Biomedical Engineering Reference
In-Depth Information
backward and determining how they were affected on their way from the light source illuminating the
molecular structures in the image. In addition, PyMol supports the Python scripting language (hence
the name), allowing automated processing of images.
SWISS-PDBViewer was acquired by GlaxoSmithKline and then made available to non-commercial
users at no cost. Like RasMol, SWISS-PDBViewer emphasizes ease of use over power and
functionality. Even so, as illustrated in
Figure 5-13
, SWISS-PDBViewer is feature-laden. In terms of
functionality, it's somewhere between RasMol and Pymol. As such, computer hardware requirements
are moderate. Like RasMol, it's capable of reasonable performance on a low-end desktop or a laptop
computer. The graphical user interface provides access to a variety of features. Unlike Pymol,
however, there is no scripting language, which limits extensibility of the program.
Figure 5-13. SWISS-PDBViewer. The Preferences menu hints at the
extensive rendering capabilities of the program. The image in the
background is a wireframe view of Deoxy Hemoglobin.
Chimera is a high-end, highly extensible rendering program from the Computer Graphics Laboratory,
University of California, San Francisco. Of the programs reviewed here, Chimera is clearly the most
powerful, most feature-packed, and most demanding application. Features include multiple view
tools, labeling of amino acids by a variety of criteria, alignment of molecules, and the ability to mix
multiple renderings, such as transparent surfaces with ball-and-stick views. In addition to extensive
online user documentation, there is an online programmer's guide that describes how the plug-in can
be integrated with custom applications. The prices for this functionality are a relatively steep learning
curve and the need for a high-end workstation for productive work. For example, the download is
over 27 MB, and the developers recommend a 1 GHz Pentium with high-end video hardware. One of
the downsides of Chimera is that it is still under development, so some of the features may not be
fully implemented. Chimera is the successor to the popular UCSF Midas and MidasPlus programs.
