3D Molecular Visualization Module
The 3D Molecular Visualization module (3DMV) within the Smartwork system allows students to visualize, manipulate, and analyze three-dimensional structures of proteins and nucleic acids that have had their three-dimensional structures solved and deposited into the Protein Data Bank (pdb). Many chapters of the Biochemistry textbook have one or more associated “PDB” questions that use the 3DMV. For these questions, the pdb coordinates, and structure, of a biological macromolecule discussed in the textbook have been loaded into the introduction of the question, shown in the Figure 1 below.
In order to manipulate this structure in the 3D molecular visualization, you can either work within this window or open a new separate window that has the 3D molecular visualization viewer. To open up a separate window to view the structure, hover over the structure and double-click the left button of your mouse.
Moving the Molecule and Selecting Components
To rotate the view of the molecule in the 3DMV Designer, left-click and continue holding the left mouse button down as you move your mouse around. This will rotate the molecule. If you are using a device with a touch screen, then you can rotate the molecule with finger dragging.
To zoom in or out of the molecule in the 3DMV Designer, use the scroll button on the mouse or, if you are using a device with a touch screen, use the finger and thumb “pinching in and out” method.
To select components
Along the bottom there are words in blue indicating specific components of the structure, and each has two boxes next to it. (This is shown by the red circle and arrow in Figure 3 below). The component titles are labelled in parenthesis as indicated in Figure 2:
- Protein structures: “amino” for amino acids
- DNA or RNA structures: “nucl” for nucleic acids
- Co-factors: various names
The first box, if checked, selects that component such that it is visualized on the screen. When analyzing more complicated structures, it is useful to “hide” parts of the structure by unchecking this box.
Figure 3 below shows a structure that contains proteins, nucleic acids, and several co-factors. The names of the different parts of the complex along the bottom of the viewer are zoomed in for clarity. The user may need to scroll across in order to see all the names.
The second box after these names along the bottom of the viewer allows the user to select or de-select all of the parts of that particular component. Selection of the component is indicated by green “x’s” on the structure (see Figure 4). This selection must be done if the user wants to change the display type or coloring of that part of the molecule.
Dropdown Menu Basics: Coloring and Display Style
The dropdown menu is found in the upper right-hand corner of the structure viewing window, circled in red in Figure 4 below.
Once selected, the user can use the dropdown menu to change the display or coloring of the molecule. Click the left button of your mouse to display the dropdown menu, shown below.
To change how the structure is displayed, first click on its current representation (ribbon in this figure), and then click on the preferred selection (Figure 6).
After you have made your display and coloring selections, deselect (uncheck) the second box after the name of the component you are working with (“b(amino)” in this example).
Selecting Specific Areas or Residues
Two other toolboxes in the dropdown menu, the “Labels” tools and the “Measure” tools are used in many types of problems, but they generally have limited utility if all atoms in a structure are selected. To make good use of these tools, the user must select specific atoms.
To select a specific area of the molecule, first method: To select a certain region of a molecule, hover over the area, right-click your mouse, and continue holding the right button down as you expand the resulting "black box" to cover the area you are interested in. Release the mouse button when the area is where you desire. A small green x (or green x's) should appear in your selected area.
To select a specific residue of the molecule, second method: View the particular residue or sequence of residues (amino acid for protein structure, or nucleotide for nucleic acid structure), and select "View" and "Sequence View" on the dropdown menu. To select a particular residue for labeling, hold down the left button on your mouse while you scroll over that residue, or residues. Small green x’s should appear in the viewer once you do this, while the letters representing the residues in the sequence viewer will become highlighted in blue and surrounded by blue “thought bubbles.”
Now that two methods of selecting specific areas of residues of your structure are clear, let’s explore the labeling and measuring tools from the dropdown menu.
First, for labeling, you can label your selected component by, from left to right after “Labels,” the atom (“ATOM hb1”), the residue (“RES A5”), or the site (“SITE S”); see Figure 14. Atom and site labeling are self-explanatory, while residue labeling means labeling by either amino acid or nucleotide, using the 1 letter code and the number on the residue in the structure (1 = N terminus, or 1 = 5’ end).
To label: After selecting the general area, or individual residues you want to label (should have green x’s in the visualization window), scroll to “Labels” in the dropdown menu and select which labeling you want. You may have to rotate your molecule to view the labels well.
The measuring tools from the dropdown menu, from left to right are: distance, planar angles, torsion angles, and delete all measurements.
To Measure: First, the molecule should be displayed either in ball and stick or CPK representation. Next, deselect all residues in your molecule (there should not be any green x’s on the structure). Click on the measure tool from the dropdown menu. To measure between two atoms, click on the first and then the second atom. A small green x will appear on the atom (s) you selected, and a black line with a distance measurement will appear next to it. In order to ensure you have measured the correct component, it is often helpful to label relevant residues prior to measuring.
There are other functions in the 3D Molecular Visualization Module, especially in the dropdown menu. However, the abilities to select certain components of a structure, to select areas or specific residues of a structure, to change the display type, to label components, and to use the measuring tools are by far the most important functionalities to understand in order to complete Smartwork questions using this module.