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• repindex molecule number name: Return the rep number for the rep with the given name,
or -1 if no rep with that name exists in that molecule.
• selupdate rep number molecule number [onoff]: Update the selection for the specified rep
each time the molecule’s timestep changes. If onoff is not specified, returns the current update
state.
• colupdate rep number molecule number [onoff]: Update the calculated color for the specified
rep each time the molecule’s timestep changes. If onoff is not specified, returns the current
update state.
• drawframes molecule number rep number [frame specification]: Draw multiple trajectory
frames or coordinate sets simultaneously. This setting allows the user to select one or more
ranges of frames to display simultaneously. The frame specification takes one of the following forms now, frame number, start:end, or start:step:end. If the frame specification is not
specified, the command returns the currently active frame selection text.
• smoothrep molecule number rep number [n]: Get/set the window size for on-the-fly smoothing of trajectories. Instead of drawing the specified rep from the current coordinates, VMD
will calculate the average of the coordinates from the n previous and subsequent timesteps. If
n is zero then no smoothing is performed. Note that this smoothing does not affect any label
measurements, and does not change the values of the coordinates returned by atom selections
or written to files; it only affects how the rep is drawn. Smoothing can be especially useful
in visualizing rapidly fluctuating molecules or making movies.
• scaleminmax molecule number rep number [min max | auto]: Get/set the color scale range
for this rep. Normally the color scale is automatically scaled to the minimum and maximum
of the corresponding range of data. This command overrides the autoscaled values with the
values 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 or
hidden. Hidden reps cannot be picked and do not show any graphics.
• volume molecule number <volumeset name> <Origin> <a> <b> <c> #a #b #c <Data> Add
a volumetric data set to the current molecule. Origin, a, b, and c are vectors setting the origin
and the three cell vectors. #a, #b, and #c are the number of grid points in the respective cell
vector directions and finally the data has to be provided as one list with the data following
the grid points along the c-axis fastest, then the b-axis and finally the a-axis.
9.3.20
molecule
Same as mol.
9.3.21
molinfo
The molinfo command is used to get information about a molecule (or loaded file) including the
number of loaded atoms, the filename, the graphics selections, and the viewing matrices. It can
also be used to return information about the list of loaded molecules.
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