VMD User's Guide

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3.4 Raster3D file formatIn addition to the molecular file formats, VMD can read the input file for Raster3D. (Raster3Dconverts an input file into a shaded raster image for use in making high quality pictures. It is oftenused with MolScript.) The ability to read Raster3D allows users to view MolScript files in 3D andincorporate special images into the display without having to edit the VMD code. The file format,which is part of the Raster3D documentation, describes a simple collection of triangles, spheres,and cylinders with either flat or spherical ends. Each shape is colored by an RGB triplet.Certain newer Raster3D objects are ignored, such as quadrics. Also, nearly all of the headerinformation is ignored—most notably, the viewing matrix. Raster3D uses many cylinders withspherical (rounded) ends. VMD deliberately omits these rounded ends since the resultant imagewould be very slow to render interactively. VMD uses a fixed size palette of colors, each triplet isconverted into its “nearest” indexed color. This may cause images to be colored slightly differentlythan expected.22
Chapter 4User Interface ComponentsVMD provides several methods for the user to control and interact with the molecular display. Theprimary methods are by using the mouse, either in the graphics window or in the different graphicaluser interface (GUI) forms provided by the program. In addition to the mouse, VMD also supportsa number of more advanced input devices such as the Spaceball, Magellan, and Phantom, whichprovide the ability to manipulate molecules with six degrees of freedom. Some devices such as thePhantom can also provide haptic (sense of touch) force feedback. VMD also provides a text consoleinterface for executing built-in commands or running scripts. This chapter describes how to usethe mouse-based user interfaces, and some of the advanced input devices supported in VMD. Thethe text and scripting interface is described fully in chapter 8.4.1 Using the Mouse in the Graphics WindowThe graphics window is labeled VMD OpenGL Display and contains a view of the molecules andother objects which make up the scene. When the mouse is in the graphics display window, it maybe used to perform the following actions such as:• Rotate, translate, or scale the displayed molecules• Select, or ‘pick’ atoms or other objects in order to move them, or label them• Translate and rotate a set of atoms• Apply a force (acceleration) to a set of atoms• Move the lightsUser-defined keyboard accelerators, or hot keys, are also available when the mouse is in the graphicsdisplay window. These keys are bound to VMD text commands, which are executed when the keyis pressed. VMD has many built-in default hot key commands (see Tables 4.1, 4.2, 4.3 and 4.4).Users can add new hot keys, overriding default settings if desired.4.1.1 Mouse ModesThe mouse is in one of several modes at any time; the current mouse mode determines the effect ofpressing and releasing mouse buttons or the mouse wheel while the mouse is in the graphics window.23
Page 1 and 2: VMD User’s GuideVersion 1.8.6Apri
Page 3 and 4: 4.4.4 Molecule File Browser Form .
Page 5 and 6: 8.3.20 molecule . . . . . . . . . .
Page 7 and 8: List of Figures2.1 Sample VMD sessi
Page 9 and 10: Chapter 1IntroductionVMD is a molec
Page 11 and 12: 1.4 AcknowledgmentsThe authors woul
Page 13 and 14: • TachyonThe Tachyon multiprocess
Page 15 and 16: Figure 2.1: Sample VMD session disp
Page 17 and 18: 2.5 An Introduction to Atom Selecti
Page 19 and 20: selection: protein and (name CA or
Page 21: no coordinate information. It must
Page 25 and 26: • Center (hot key ’c’)This mo
Page 27 and 28: 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
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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
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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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