VMD User's Guide

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9.6.2 MoleculeRep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1459.6.3 Draw Style Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1459.6.4 Saving and Restoring Molecule State . . . . . . . . . . . . . . . . . . . . . . . 14610 Vectors and Matrices 14710.1 Vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14710.2 Matrix routines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15010.3 Multiplying vectors and matrices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15310.4 Misc. functions and values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15311 Molecular Analysis 15511.1 Using the molinfo command . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15511.2 Using the atomselect command . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15611.3 Analysis scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16111.4 RMS Fit and Alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16411.4.1 RMS Fit and Alignment Extension . . . . . . . . . . . . . . . . . . . . . . . . 16511.4.2 RMS and scripting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16611.5 VMD Script Commands for Colors . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16811.5.1 Changing the color scale definitions . . . . . . . . . . . . . . . . . . . . . . . 16811.5.2 Creating a set of black-and-white color definitions . . . . . . . . . . . . . . . 16911.5.3 Revert all RGB values to defaults . . . . . . . . . . . . . . . . . . . . . . . . 16911.5.4 Coloring Trick - Override a Coloring Category . . . . . . . . . . . . . . . . . 17012 Customizing VMD Sessions 17112.1 VMD Command-Line Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17112.2 Environment Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17312.3 Startup Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17612.3.1 Core Script Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17612.3.2 User Script Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17612.3.3 .vmdrc and vmd.rc Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17612.4 Using VMD as a WWW Client (for chemical/* documents) . . . . . . . . . . . . . . 17712.4.1 MIME types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17712.4.2 Setting up your .mailcap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17712.4.3 Example sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178Index 1796
List of Figures2.1 Sample VMD session displaying myoglobin. . . . . . . . . . . . . . . . . . . . . . . . 154.1 The Main form . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 304.2 The Main form animation controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . 324.3 The Molecule File Browser form . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 334.4 The Display menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 364.5 Relationship between screen height (SCRHEIGHT), screen distance to origin (SCRDIST),and the viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 394.6 The Graphics form (in Draw Style mode) . . . . . . . . . . . . . . . . . . . . . . . . 404.7 The Graphics form (in Selections mode) . . . . . . . . . . . . . . . . . . . . . . . . . 414.8 The Labels form . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 434.9 The Color form . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 454.10 The Material Form . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 474.11 The Render form . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 484.12 The Tool form . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 484.13 The Sequence form . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 534.14 The RamaPlot Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 555.1 RGB color scale: the three plots shows the contributions of each color, and theresulting colors are on the bottom. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 695.2 The shift to the red component of the RGB scale caused by the value of “min”. . . . 6911.1 RMS calculation and alignment extension . . . . . . . . . . . . . . . . . . . . . . . . 1657
Page 1 and 2: VMD User’s GuideVersion 1.8.6Apri
Page 3 and 4: 4.4.4 Molecule File Browser Form .
Page 5: 8.3.20 molecule . . . . . . . . . .
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 and 22: no coordinate information. It must
Page 23 and 24: Chapter 4User Interface ComponentsV
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
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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
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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
Page 185 and 186:
short circuit logic, 72, 75sleepcom
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