VMD User's Guide

More documents

Recommendations

Info

changing, 81<strong>VMD</strong>as MIME helper application, 177command line options, 171compile options, 115copyright, 11customizing, 26, 171vmdinfocommand, 114, 120volmapcommand, 115, 120volumetric data, 63, 64generating, 115waitcommand, 118, 120XPLORfiles, 20, 34186
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 and 122:
Sourceraster3dmsmsfaqbiocoretachyon
Page 123 and 124:
Table 8.4: Description of Tcl callb
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: short circuit logic, 72, 75sleepcom
show all

VMD User's Guide

Create successful ePaper yourself

Delete template?

Save as template?