9.5.2 axesPython operations available from the axes module, used to change where the axes are displayed inthe graphics window.String constants de-• OFF, ORIGIN, LOWERLEFT, LOWERRIGHT, UPPERLEFT, UPPERRIGHT:fined in the axes module for setting the location of the axes.• get location():Returns a string object corresonding the current location of the axes.• set location(location):the module.Set the location of the axes, using one of constants defined in9.5.3 colorPython operations available from the color module, used to change the color definitions, color maps,or edit the color scale. All rgb and color scale values should be in the range 0 to 1.• categories():Returns a list of available color categories.Returns a dictionary of name/color pairs for the given color cate-• get colormap(name):gory.• set colormap(name, dict): Change the color definitions for the colors in the given colorcategory. The keys in dict must come from the keys listed by get colormap for that colorcategory, though not all keys need be listed. The values must be legal color names.• get colors(): Returns a dictionary whose keys are all the legal color names and whosecorresponding values are the RGB values of the color, represented as a 3-tuple.• set colors(dict): Changes RGB values for colors in <strong>VMD</strong>. Keys must be chosen from thekeys returned by get colors(). Values must be 3-tuples of floats.• scale method():• scale methods():Returns the current color scale method.Returns a list of all available color scale methods.• scale midpoint():Returns the current color scale midpoint.• scale min():• scale max():Returns the current color scale minimum.Returns the current color scale maximum.• set scale(method, midpoint, min, max): Change the color scale method, midpoint, minimum,or maximum. All properties may be set using keyword arguments.9.5.4 displayPython operations available from the display module, used to control the <strong>VMD</strong> camera as well asscreen updates.• update():Force a display update, without checking the <strong>VMD</strong> FLTK menus134
• update ui():• update on():Update the display as well as any other user interfaces.Tell <strong>VMD</strong> to regularly update the display and the FLTK menus• update off(): Tell <strong>VMD</strong> not to regularly update the display. The display will be updatedonly when display.update() is called.• stereomodes():Returns a list of the available stereo modes.• PROJ PERSP, PROJ ORTHO: String constants defined in the display module for setting theprojection keyword in the set method.• set(**keywordlist):• get(key): set() and get() control various display properties. The following keywords accept/returnfloating-point values: eyesep, focallength, height, distance, nearclip,farclip. The following keywords accept boolean values for on or off, respectively: antialias,depthcue, culling. stereo should be one of the values returned by stereomodes().projection should be one of the PROJ constants defined in this module. size shouldbe a list of two integers corresponding to the width and height of the display in pixels.9.5.5 graphicsPython operations available from the graphics module, used to create custom 3-D objects fromgraphics primitives. The first argument to all operations is the id of a Graphics molecule. Graphicsmolecules are created using the load() command in the molecule module: load(’graphics’,’test’) creates a Graphics molecule named ’test’. For vertices and normals, a tuple with threefloat items is required.• triangle(id, v1, v2, v3):Draw a triangle with the given vertices.• trinorm(id, v1, v2, v3, n1, n2, n3):vertex normals.Draw a triangle with the given vertices and• cylinder(id, v1, v2, radius=1.0, resolution=6, filled=0): Draw a cylinder withendpoints specified by the given points. Radius, resolution, and filled (whether the endsshould be capped or not) may be optionally specified with keyword arguments.• point(id, v):Draw a point at the given coordinates.• line(id, v1, v2, style=’solid’, width=1): Draw a line between the given vertices.Optionally, the line style may be specified as either ’solid’ or ’dashed’, and width may be anypositive integer.• materials(id, onoff): Turns materials on/off for subsequent graphics primitives. Primitiveslying earlier in the stack are not affected. onoff should be either 0 (off) or 1 (on).• material(id, name): Sets the material for all graphics primitives in this molecule. nameshould be one of the material names returned by material.listall().• color(id, color): Set the color for subsequent graphics primitives. color may be (1)a tuple containing three floats specifying the RGB value, (2) an integer corresponding to acolor index, or (3) a string corresponding to a color name.135
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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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short circuit logic, 72, 75sleepcom