• cone(id, v1, v2, radius=1.0, resolution=6): Draw a cone with base at v1 and pointat v2. radius and resolution may optionally be specified with keyword arguments.• sphere(id, center=(0.0, 0.0, 0.0), radius=1.0, resolution=6): Draw a sphere.The sphere center, radius, and resolution may optionally be specied with keyword arguments.• text(id, pos, text, size=1.0): Draw text at the given position (specified by a tupleof three floats, using the string text. Size may optionally be specified using keyword arguments.• delete(id, index): Deletes the graphics primitive with the given index. Alternatively, ifthe string ’all’ is passed as the index, all graphics primitives will be deleted.• replace(id, index): Deletes the graphics primitive with the given index. The next graphicsprimitive added will go in the newly vacated position. Subsequent graphics primitives willresume at the end of the list.• info(ind, index): Returns a string describing the graphics primitive with the given index.If the index is invalid, an IndexError exception is raised.• listall(ind):Returns the indices of the valid graphics primitives in a list.9.5.6 imdPython operations available from the imd module, used to display and interact with a molecule ina molecular dynamics simulation.• connect(host, port): Connect to a simulation running on host host and listening forincoming connections on port port.• pause():If connected, cause the simulation to pause.• detach(): If connected, detach from the simulation. The simulation will continue to run,but no more frames will be received until a connection is re-established.• kill():If connected, terminate the simulation. The connection will also be abolished.• transfer(rate): Set/get how often the remote simulation sends coordinate frames to <strong>VMD</strong>.If rate is omitted or is negative, no action is taken and the current value is returned. A valueof 1 corresponds to every frame being sent; a value of 2 corresponds to every other frame,etc.• keep(rate): Set/get how often received coordinates frames are kept by <strong>VMD</strong> as part ofan animation. If rate is omitted or is negative, no action is taken and the current value isreturned. A value of 0 means no frames are saved. A value of 1 corresponds to every framebeing saved; a value of 2 corresponds to every other frame, etc.136
9.5.7 labelPython operations available from the label module, used to create, show/hide, and delete labels foratoms, bonds, angles, or dihedrals.• ATOM, BOND, ANGLE, DIHEDRAL: Label types defined by the label module, for use as the firstargument to the add, listall, show, hide, and delete methods.• add(type, molids, atomids): Create a label of the given type. molids and atomids mustbe tuples containing 1, 2, 3, or 4 integers for ATOM, BOND, ANGLE, or DIHEDRAL labels,respectively. If the label already exists, no action is performed. Returns a dict correspondingto the referenced label that can be used in the show(), hide(), delete(), and getvalues()methods.• listall(type): Returns a list of labels of the given type. The elements of the list arepython dictionary objects, with the following keys: molid, atomid, value, on. The valuesfor molid and atomid are tuples containing the molecule id and atom id for the label. valueis the numerical value of the geometry label, or zero for ATOM labels. on is 1 if the label isshown, and 0 if the label is hidden.• show(type, label): Turn the given label on. label must be a dictionary containing molidand atomid keys whose values are tuples. If the tuples match the molecule ids and atom idsof the atoms in an existing label, the label will be turned on. Raises ValueError if the labeldoes not exist.• hide(type, label): Turn the given label off. label must be a dictionary containing molidand atomid keys whose values are tuples. If the tuples match the molecule ids and atom idsof the atoms in an existing label, the label will be turned off. Raises ValueError if the labeldoes not exist.• delete(type, label): Delete the given label. label must be a dictionary containing molidand atomid keys whose values are tuples. If the tuples match the molecule ids and atom idsof the atoms in an existing label, the label will be deleted. Raises ValueError if the label doesnot exist.• getvalues(type, label): Returns a list of values of the given label for each coordinateframe in the label. If the atoms in the label belong to different molecules, only the coordinatesof the first molecule will be cycled. If the labels don’t have values (like atom labels), None isreturned.9.5.8 materialPython operations available from the material module, used to create and modify material propertiesof molecular representations.• listall():Returns a Python list of the names of all available materials.• settings(name):the given name.Returns a Python dictionary of the material settings for material with137
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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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