The controls allow selection the molecule used for the calculation. The graphical display of residues and timesteps can be scrolled and zoomed as necessary to see results for large structures and long trajectories.
The controls allow selection the molecule used for the calculation. The graphical display of residues and timesteps can be scrolled and zoomed as necessary to see results for large structures and long trajectories.
Brief Tutorial Example:
Start VMD
Load a trajectory (e.g. sample.psf and sample-traj.dcd)
Select Extensions:timeline from "VMD Main" window.
Calculate and display graphs: To display a 2D graph of secondary structure vs. time, select Calculate:Calc Sec. Struct. from the "VMD Timeline" window. A color-coded map of secondary structure should appear. The horizontal axis is time (frame number), the vertical axis is residue number / chain.
Graph zooming: Control the residue numbering as for the Sequence Viewer [link to section]. The top left horizontal slider sets the scale for both axes simultaneously. The left horizontal slider below it sets the scale only for the horizontal axis. "Fit all" will fit both the vertical and horizontal graphs into the window.
To change displayed frame: Scrub left and right over the graph to change the frame displayed in the GL window. A gray bar will overlay the current time in the graph.
To highlight an 'event': Click and drag a marquee box with the left mouse button. A blue box will appear in the graph to show the residues and time range selected. Shift-Click-drag out another box to select more residues; several sets of residues may be selected, but only one frame range. The trajectory will animate through the selected frame range three times after each selection.
The selected residues will appear as bonds; change their color and draw style by changing the associated representation in the "Graphical Representations" window.
Other per-residue calculations are available besides secondary structure:
Calculate:Calc X position : simple demonstration of per-reside information
Calculate:Calc. Phi: per-res Phi angle
Calculate:Calc. Delta Psi: per-res change in Psi angle from initial frame
Calculate:Calc. per-res RMSD: broken, brings up Ramaplot instead
These are intended as demonstration calculations. A method to specify arbitary calculations is planned, currently other calculation results can only be displayed via loading data files (see below).
Residue number vs. frame number data files can be saved and loaded.
File: Load Data file: saves current per-res data for entire trajectory
File: Save Data file: loads per-res data for entire trajectory