VMD User's Guide

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X-PLOR Wildcard Description Regular Expression* matches any string .*% matches a single character .+ matches any digit [0-9]# matches any number [0-9]+Table 5.10: Regular expression conversions.80
Chapter 6Viewing ModesThere are many different viewing modes available. These show the scene in orthographic or perspectiveviews, and in several mono- and stereo- graphic displays. The stereo mode can be changedusing the stereo entry in the Display form or the text command display stereo mode.6.1 Perspective/Orthographic viewsIn the perspective view (the default), objects which are far away are smaller than those nearby.In the orthographic view, all objects appear at the same scale. Since some prefer one over theother, both options are available. Perspective viewpoints give more information about depth andare often easier to view because you use perspective views in real life. Orthographic viewpointsmake it much easier to compare two parts of the molecule, as there is no question about how theviewpoint may affect the perception of distance.6.2 Monoscopic ModesWhen you normally look at objects, your two eyes see slightly different images (because they arelocated at different viewpoints). Your brain puts the images together to generate a stereoscopicviewpoint. When generating a single image for the computer display, the default calculations (modeStereo Off) assume there is one eye centered between where two eyes would be. For stereo, the leftand right eye views need to be generated independently. Choosing mode Left produces the left eyeviewpoint, while Right produces the right eye viewpoint. The left and right monoscopic modes aremost useful when exporting scenes to external ray tracers.6.3 Stereoscopic ModesMolecules may be rendered in stereo, which can greatly enhance the appearance and visual contentof the displayed systems. There are several stereo formats available:1. Side-by-side cross-eyed stereo;2. Side-by-side wall-eyed stereo;3. Anaglyph stereo (requires stereo-capable monitor, quad-buffered stereo video board, and redbluehorror-movie-style stereo glasses).81
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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
Page 29 and 30: Hot Key Command Purpose+,f,F animat
Page 31 and 32: information. Atoms shows the number
Page 33 and 34: Animation SpeedThe rate of playback
Page 35 and 36: can change the view of the scene, e
Page 37 and 38: • Perspective - The view of the s
Page 39 and 40: 4/3 SCRHEIGHTi.e. 8.0YViewer’sEye
Page 41 and 42: Hiding a rep. To hide a rep, double
Page 43 and 44: Periodic TabThe Periodic tab contro
Page 45 and 46: • Name - the name of the atom as
Page 47 and 48: Figure 4.10: The Material Formslide
Page 49 and 50: force-feedback (haptic) devices suc
Page 51 and 52: the simulated spring is connected t
Page 53 and 54: Figure 4.13: The Sequence formmolec
Page 55 and 56: • 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
Page 61 and 62: segment pieces are colored accordin
Page 63 and 64: • Representation Method - The sur
Page 65 and 66: 5.1.19 BeadsA bounding sphere is dr
Page 67 and 68: 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: FunctionDescriptionsqr(x) square of
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
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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)
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ef=AtomSel(’backbone’,frame=0)f
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functions (e.g., listall()) overlap
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• update ui():• update on():Upd
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9.5.7 labelPython operations availa
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• add volumetric(molid, name, ori
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• set colorupdate(molid, rep, ono
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9.6 High-level Python InterfaceVMD
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9.6.2 MoleculeRepThe MoleculeRep cl
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Chapter 10Vectors and MatricesTcl d
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• veccross v1 v2 - Returns the ve
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• transaxis amount [deg|rad|pi]
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-axiszamount [rad|deg|pi] - Adds a
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Chapter 11Molecular Analysis11.1 Us
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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
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