• get(attr1, attr2, ...): Takes any number of string arguments, which should correspondto a valid atom property such as ”name”, ”x”, or ”water”. Returns a list of the value of theproperty for each atom in the selection. For boolean properties such as ”water”, the returnedvalue will be 1 if true and 0 if false.>>> x, y, z = sel.get(’x’, ’y’, ’z’)• set(attr, val): Set the atom property corresponding to attr using the values in val. Thenumber of elements in val should be either 1 or the number in the atom selection.>>> len(sel)12>>> sel.set(’beta’,3)>>> sel.set(’beta’,(1,2,3,4,5,6,7,8,9,10,11,12))• write(filename, filetype=None): Write the atoms in the selection to filename. Filetypeis guessed from the filename, or can be specified with filetype.• sel1 & sel2:• sel1 | sel2:Create a new atom selection using the atoms found in both sel1 and sel2.Create a new atom selection using the atoms found in either sel1 or sel2.• -sel:Create a new atom selection using the atoms not found in sel.• len(sel):Returns the number of atoms in the selection.Index and slice operations return the corresponding atoms in the selec-• sel[0], sel[0:3]:tion.• center(weight=None): Return the center of the selected atoms, possibly weighted byweight, which must be a sequence.• sasa(srad, samples=-1, points=None, restrict=None): Returns the solvent-accessiblesurface area (SASA) of atoms in the selection using the assigned radius for each atom, extendingeach radius by srad to find the points on a sphere that are exposed to solvent. Ifa restrict selection is given, only solvent-accessible points near that selection bill be considered.The points parameter can be used to collect the points which are determined to besolvent-accessible; this must be a list variable.• getbonds():Returns a list of the atoms bonded to each atom in the selection.• setbonds(bonds): Set the bonds for the atoms in the selection. bonds must be a list ofthe same length as the selection; each element in the list must be a sequence containing theindices of the atoms to which the atom has a bond.• minmax(): Returns the minimum and maximum coordinates of the atoms in the selectionas a tuple of the form (xmin, ymin, zmin), (xmax, ymax, zmax).• rmsd(sel, frame=None, weight=None): Returns the root-mean-square distance of theatoms in sel from the selection. If frame is given, the coordinates from the correspondingframe will be used (see the example). If weight is given, the computed RMSD will be weightedusing the values in weight.126
• align(ref=None, move=None, frame=None, weight=None): Finds the transformationthat aligns the atoms in the selection with the atoms in ref, with optional weights weight,and applies this transformation to the atoms in move. The following default values for allarguments are provided:– ref: Same molecule and atoms as selection, but always using the– align(ref=None, move=None, frame=None, weight=None):Finds the transformation that aligns the atoms in the selection with the atoms in ref,with optional weights weight, and applies this transformation to the atoms in move.The following default values for all arguments are provided:∗ ref: Same molecule and atoms as selection, but always using the first timestep inthe molecule.∗ move: All atoms in the selection molecule.∗ frame: overrides both the selection’s frame and the move frame, but does not affectthe ref frame.∗ weight: Defaults to uniform weights on all atoms in selection.first timestep in the molecule.– move: All atoms in the selection molecule.– frame: overrides both the selection’s frame and the move frame, but does not affect theref frame.– weight: Defaults to uniform weights on all atoms in selection.• contacts(cutoff, sel=None): Returns pairs of of atoms within cutoff of each other.If sel is None, atoms in the pairs must be in the selection; otherwise, the first atom in eachpair will be from the selection, and the second will be from sel.9.3.3 An atom selection exampleIn the first example, we load the molecule alanin.pdb, and create an atom selection consistingof the alpha carbons. Note that AtomSel is the name of the class which generates atom selectioninstances. We show the string representation of the object by entering its name and pressing return;this shows the text used in the selection.Next we demenstrate how atom selections act like tuples: we can get their length using the builtinlen() command,and return a copy of the selected atoms in a tuple by using the slice operator[:].Finally, we demonstrate the get and set operations. The get() operation takes any number ofstring arguments; for each argument, it returns a Python list of values corresponding to that string.The set() operation allows only one property to be changed at a time. However, you can pass ineither a single value, which will be applied to all atoms in the selection, or a tuple or list of the samesize as the atom selection, in which case values in the list will be assigned to the correspondingatom in the selection. We take advantage of this behavior in the following example by first savingthe current value of beta for the selection, then setting the value of beta to 5 for all selected atoms,and finally resetting the original values using the results of the get().>>> from molecule import *>>> from AtomSel import AtomSel127
- 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: version (2.2). Thus if you have Pyt
- 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