Overview

The pace of structural biology has accelerated rapidly in recent years. Since February 1999, the Protein Data Bank (PDB), according to its Web site, has received over 3,000 new structures for publication (an average of 6.4 every day). More scientists are integrating structural biology into their own research projects, and more students need to learn structural biology concepts and techniques. Scientists, educators, and students need powerful molecular-modeling tools that are inexpensive, easy to learn, and usable on a PC. Swiss-PdbViewer fits this description nicely. While it may never replace expensive, commercial modeling software, it is free, offers an intuitive graphic interface, can handle complex operations with minimum delay, and is small in size. It is cross-platform with impressive online support, both technical and educational, and it is compatible with many other molecular modeling resources such as FASTA, GRASP, X-PLOR, and PDB.

How Long Did It Take to Learn to Use It Productively?

The basic tutorial took me about two hours to complete (I have over three years of experience in molecular visualization and modeling software). It provided a working knowledge of the menu options, mouse actions, and how to perform most of the basic operations. The tutorial also includes a number of practical examples, showcasing important features of the software. For a novice, the entire tutorial might take 5 to 6 hours. A Web site, aimed specifically at students and maintained by Gale Rhodes (author of Crystallography Made Crystal Clear), has a more extensive tutorial that may take several days to complete.

Product Quality

Customizability

Nearly all features of the software are highly customizable, including loading, modeling, and rendering. Swiss-PdbViewer allows you to save different sets of preferences to accommodate multiple users.

Ability to Program in Scripts, Add Extension Modules, etc.

None.

Ability to Import and Export in Different File Formats

Opens/Imports: PDB, MMCIF, and MOL files; text files (sequences); molecular- surface, electrostatic-potential (including GRASP), and electron-density (including X-PLOR) maps.

Saves/exports: all of the above, plus FASTA and aligned-sequence files; Ramachandran plots; picture files; and POV-Ray scenes.

Useful or Unusual Features

Swiss-PdbViewer has a host of useful features. It provides numerous resources for aligning, superimposing, and fitting molecules. It allows you to "mutate" amino acids in a protein, change the conformation of amino-acid side chains via the Ramachandran plot, model hydrogens onto a structure, and build functional multimers from a single monomer. You can build crystal symmetries to view a protein in its crystal unit and analyze crystal contacts. You can even use Swiss-PdbViewer to fit a sequence onto an electron-density map.

Swiss-PdbViewer also allows you to load and manipulate multiple structures, or even merge them into a single file. You can move one region of a protein relative to another and view the consequences graphically. In conjunction with POV-Ray, you can create high-quality images.

Swiss-PdbViewer boasts a direct connection to the Swiss-Model database, which allows easy homology modeling. The Swiss-PdbViewer tutorial includes step-by-step instructions for this procedure. Essentially, loading a raw protein sequence allows you to submit the sequence to the database, retrieve the 3D structures of homologous proteins, thread the raw sequence onto the structures, tweak the fit manually, validate your alignment, and submit a request to model the structure.

Limitations

The current version allows you to generate but not save a molecular surface. It does not retain the PDB header when saving a PDB file, and it loses hydrogens during certain procedures (for example, during fixing selected side chains). On the Macintosh, it sets the display to 256 colors.

Basic installation was fast and very easy, but installing the tutorial, database, and various extra PDB files was slightly more cumbersome, since they had to be downloaded and then manually placed in the proper directories. Offering the full installation as a single package would be a nice feature.

Comparisons with Similar Software

Swiss-PdbViewer offers a combination of extensive modeling functions and high-quality image rendering that similar free programs do not. It is not as flexible as RasMol or Chime in customizing the display of the structure, but it can render final images in much higher resolution.

Technical Support and Documentation

Documentation, in general, is excellent, with very useful Web resources. There is also a discussion group for Swiss-PdbViewer users. Traditional technical support is not offered, but for basic operations, the software is fairly intuitive. The high-powered features, especially the homology-modeling functions, are more complex. The tutorial was extremely helpful in performing these functions. Local and Web help are available from the Help (Windows) or Apple (Macintosh) menus. Novices may need to visit Gale Rhodes' Web site.

Target Users

Anyone with an interest in structural biology will appreciate Swiss-PdbViewer. Although dedicated research labs involved in intensive molecular modeling will find more powerful and expensive software to use, for the enthusiast, the research scientist with some molecular modeling to do, or the science educator, this is an invaluable software package.