VMD User's Guide

• drawframes molecule number rep number [frame specification]: Draw multiple trajectoryframes or coordinate sets simultaneously. This setting allows the user to select one or moreranges of frames to display simultaneously. The frame specification takes one of the followingforms now, frame number, start:end, orstart:step:end. If the frame specification is notspecified, the command returns the currently active frame selection text.• smoothrep molecule number rep number [n]: Get/set the window size for on-the-fly smoothingof trajectories. Instead of drawing the specified rep from the current coordinates, VMDwill calculate the average of the coordinates from the n previous and subsequent timesteps. Ifn is zero then no smoothing is performed. Note that this smoothing does not affect any labelmeasurements, and does not change the values of the coordinates returned by atom selectionsor written to files; it only affects how the rep is drawn. Smoothing can be especially usefulin visualizing rapidly fluctuating molecules or making movies.• scaleminmax molecule number rep number [min max | auto]: Get/set the color scale rangefor this rep. Normally the color scale is automatically scaled to the minimum and maximumof the corresponding range of data. This command overrides the autoscaled values with thevalues you specify. Omit the min and max arguments to get the current values. Use “auto”instead of a min and max to rescale the color scale to the maximum range again.• showrep molecule number rep number [on | off]: Get/set whether the given rep is shown orhidden. Hidden reps cannot be picked and do not show any graphics.• volume molecule number #a #b #c Adda volumetric data set to the current molecule. Origin, a, b, and c are vectors setting the originand the three cell vectors. #a, #b, and #c are the number of grid points in the respective cellvector directions and finally the data has to be provided as one list with the data followingthe grid points along the c-axis fastest, then the b-axis and finally the a-axis.8.3.20 moleculeSame as mol.8.3.21 molinfoThe molinfo command is used to get information about a molecule (or loaded file) including thenumber of loaded atoms, the filename, the graphics selections, and the viewing matrices. It canalso be used to return information about the list of loaded molecules.Each molecule has a unique id, which is assigned to it when it is first loaded. These start atzero and increase by 1 for each new molecule. When a molecule is deleted, the number is not usedagain. There is one unique molecule, called the top molecule [§4.4.2], which is used to determinesome parameters, such as the center of view, the data in the animation form, etc.• list: Returns a list of all current molecule id’s.• num: Returns the number of loaded molecules.• top: Returns the id of the top molecule.110