VMD User's Guide

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Figure 4.6: The Graphics form (in Draw Style mode)occur when the Apply button is pressed. Changing the drawing method brings up method-specificcontrols and defaults. If you go back to the previous draw style, <strong>VMD</strong> restores any changes thatyou may have made to the settings. Pressing the Default button will restore the default settings.The display will be updated after every change.Adding a rep. To add a new representation of the molecule, enter the selection into the AtomSelection text area (or keep what is there) and press Create Rep. This adds the representation tothe currently selected molecule.Deleting a rep. To delete a representation, select the representation in the browser and pressthe Delete button. Bear in mind that this does not delete the molecule, it only deletes one of itsgraphical representations.40
Hiding a rep. To hide a rep, double-click its entry in the browser. The text will turn pink toindicate that the rep is hidden. Turn the rep back on by double-clicking again on the same line.Hidden reps will not recalculate their geometry if the animation frame changes until the rep isturned back on.Selections TabFigure 4.7: The Graphics form (in Selections mode)The Selections tab provides access to browsers which display the lists of atom names, residuenames, and so forth for the selected molecule. When the Selections tab is pressed, several browsersappear in place of the drawing and coloring method controls. These are used to list the availablekeywords, macros, and values for use in selecting atoms for the associated representation. Thetop browser lists singlewords and macros such as all, water, andhydrophobic. The botton leftbrowser contains a list of the keywords and functions understood by the selection command [§5.3].If a keyword is selected which can take on a value (for instance, name and index), then the possible41
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 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: 4/3 SCRHEIGHTi.e. 8.0YViewer’sEye
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 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
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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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