Biomedical Engineering Reference
In-Depth Information
The minimum functionality of the open-source (source code is available for free or low-cost non-
commercial) rendering programs available on the Web includes the selective viewing and
manipulation of subsets of atoms, wireframe, ball-and-stick, or ribbon renditions of a protein. Each
representation emphasizes different protein properties. For example, the ball-and-stick PyMol
rendering of Glutamine Synthetase in
Figure 5-7
emphasizes atoms and bonds. Wireframe views,
such as the PyMol renderings in
Figures 5-8
and
5-9
, emphasize the molecular bonds. Ribbon
diagrams, such as the Chimera rendering of Glutamine Synthetase shown in
Figure 5-10
, emphasize
the protein's secondary structure, whereas the Van der Waals surface diagram of Deoxy Hemoglobin
in
Figure 5-11
rendered in SWISS-PDBViewer emphasizes the atomic volumes. Another popular
format is the backbone, which shows the overall molecule structure (see
Figure 5-12
).
Figure 5-7. Ball-and-Stick Display of Glutamine Synthetase Rendered in
PyMol. A close-up of the center of the molecule is shown on the right. The
ball-and-stick format emphasizes atoms and bonds.
