VMD Tutorial-Drawing Style

Introductions

VMD is a molecular visualization program that uses 3D graphics and built-in scripts to display, animate, and analyze large biomolecular systems. VMD is a very small and sophisticated visualization tool and a powerful molecular dynamics visualization software that is very commonly used in the industry.

Tutorial

  • After opening the pdb file, we see the molecular model consisting of the lines shown below:

VMD Tutorial-Drawing Style

  • In the main VMD window, select "Graphics>>Representations..." menu option. The "Graphical Representations" window will pop up, where the default display state of the current molecule is highlighted (yellow-green, a).
  • In the Draw Style tab (b), we can change the display style (d) and color (c). Let's start with the Drawing Method. Each Drawing Method has its own parameters. For example, in the Lines style, the thickness of the lines (Thickness) can be modified using the parameter control in the lower right corner of the window (e).
  • Clicking on the Drawing Method brings up a list of options. By selecting VDW (van der Waals), each atom is displayed as a sphere, which makes it easier to see the spatial distribution of the proteins.
  • VMD Tutorial-Drawing Style

  • When VDW is selected as the drawing method, two new parameter controls (g) will appear in the lower right corner. Use these controls to change the Sphere Scale to 0.5 and the Sphere Resolution to 12. Note that the higher the resolution, the slower the graph will be displayed.
  • Pressing Default will return you to the default properties of the current drawing method.
  • To display a more abstract protein pattern, you can select Tube in the Drawing Method and watch the protein skeleton change.
  • In the Graphical Representation window, select "Drawing Method>>NewCartoon" and you can easily identify how many alpha-helices, beta-folds and other pipelike structures there are in the protein.
  • Ubiquitin protein structure: Ubiquitin protein contains three semi-a-helices (residues 23-34, three of which are hydrophobic), a short 310-helix (residues 56-59), a β-folded fragment with five round trips (residues 1-7, 10-17, 40-45, 48-50, and 64-72), and seven inverted linkage segments. VMD uses the STRIDE program to calculate the secondary structure of the protein based on a heuristic algorithm.

  • Each drawing style can be selected with a different coloring method (Coloring Method). In the Graphical Representation window, the default coloring method is Name, in which you can see that different atoms have different colors if you select a coloring style that shows individual atoms: O (oxygen) is red, N (nitrogen) is blue, C (carbon) is cyan, S (sulfur) is yellow, etc.
  • Select Coloring Method>>ResType, which distinguishes between non-polar residues (white), basic residues (blue), acidic residues (red), and polar residues (green).
  • VMD Tutorial-Drawing Style

  • Select ColoringMethod>>Secondary Structure, this coloring method is usually used with the NewCartoon style.

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Applications of Visual Molecular Dynamics Software

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