Interface and controls

This general description of the Timeline interface should help with navigating in Section 3, ``Trajectory Analysis''.

Figure 5: The Timeline 2D data plot. Main interface features are indicated.

Figure 6: Parts of the Timeline interface. a) Horizontal and both-axis zoom sliders, b) Vertical axis zoom slider, c) Threshold count plot, d) Fixed-zoom buttons, e) Highlight Details panel, f) Molecule ID and Analysis selection, g) Key/Scale, h) Key Scale (secondary structure), i) Threshold minimum/maximum, j) Threshold count, high, total k) Current structure highlight, l) Current frame highlight

Figure 7: Highlight Details panel.

See a closer view of parts of the interface in Figure 6, and descriptions of these in Table 1. A diagram of the Highlight Details panel is in Figure 7. The top-level Timeline menus are described in Table 2.

Table 1: Timeline main interface features

Interface element	Description	See Figure
Current highlight selection cursor	This 2D highlight cursor determines the structure that is highlighted in the 3D molecule view, and which is described in the Highlight Details panel. Left mouse button click or drag to change the current highlight selection.	5
Horizontal axis zoom slider.	Scales the 2D data plot horizontally. Useful for changing time range viewed without changing structure range.	6a
Both-axis zoom slider.	Scales both axes simultaneously. Combine with resizing Timeline window to fit a larger trajectory or structure in less screen area.	6a
Vertical axis zoom slider.	Scales the 2D data plot vertically. Useful for changing range of structure data displayed, without changing time range.	6b
Fixed-zoom buttons.	The fit all button scales the entire loaded trajectory to display within the default window size. The every residue button scales the vertical axis to show an axis label for every residue.	6d
Molecule ID	Specifies the molid of the molecule to analyze.	6f
Analysis selection	A VMD selection string, specifies what part of the current molecule to use for per-residue analysis. Default is ``all''.	6f
Threshold count plot	Graphs number of items (residues or selections) in each frame that are within the threshold range for each frame. The max value is normalized to the height of the graph. First instance of max. (min.) value marked with a green (red) line.	6c
Key/Scale	Displays the analysis method, units, and numerical range of currently displayed colors.	6g
Key/Scale (sec. struct.)	When displaying Secondary Structure, displays the structure coloring codes. The one-letter code descriptions are listed in Help $\rightarrow$ Structure codes... and in Figure 9.	6h, 9
2D Data Plot	This is a plot of structural elements (residues or selections) vs. time. Exploring this plot for changes, transitions, and visually-detectable correlations helps the user find events in the trajectory.	5
Threshold min./max.	Set the range for Threshold plot. The Threshold plot will change as you drag these sliders. The limits of the sliders are adjusted for the range of the loaded data set.	6i
Threshold count, high, and total	Shows the threshold count for the currently highlighted frame, the highest threshold count in the trajectory, and the total number of items in the structure.	6j
Current frame bar	The long vertical black bar indicates the current frame, and helps to visually locate the highlight cursor.	5
Current frame highlight	Highlight box in the horizontal axis to indicate current frame	6l
Current structure highlight	Highlight box in the vertical axis to indicate current structure	6k
Mouse zoom-in/zoom-out.	Zoom in with right-button click-and-drag; this creates a rectangle selection, the contents of which will expand to fill the 2D plot. Zoom out with right click, or with the zoom slider and fixed zoom controls.
Scroll Bars	Use to move around the 2D data block, whenever either scale is zoomed in beyond the ``fit all'' size. Moves thorugh the structure and the trajectory.	5
Current structure highlight	The long vertical black bar indicates the current frame; this along with highlights in the horizontal and vertical axes labels helps visually locate the highlight cursor.	5
Highlight Details panel	Description of the residue/selection beneath the 2D cursor. The current residue number, residue name, chain, segment, and frame, data value for the selected residue, and current analysis method.	6e, 7

Table 2: Timeline Top-level Menus

Title	Description
File	Allows saving and loading formatted data sets, and printing of the 2D data plot.
Calculate	Provides several built-in calculation options, access to user data fields, and user-defined per-residue functions.
Threshold	Allows direct entry of values for threshold graph, and clearing/recalculating the graph.
Analysis	Allows a user to enter the user-defined per-residue function, and to set the frame range to which to apply the chosen analysis method.
Appearance	Sets the value range for scaling on the 2D data plot, the shading pallette (greyscale or rainbow), and other user interface details.
Data	File list of the current data collection, for quick browsing between .tml files in a designated directory.