VMD User's Guide

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RenderMan, 85stereo, 87STL, 85Tachyon, 11, 13, 16, 86, 112TachyonInternal, 112VRML, 85rendering modes, 97rendermode, 38representation, 57, 107add new, 40adding, 40auto-update, 42Beads, 65Bonds, 58Cartoon, 62changing, 17, 39, 108clipping planesuser defined, 108CPK, 60deleting, 40dotted van der Waals, 65draw multiple frames, 110DynamicBonds, 59examples, 18HBonds, 59hiding, 40Isosurface, 64Licorice, 60Lines, 58list of available, 58MSMS, 63NewCartoon, 62NewRibbons, 61Points, 59Ribbons, 61show/hide, 110, 141solvent representation, 65style, 15, 39, 57, 108Surf, 62Trace, 60Tube, 60van der Waals, 59VolumeSlice, 63representionauto-update, 109reset view, 36, 96restoreviewpoint, 155vmd state, 19RMSFit, 164RMS:Alignment, 164RMSD, 126, 127, 129, 163, 166, 167rock, 33command, 112, 120rotatecommand, 113, 120side chain, 160rotationcontinuous, 24hot keys, 28stop, 24using mouse, 24saveconfiguration, 19viewpoint, 155vmd state, 19, 146scalecommand, 113, 120scalingusing mouse, 24screen parameters, 38scriptsplay, 89source, 89secondary structure codes, 53selection, 15, 17, 39, 57, 91, 108, 156comparison, 74keywords, 41, 70, 77boolean, 72logic, 72math functions, 79modes, 70text, 156volumetric data, 79sensor configuration file, 49sensors, 49sequence, 52caveats, 54dna, 52form, 52zooming, 54184
short circuit logic, 72, 75sleepcommand, 118, 120sourcecommand, 89spaceballdriver, 11, 27MacOS X, 27Unix, 27Windows, 27modes, 27using, 27stage, 37command, 113, 120startup files, 26, 173, 176stereomode, 82cross-eyed, 82CrystalEyes, 83DTI side-by-side, 82scanline interleaved, 82side-by-side, 82off, 81parameters, 37, 83, 96, 97stop rotation, 36stride, 12surf, 12surfacemolecular, 65solvent accessible, 65Tachyon, 13Tcl, 90tclcommands,90textdisplayed, 99Tk, 90toolCAVE, 49command, 113, 120form, 48FreeVR, 49Spaceball, 49VRPN, 49tools, 50topology files, 20trajectorydraw multiple frames, 42, 110files, 20read, 34smoothing, 42, 110, 141write, 31transPython module, 141translatecommand, 114, 120translationchange atom coordinates, 160using mouse, 24transparency, 39unit cell information, 43universal sensor locator, 49usercommand, 114, 120user interfacespython, 124text, 89USL, 49variablesenv, 173, 176M PI, 153trace, 118vector commandcoordtrans, 153vecadd, 147veccross, 149vecdist, 149vecdot, 148vecinvert, 150veclength, 149veclength2, 149vecmean, 148vecnorm, 149vecscale, 148vecstddev, 148vecsub, 147vecsum, 148vectrans, 153veczero, 147vector routines, 147view, 107viewing modes185
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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
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• Perspective - The view of the s
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4/3 SCRHEIGHTi.e. 8.0YViewer’sEye
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Hiding a rep. To hide a rep, double
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Periodic TabThe Periodic tab contro
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• Name - the name of the atom as
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Figure 4.10: The Material Formslide
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force-feedback (haptic) devices suc
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the simulated spring is connected t
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Figure 4.13: The Sequence formmolec
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• Selections by chain: When there
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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
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
Page 139 and 140: • add volumetric(molid, name, ori
Page 141 and 142: • set colorupdate(molid, rep, ono
Page 143 and 144: 9.6 High-level Python InterfaceVMD
Page 145 and 146: 9.6.2 MoleculeRepThe MoleculeRep cl
Page 147 and 148: Chapter 10Vectors and MatricesTcl d
Page 149 and 150: • veccross v1 v2 - Returns the ve
Page 151 and 152: • transaxis amount [deg|rad|pi]
Page 153 and 154: -axiszamount [rad|deg|pi] - Adds a
Page 155 and 156: Chapter 11Molecular Analysis11.1 Us
Page 157 and 158: vmd> set sel [atomselect top "water
Page 159 and 160: The decimal in ”1.0” is importa
Page 161 and 162: # get the sidechain atoms (CB and o
Page 163 and 164: Applying this to the alanin.pdb coo
Page 165 and 166: have the same number of atoms, then
Page 167 and 168: set transformation_matrix [measure
Page 169 and 170: }display update offfor {set i 0} {$
Page 171 and 172: Chapter 12Customizing VMD SessionsT
Page 173 and 174: • -nt : Do not display the VMD ti
Page 175 and 176: • VMDIMMERSADESKFLIP : Enable a s
Page 177 and 178: axes location lowerleftstage locati
Page 179 and 180: Index.mailcap, 177.vmdrc, 26, 89, 1
Page 181 and 182: VMDHTMLVIEWER, 174VMDIMAGEVIEWER, 1
Page 183: move, 35atom, 35fragment, 35highlig
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