VMD User's Guide

More documents

Recommendations

Info

Keyword Aliases Arg Set Descriptionid int N molecular idindex int N index on the molecule listnumatoms int N number of atomsname str N the name of the molecule (usually the name of the file)filename str N list of filenames for all files loaded for this moleculefiletype str N list of file types for this moleculedatabase str N list of databases for this moleculeaccession str N list of database accession codes for this moleculeremarks str N list of freeform remarks for this moleculeactive bool Y is/make the molecule activedrawn displayed bool Y is/make the molecule drawnfixed bool Y is/make the molecule fixedtop bool Y is/make the molecule topcenter vector Y get/set the coordinate used as the centercenter matrix matrix Y get/set the centering matrixrotate matrix matrix Y get/set the rotation matrixscale matrix matrix Y get/set the scaling matrixglobal matrix matrix Y get/set the global (rotation/scaling) matrixview matrix matrix N get/set the overall viewing matrixnumreps int N the number of representationsselection i string N the string for the i’th selectionrep i string N the string for the i’th representationcolor i colour string N the string for the i’th coloring methodnumframes int N number of animation framesframe int Y current frame numbertimesteps int Y number of elapsed timesteps in an interactive simulationbond float N the bond energy (for the current frame)angle float N the angle energydihedral float N the dihedral energyimproper float N the improper energyvdw float N the van der Waal energyelectrostatic elec float N the electrostatic energyhbond float N the hydrogen bond energykinetic float N the total kinetic energypotential float N the total potential energyenergy float N the total energytemperature temp float N the overall temperaturepressure float Y the simulation pressurevolume float Y the simulation volumeefield float Y efieldalpha float Y unit cell angle alpha in degrees (for the current frame)beta float Y unit cell angle beta in degrees (for the current frame)gamma float Y unit cell angle gamma in degrees (for the current frame)a float Y unit cell length a in Angstroms (for the current frame)b float Y unit cell length b in Angstroms (for the current frame)c float Y unit cell length c in Angstroms (for the current frame)Table 8.3: molinfo set/get keywords122
Table 8.4: Description of Tcl callback variables in <strong>VMD</strong>.When called Name New valueMolecule molid was deleted vmd molecule(molid) 0Molecule molid was created (data vmd molecule(molid) 1may not have been loaded yet)Molecule molid was renamed vmd molecule(molid) 2Structure file loaded vmd initialize structure(molid) 1Coordinate file loaded vmd trajectory read(molid) name of coordinate fileMolecule molid changed animation vmd frame(molid)new animation frameframesAny <strong>VMD</strong> command executed vmd logfile Tcl text equivalent ofcommandBond, angle or dihedral label added vmd pick value Value of geometry labelAtom picked vmd pick mol id of picked moleculeAtom picked vmd pick atom id of picked atomPointer moved. vmd pick client name of pointerPointer moved. vmd pick mol silent id of nearby molPointer moved. vmd pick atom silent id of nearby atomAtom picked vmd pick shift state 1 if shift key down duringpick, 0 otherwiseIMD coordinate set received vmd timestep(molid) frame containing newcoordinatesSet of labels to be graphedvmd graph label {labeltype labelid}{labeltype labelid} ...Tcl interpreter is shutting down vmd quit 1123
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 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
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
Page 105 and 106: the area contributions are coming f
Page 107 and 108: 8.3.19 molLoad, modify, or delete a
Page 109 and 110: • modselect rep number molecule n
Page 111 and 112: • index n: Returns the id of the
Page 113 and 114: 8.3.26 rockRotate the current scene
Page 115 and 116: 8.3.33 vmdinfo(Tcl) Returns informa
Page 117 and 118: • -minmax {{ x min y min z min }
Page 119 and 120: In the VMD script library at http:/
Page 121: Sourceraster3dmsmsfaqbiocoretachyon
Page 125 and 126: version (2.2). Thus if you have Pyt
Page 127 and 128: • align(ref=None, move=None, fram
Page 129 and 130: esid5.frame()50>>> resid5.frame(22)
Page 131 and 132: 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 and 184:
move, 35atom, 35fragment, 35highlig
Page 185 and 186:
short circuit logic, 72, 75sleepcom
show all

VMD User's Guide

Create successful ePaper yourself

Delete template?

Save as template?