What follows will be a very brief introduction to what can be done with VMD. Only the most basic viewing functionality will be discussed. For a complete description of the capabilities of VMD and how to use them, please refer to the
VMD web site .
In this section, a human leukocyte-associated antigen, HLA-AW (PDB structure ID 2HLA), will be shown under various rendering methods in VMD. This section is intended to convey, first, a general idea of the types of visual representations that are available for protein structures, and second, what information is and is not conveyed by each representation.
VMD allows the user to load and view molecule description files in a wide variety of common formats, including trajectory files with multiple structures of the same molecule, such as might be generated by a simulation. Once the molecules are loaded, the way each molecule is rendered may be controlled using the Graphical Representations menu:
Vmd graphical representations menu
This menu allows the user to control in detail how each molecule is rendered.
Vmd atom coloring methods
Coloring schemes to highlight features of interest.
Vmd molecule drawing methods
Rendering methods in VMD. Which one to use depends on the features to highlight.The built-in rendering options of VMD.
Molecules may be displayed by various rendering modes:
Hla-aw. drawing method: lines. coloring method: name
In this representation, each line represents a bond between two atoms. The color of each half-bond corresponds to the element of the atom at the corresponding end of the bond (red for oxygen, blue for nitrogen, yellow for sulfur, and teal for carbon). Line representation gives a clear idea of the molecule's connectivity, but for large molecules it can be difficult to isolate protein sub-structures.
Hla-aw. drawing method: vdw. coloring method: name
Here each atom is represented by a sphere whose radius is the
Van der Waals radius of the atom. The Van der Waals radius is half the separation of unbonded atoms packed as tightly as possible, and provides a rough notion of a collision radius, although it is not a firm barrier. This representation of the molecule gives a rough sense of its shape, and is sometimes called a
space-filling model.
This rendering is the same as in the previous figure, except that now the atoms are colored based on which polypeptide chain they belong to. HLA-AW consists of two chains, the alpha chain (blue), which folds into three domains and the smaller β2 microglobulin (red), which is a component of a whole class of HLA proteins. Coloring by chain allows an inspection of how the polypeptide subunits come together to form the whole quaternary structure of the protein. The black balls are water molecules near the surface of the protein that always appear in the same place in crystal structures, and may therefore be considered part of the structure for some applications.
The Surf drawing mode renders a surface swept out by a sphere of some set size skimming the protein. Usually, this size is approximately that of a water molecule, in which case the rendered surface is very similar to the
solvent-accessible surface .
Note that it is impossible to deduce the connectivity of the atoms from this image or from the space filling image in the previous figure. Overall shape, rather than connectivity, is the information conveyed by these representations. Hence, both backbone-based and surface-based renderings are necessary to fully understand a protein's structure.
Here the protein has been rotated approximately 90 degrees toward the viewer, so that, compared to the previous image, we are looking down from above. The deep groove running from the top left to lower right is the
binding pocket of the protein.
Cartoon rendering places an emphasis on secondary structure. Beta sheets appear as flattened arrows, and alpha helices appear as cylinders. These are common conventions in representing protein secondary structure. By examining this image, we can see that the walls of the binding pocket observed in the previous figure consist of alpha helices, and the floor is an
anti-parallel beta sheet. In anti-parallel beta sheets, adjacent strands run in the opposite direction (notice the arrow points alternate in direction). Note that this representation only conveys information about the backbone connectivity of the protein. Side chain atoms are omitted, and therefore the overall shape is only a very coarse approximation.
Alternative coloring methods can provide additional insight into a protein's structure and function. Here each atom is colored based on whether the side chain of the amino acid residue to which it belongs is acidic (red), basic (blue), polar neutral (green), or apolar (gray). Note that residues on the surface of the protein tend to be hydrophilic (attracted to water, in red, blue, and green), whereas residues closer to the core of the protein tend to be hydrophobic (greasy or water repellant, in gray). This is characteristic of proteins that exist in aqueous solution in nature. Their native structure is stabilized by a tendency for the hydrophilic residues to interact with the solvent water molecules, while the hydrophobic residues are driven together away from the solvent. Clusters of hydrophobic residues on the surface often indicate a location that is usually protected from solvent in the natural state, either by interaction with another molecule or by part of the protein itself.
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Source:
OpenStax, Geometric methods in structural computational biology. OpenStax CNX. Jun 11, 2007 Download for free at http://cnx.org/content/col10344/1.6
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