VMD User's Guide

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• Move → Molecule (hot key ’8’)This mode may be used to move all the atoms in a selected molecule at the same time.Select an atom in a molecule, and move it to a new position while keeping the mouse buttonpressed. All the atoms in the same molecule as the selected one will be moved the sameamount. Holding down the ¡shift¿ key and the left mouse button while moving the mousewill rotate the atoms in the molecule about the selected atom. If the middle mouse buttonis held down instead, the atoms in the molecule will rotate about a line drawn through thepicked atom and parallel to a line coming directly out of the screen. This behavior is similarto the usual Rotate mode, except that coordinates of atoms are changed.• Move → Rep (hot key ’9’)This mode may be used to move all the atoms in a selected representation at the same time.You select a representation by clicking on one of the reps in the browser window of theGraphics form. In order to move the atoms in this rep, the atom you pick with the mousemust be selected by that rep.When you have clicked on an atom in the rep, move the mouse to a new position while keepingthe mouse button pressed. All the atoms selected by the highlighted rep will be moved thesame amount. Holding down the ¡shift¿ key and the left mouse button while moving themouse will rotate the atoms in the rep about the selected atom. If the middle mouse buttonis held down instead, the atoms in the rep will rotate about a line drawn through the pickedatom and parallel to a line coming directly out of the screen. This behavior is similar to theusual Rotate mode, except that coordinates of atoms are changed.4.1.3 Hot KeysWhen the mouse is in the graphics window, many commands are accessible via programmable hotkeys. Hot keys allow you to do things like change mouse modes or advance the animation by aframe by simply pressing a key. There are a number of predefined hot keys, as listed in tables 4.1,4.2, 4.3, and 4.4. They can be printed out with the command user print keys. The commandslisted are the text commands which are executed when the hot key is pressed; these text commandsare explained in section 8.3.To add or modify a hot key, use the command user add key key command. Thekey parametermust be a single character. If command contains more than one word, it must be enclosed in bracesso that the subsequent command words are not ignored. When that key is pressed while the mousecursor is in the graphics display window, the associated command will be executed. Once youhave a set of commands which are particularly useful and familiar for you, you will want these hotkey commands automatically available every time you run VMD. This can be done by placing thecommands to add these items in your .vmdrc file, which is a file containing VMD text commandsthat is executed every time VMD starts up. The basic method for setting up this file is describedin section 12.3.3. Once you have such a file, put the user add commands in it.26
Hot Key Command Purposer, R mouse mode 0 0 enter rotate mode; stop rotationt, T mouse mode 1 0 enter translate modes, S mouse mode 2 0 enter scaling mode0 mouse mode 4 0 query itemc mouse mode 4 1 assign rotation center1 mouse mode 4 2 pick atom2 mouse mode 4 3 pick bond (2 atoms)3 mouse mode 4 4 pick angle (3 atoms)4 mouse mode 4 5 pick dihedral (4 atoms)5 mouse mode 4 6 move atom6 mouse mode 4 7 move residue7 mouse mode 4 8 move fragment8 mouse mode 4 9 move molecule9 mouse mode 4 13 move highlighted rep% mouse mode 4 10 apply force on atom∧mouse mode 4 11 apply force on residue& mouse mode 4 12 apply force on fragmentTable 4.1: Mouse control hot keys.4.2 Using the Spaceball in the Graphics WindowVMD provides optional support for Spaceball six-degree-of-freedom input devices. The Spaceballmay be used to rotate, translate, and scale molecules, using up to 6 control axes simultaneously (3axes in translation, 3 in rotation). The Spaceball can be used independently and simultaneouslywith the mouse. With the spaceball in one hand and the mouse in the other, a user can performcomplex picking and identification operations more efficiently, since the mouse can be left in pickmode (for example) while the Spaceball is used to perform rotations, translations, and scalingoperations with the other hand.The Spaceball can be run in one of several modes within VMD. The Spaceball interface currentlyprovides two methods of rotation and translation, and a scaling mode. The Spaceball interfacecurrently uses Button 1 (known as Function 1 in the SpaceWare driver) to reset the view, andButton 2 to cycle through the available Spaceball interface modes.4.2.1 Spaceball DriverVMD interfaces to the Spaceball in one of two ways; either by communicating directly with theSpaceball using built-in serial interface software, or vendor provided drivers. Unix and Mac OS Xversions of VMD use the built-in serial Spaceball driver. At startup, VMD checks for the existenceof an environment variable VMDSPACEBALLPORT. This environment variable must be set tothe Unix device name of the serial port to which the Spaceball is attached. The serial port devicepermissions must be set to allow the VMD user to open the device for reading and writing. Intypical usage, this usually requires performing a chmod 666 /dev/somettyname on the appropriatedevice as root. One restriction with the use of the built-in Spaceball driver is that only one VMDprocess may safely use the Spaceball at a time. If multiple VMD sessions are started on the samemachine and all are set to open the Spaceball, it will behave very erratically.27
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: • Center (hot key ’c’)This mo
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
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
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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
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short circuit logic, 72, 75sleepcom
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