VMD User's Guide

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Note that if the zoom factor is smaller than 1.0, the single-residue sequence highlight will be shorterin height than a full line of text. Once the Sequence window has been opened, any “Pick” willcreate or add to selections, until highlighting is turned off[§ 4.4.14].Sequence ZoomingLarger molecules contain thousands of residues, too many to display in a linear text list all at once.The sequence form can only list about 40 text lines; to work with a molecule of more than 40residues use the scroll bars to scroll through the long list, or use the Zoom controls to fit the datafromalonglistintoasmallspace.The Zoom slider, and the Fit all, Every Residue buttons, zoom in and out of a long sequence listto allow viewing and selecting from the entire list all at once. To represent more than 40 residueson the form, the text list seems to “skip” residues, but selections, highlights and color-coded dataare still active for all residues.By setting the Zoom slider to a value smaller than 1.0, or by pressing the Fit all button, moreor all of the sequence information for a large molecule can be seen at once. To show a text line forevery residue in the sequence (zoom factor = 1.0), click on the Every Residue button. The Zoomslider can be dragged with the left mouse button (to re-scale sequence smoothly) or it can jump toa given value by clicking along the slider track with the middle button (this is useful to work morequickly with very long sequences).For a multi-thousand residue protein with Fit all selected, hundreds of residues can be selectedat once, and trends in B-value and structure across the entire protein sequence can be detected.In the screen-shot above, a section of 70 residues with lower B-values than surrounding sequenceis selected, by dragging a rectangle around the green stretch in the B-value column.Other controls include:• Toggle display of 3-letter and 1-letter codes – Click on 1-letter code to switch from3-letter to 1-letter amino acid codes. The same button then reads 3-letter code, click it toswitch back from 1-letter to 3-letter codes.• Print contents of sequence window – Select File:Print to File to create a postscript filecontaining the current sequence listing and highlighting.Turn off highlighting / Change highlight styleTo clear all highlights, reselect the current molecule from the Molecule pop-up menu. To turnthe highlight representation off completely for a given molecule, find the representation in theGraphics form which the Sequence form has created (appears with “Bonds ColorID 4”) and setthe style to “none”. To change highlighting style, set this same representation to your preferredstyle and coloring. The selection for this representation will still change whenever the sequenceform selection changes. Example application: specify Multiple Frames in the Trajectory tab of thehighlight representation. This will display the trajectory motions of the residues clicked on in themain <strong>VMD</strong> window, or in the Sequence window.Caveats• Pause on first use: Since the sequence form displays secondary structure of loaded molecules,there may be a pause for structure calculation the first time the sequence for a protein isdisplayed.54
• Selections by chain: When there are multiple segments in a chain, it is possible for severalresidues to have the same residue number and chain name. These residues will be highlighted/selected/deselectedtogether.• B-values can be user assigned: To use the B-value column to view arbitrary data, use theselection set beta commands to change B-values. To refresh the displayed B-value data,re-select the currently displayed molecule from the Molecule pop-up menu.4.4.15 RamaPlotFigure 4.14: The RamaPlot WindowThe RamaPlot window displays a Ramachandran plot for a selected molecule. If you animateyour molecule over a range of frames , RamaPlot will update the Ramachandran plot automatically.You can select a range of residues to be displayed in the plot. Clicking on a point in theRamachandran plot will show the trajectory of the selected residue in Ramachandran space overall frames . Fields on the right of the window show the computed value of phi and psi for the mostrecently selected residue. Finally, you can create a PostScript image of the current Ramachandranplot. RamaPlot functionality is summarized in Fig. 4.14.Using RamaPlotStart RamaPlot by typing “ramaplot” in the <strong>VMD</strong> text console, or by selecting the ramaplot menuitem in the Extensions menu. The main window contains a Ramachandran graph, with phi and psirunning along the horizontal and vertical axis, respectively, from -180 to 180 degrees. The mostallowed region of Ramachandran space is colored blue; partially allowed regions are colored green.55
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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 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: Figure 4.13: The Sequence formmolec
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
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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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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