VMD User's Guide

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7.6 Making a MovieIt is possible to make movies with VMD, through the use of Tcl or Python scripts, or with the“vmdmovie” extension included with VMD. Several movie making scripts are provided in the VMDscript library on the VMD home page. These scripts can be used as-is, or they can be customized toperform complex animation tasks beyond the scope of this user guide. In general, movies are createdby driving render commands with a script, producing a sequence of individual image files. Whenthe script has completed rendering all of the individual frames, the images are ready for importinto an animation package, or can be converted to one of several popular compressed movie formatsby further processing. The “vmdmovie” extension provided with VMD completely automates themovie creation process, though it requires a number of software packages be installed in order todo the job. Please see the separate documentation on the movie scripts and “vmdmovie” in theVMD script library.88
Chapter 8Tcl Text InterfaceThe Tcl text interface provides complete access to all the VMD commands. Anything that can bedone from the menus can be done with VMD text commands.8.1 Using text commandsText commands can be entered into VMD in several ways:• Commands can be entered by typing them at the VMD prompt in the text console window.This window normally contains the prompt vmd > . When other text (e.g., from a mousepick) is displayed to the screen, it will scroll the screen up so the prompt is not at the lastline of the screen. To make it reappear, press enter. When entering multi-line commands,an alternate prompt appears, ? , and will not disappear until the command is finished.Sometimes it is waiting for a close to a double quote, open brace, or open bracket, while atother times it is waiting for a line that doesn’t end in a backslash.• Since you may not want to retype all the data in every time, there are two ways to read thedata in from a text file. One is the play command. This reads a line from the file, executesit, then updates the screen and checks for any changes in the mouse or forms input, so thatVMD stays interactive during execution of the script. The second way is the Tcl commandsource. This reads the whole file before allowing the mouse and forms to respond to newinput. This is often more efficient when your script contains many lines.• On Unix/Linux platforms, if the file .vmdrc (see section 12.3.3) exists in your home directory,it is played at VMD startup. If you don’t have a .vmdrc file, VMD uses a default script inthe VMD installation directory. Similarly, at startup the -e command line flag can be usedto specify an input file to be played after reading the .vmdrc file. The Windows version ofVMD works similarly, though the startup file is named vmd.rc.A good use of the .vmdrc file is to specify which VMD menus you would like to have openwhen you start VMD and where they should be placed; see section 8.3.18) for information onusage.89
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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
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 and 80: FunctionDescriptionsqr(x) square of
Page 81 and 82: Chapter 6Viewing ModesThere are man
Page 83 and 84: sci-fi and horror movie showings. T
Page 85 and 86: Name Description Default Render Com
Page 87: • Dotted spheres are not drawn wi
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)
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
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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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