 1 ‖)149
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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
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 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
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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: Chapter 10Vectors and MatricesTcl d
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 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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