VMD User's Guide

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9.6.4 Saving and Restoring Molecule StateMolecule and MoleculeRep instances can be saved used the pickle module from the Python standardlibrary. Molecules will be saved with information about their name, files, and reps. The filesthemselves are not saved with the molecule; they will be reloaded when the molecule instance isrecreated using pickle.load(). MoleculeRep instances can also be pickled; when restored theywill be unassigned to any Molecules.146
Chapter 10Vectors and MatricesTcl does not handle mathematical expressions very well. It is slow at evaluating expressions, andprovides no facility for handling vectors or matrices. Since the latter two are needed for structureanalysis, we have added routines to manipulate them.A vector in VMD is a list of numbers. All of the vector routines but one will work with vectorsof any length; veccross will only use vectors of three numbers. A matrix is a 4x4 collection ofnumbers stored as a list of 4 vectors of 4 numbers, in row-major form.Following are descriptions and examples of all the commands. For more examples of vectors,though without much documentation, the script used to test the vectors implementation is locatedat $env(VMDDIR)/scripts/vmd/test-vectors.tcl.Since Tcl is slow at math, some of these commands have been reimplemented in C++. (Theoriginal definition is in the vmd script distribution, but it is redefined later on inside VMD). Attimes, the speedup is a factor of 40 or more. These commands are noted by (C++).10.1 Vectors• veczero – Returns the zero vector, {0 00}Example:vmd > veczero0 0 0• (C++) vecadd v1 v2 [v3 ... vn] – Returns the vector sum of all the terms.Examples:vmd > vecadd {1 2 3} {4 5 6} {7 8 9} {-11 -11 -11}1 4 7vmd > vecadd {0.1 0.2 0.4 0.8} {1 1 2 3} {3 1 4 1}4.1 2.2 6.4 4.8vmd > vecadd 4 59• (C++) vecsub v1 v2 – Returns the vector subtraction of the second term from the first147
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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
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: 9.6.2 MoleculeRepThe MoleculeRep cl
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
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