VMD User's Guide

More documents

Recommendations

Info

• set center(molid, vector):as a Python list.Get/set the coordinates of the center of the given molecule• get scale(molid):• set scale(molid,scale):Get/set the scale factor used to display the given molecule.• get rotation(molid):• set rotation(molid, matrix): Get/set the rotation matrix for the given molecule as a16-element Python list in row-major order.• get trans(molid):• set trans(molid, vector):as a Python list.Get/set the global translation applied to the given molecule• is fixed(molid): Returns whether the molecule with the given id is fixed; that is, whetherit is affected by translation, rotation, or scaling. Fixed molecules may still be animated (seeis active in the animate section).• fix(molid, trueorfalse):Make the molecule with the given id fixed or not.• is shown(molid):Returns whether the molecule with the given id is shown or not.• show(molid, trueorfalse):Make the molecule with the given id shown or not.9.5.13 vmdnumpyThis optional module is made available from within the toplevel VMD module if VMD detects aNumeric Python installation in the Python search path. When present, the following methods areprovided:• timestep(molid, frame): Returns a single-precision Numeric array containing a directreference to the given set of atom coordinates. Atom coordinates are arranged xyzxyzxyz...for each atom in the molecule. No copy of VMD’s internal coordinates is made; therefore,modifications to this array will directly affect atom coordinates in VMD. Using the array afterthe timestep has been deleted will likely cause VMD to crash. The advantage is maximumefficiency and the ability to easily modify atom coordinates without going through the atomselection interface.• atomselect(molid, frame, selection): Returns an array of int’s representing flags foron/off atoms in the given atom selection. The syntax for the selection is the same as forthe AtomSel class. An array of this form can be used in conjunction with the Numeric takefunction to get selected coordinates from a timestep. Creating the array in this way can be50-100 times faster than converting from an AtomSel object.142
9.6 High-level Python InterfaceVMD provides three modules for accessing and manipulating VMD state with objects that representimportant entities. These objects can be thought of as references for the actual object within VMD:you can create as many references as you want and delete them, but modifying the reference changesthe actual state of VMD. This is different from the AtomSel class, where each AtomSel instanceis independent of the molecules and reps in VMD. These proxy classes are written in pure Pythonand use the lower level built-in interfaces to communicate with VMD.9.6.1 MoleculeThe Molecule class is a proxy for molecules loaded into VMD. Most operations raise ValueError ifthe proxy no longer refers to a valid molecule (i.e. if the molecule has been deleted).Molecule instances provide the following methods:• init (id=None): Creating a new Molecule instance with no arguments will create a newempty molecule in VMD. Passing a valid molecule id will make the Molecule instance mirrorthe state of the corresponding molecule in VMD.• int (): Casting a Molecule to an int returns the molecule ID.• rename(self, newname):Changes the name of the molecule.• name():Returns the name of the molecule.• delete(): Deletes the molecule corresponding to this Molecule instance. The object can nolonger be used.• load(filename, filetype=None, first=0, last=-1, step=1, waitfor=-1, volsets=[0]):Load molecule data from the given file. The filetype will be guessed from the filename extension;this can be overrideen by setting the filetype option. first, last, andstep controlwhich coordinates frames to load, if any. volsets indicates which volumetric data sets toload from the file. Raises IOError if the file cannot be loaded.• save(filename, filetype=None, first=0, last=-1, step=1, waitfor=-1, sel=None):Save timesteps to the given file. The filetype will be guessed from the filename extension; thiscan be overridden by setting the filetype option. first, last, and step control which timestepsto save. Returns the number of frames written before the command completes. Pass anAtomSel instance as sel to write only a selection of atoms to the file. Note that this differsfrom the AtomSel.write() method in that Molecule.save() writes a range of timesteps,while AtomSel.write() writes only the coordinates corresponding to the selection’s currentlyselected frame.• files():• types(): Returns a list of filenames and file types, respectively, for the files that have beenloaded into this molecule.• numAtoms(): Returns the number of atoms in the molecule.• numFrames(): Returns the number of coordinate frames in the molecule.143
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: • set colorupdate(molid, rep, ono
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

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?