VMD User's Guide

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know when to delete the temporary file containing the molecule or other data. The chemical2vmdscript starts <strong>VMD</strong> with the -e command line option which runs the saved <strong>VMD</strong> script or moleculefile.It is also possible to install the previous script in the global .mailcap file to make it accessibleto everyone. You will have to consult the documentation for your web browser(s) to find out how.12.4.3 Example sitesSome web sites that send chemical/pdb types are the Protein Data Bank at http://www.rcsb.org/and “Molecules R US” at http://www.nih.gov/htbin/pdb.178
Index.mailcap, 177.vmdrc, 26, 89, 176.vmdsensors, 49vmd.rc, 89, 176ACTC, 11AMBERfiles, 20, 34analysisscripting, 157speed, 157angles, 44animatecommand, 90, 120form, 32Python module, 133animation, 16frames , 34appending, 34delete, 32, 90, 91duplicate frame, 90goto end, 91goto start, 91hot keys, 29jump, 33, 91movie, 88play, 90read, 34, 91smoothing, 42, 110, 141speed, 33, 91step, 33style, 91loop, 33once, 33rock, 33write, 31, 91antialiasing, 37, 96atomchanging properties, 159colorauto-update, 109coordinates, 113, 114changing, 18, 159min and max, 162info, 91, 156name lists, 41picking, 17selection, 15, 17, 57, 70, 91, 156auto-update, 109changing properties, 127comparison, 74default, 108examples, 17, 70keywords, 41, 70, 77, 78logic, 72macros, 42, 92, 125math functions, 79modes, 70Python, 125quoting, 72regular expression, 73same, 75sequence, 75text, 156update, 161volumetric data, 79within, 75atomsdistance between, 18plotting, 45atomselectcommand, 91, 120, 155, 156axes, 37command, 94, 120Python module, 134Babel, 21backface culling, 37179
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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
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: axes location lowerleftstage locati
Page 181 and 182: VMDHTMLVIEWER, 174VMDIMAGEVIEWER, 1
Page 183 and 184: move, 35atom, 35fragment, 35highlig
Page 185 and 186: short circuit logic, 72, 75sleepcom
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