Reference for “Creating representations and trajectory smoothing in VMD” Software: VMD 1.9.1 Highlighting portions of the protein: 1. In the “VMD Main” window, click the “Graphics” option on the tool bar. 2. In the drop-down menu, select “Representations.” 3. In the “Graphical Representations” window, click the “Create Rep” button at the top. 4. Click the “Selections” tab underneath the “Selected Atoms” line. 5. Choose “resid” as the keyword, and double click it to add it to the “Selected Atoms” line. 6. On the right hand side at the bottom of the same window, choose the numbered residue you wish to highlight under the “Value” menu. NOTE: Steps 5 and 6 can be substituted for simply typing in the keyword and value. 7. Press ENTER/RETURN 8. With the same representation selected above (highlighted in green), click on the “Draw Style” tab next to the “Selection header.” 9. Click the “Coloring Method” drop-down menu and select “ColorID.” 10. Click the drop down menu on the right-hand side of the Coloring Method dropdown menu and select the color you wish to highlight the representation in. “Smoothing” the trajectories: 1. In the “Graphical Representations” window, select the Representation you wish to smooth by simply clicking it (highlighting it green). 2. Click the “Trajectory” tab under the “Selected Atoms” line. 3. At the bottom, click the arrows to the left and right of the “Trajectory Smoothing Window Size” to select the desired level of smoothing (interpolation of motion between frames). NOTE: 5 is generally a good value for smoothing. Make sure all of your representations in a given model have the same level of smoothing for the best visualization results. Displaying atom type in a residue(s): 1. In the “Graphical Representations” window, select the Representation you wish to display the atoms of by simply clicking it (highlighting it green). 2. Click the “Draw Style” header under the “Selected Atoms” line. 3. Click the “Drawing Method” drop down menu and select “Licorice” (same as the ligand). 4. Make sure the “Coloring Method” drop-down menu is on “Name,” which displays the various atoms in different colors. Helpful keyboard shortcuts: “=” reorients the display to its original setting. “t” allows you to translate the structure by clicking and dragging. “r” allows you to rotate the structure by clicking and dragging.
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