VMD User's Guide

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Figure 4.11: The Render formthe way to make the Raster3D render command run in the background is:(render < %s -sgi %s.rgb; ipaste %s.rgb)&4.4.12 Tool FormFigure 4.12: The Tool formThe Tool form is used to set up external 3D pointers, buttons, force-feedback devices, and theVMD “tools” that they control. VMD communicates with input devices through CAVElib, FreeVR,or via Virtual Reality Peripheral Network (VRPN), or with direct operating system interfaces.Since VRPN provides networked device abstraction, VMD doesn’t have to be running on the samecomputer that VRPN devices are attached to. With VRPN, you may use buttons, trackers, and also48
force-feedback (haptic) devices such as the PHANToM. In the CAVE or FreeVR, VMD recognizestwo types of devices: buttons and trackers. The built-in Spaceball driver can also be used to controltools.Configuring input devicesTo use input devices with VMD “tools”, you need a sensor configuration file, in your homedirectory called .vmdsensors (see the VMD Installer Guide). In this file, any number of devicescan be specified, using a universal sensor locator (USL). The format for a USL is as follows:USL – type://place/name:nums• type – the type of sensor (vrpntracker, vrpnbuttons, vrpnfeedback, cavetracker, cavebuttons,or sballtracker)• place – the machine that controls it. Devices that cannot yet be used on arbitrary computersover the network must have the keyword local here to be compatible with future versions.• name – the name of the device within that machine. If multiple devices can’t currently exist,such as with the CAVE, then a standard name should be used, such as cave, so that thesame USL will make sense in the future, when multiple devices are allowed.• nums – a comma-separated list of numbers of devices belonging to that names (optional,defaults to zero). Some devices demand only one number or a specific number but buttondevices should work correctly now.The lines of a sensor configuration file come in four flavors:• Comments begin with # and are ignored.• Empty lines are also ignored.• Device lines have the form device name USL, wherename is the name that VMD will useto refer to the device, and USL is the device’s USL.• Options tell VMD how to use the most recently listed device.supported options:Currently, there are four– “scale x” scales the position of a tracker by a factor x.– “offset xyz” adds a constant vector to the position of a tracker.– “rot right—left A 00 A 01 ...A 33 ” multiplies the orientation matrix returned by atracker on either the right or the left by the matrix A.– “forcescale x” multiplies the force applied to a force-feedback device by the amount x.Here is a simple example, showing some of the things you can do with a sensor configurationfile, for a more complete example, please refer to the .vmdsensors file that came with your VMDdistribution:### Sensable PHANTOM via VRPN### http://www.sensable.com/### The Phantom haptic device connected to the computer "odessa"device phantomtracker vrpntracker://odessa/Phantom049
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 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: Figure 4.10: The Material Formslide
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
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Page 67 and 68: those names to color the atoms. Mol
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Page 71 and 72: esname ALA to CYS TYRselects atoms
Page 73 and 74: esname ’A 1’More importantly, r
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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
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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
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short circuit logic, 72, 75sleepcom
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