Overview

WebLab ViewerPro is a well-rounded desktop molecular-graphics program for visualizing, customizing, and sharing molecular images. It offers a combination of rendering controls, molecule-sketching and minimization tools, import and high-resolution export options, and integration with other OLE-compliant applications. It can also be configured as a helper application for use with a Web browser. It is exceedingly easy to learn, especially for users with experience in related software such as RasMol or Deep View. It boasts a sleek, menu-driven interface with a lot of power under the hood, including the ability to render solvent-accessible surfaces, quickly assemble a unit crystal, and change stereochemistry - all with a click of the mouse, without needing to learn a complex command language. Select individual atoms, groups, chains, or entire molecules, and easily modify their display, color, atom identity, bond order, and more. Or build your own small molecules with WebLab ViewerPro's atom-, chain-, and ring-sketching tools, and ensure their scientific credibility with instant energy minimization. This program is so user-friendly that it will keep constant track of bond angles, torsion, chirality, stereochemistry, bond length, charges, hydrogen-bond interactions, structure validity, and more. And when you're ready to print or display your molecule, WebLab ViewerPro offers a range of options, including background color, light direction and color, and depth cueing. This software goes a long way toward bringing structural biology into the realm of everyday use. It is an outstanding value for the money.

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

The "Getting Started" tutorial included on the CD-ROM took approximately two hours to complete and provided a good level of familiarity with the software. I spent another two to three hours systematically going through the menus (including the help menu) to discover many more helpful features not mentioned in the tutorial. Almost everything in WebLab ViewerPro can be done with mouse and menu, making it exceptionally easy to use. Highly repetitive actions (such as changing an atom's identity) are also available as keyboard shortcuts. As with any software package, it does take some time to learn the correct mouse-clicks and shortcuts and to learn where all of the various menu commands are located. For users with experience in molecular modeling and visualization software, WebLab ViewerPro is learned easily. Novices may not appreciate the more subtle features of the software, such as minimization and surface rendering, but they will still be able to use the program to produce excellent molecular graphics. I did not attempt to learn how to write scripts for the software, although it is scriptable.

Product Quality

Customizability

WebLab ViewerPro has a very clean and customizable interface. Tools can be accessed from toolbars anchored to the main display window or as menu commands. Toolbars can be moved at will, anchored or made to float, made hidden or always visible, and arranged vertically or horizontally. The options included on each palette are also customizable. Windows are scalable, and multiple windows can be tiled vertically or horizontally.

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

Scripts can be written for WebLab ViewerPro to change the way a molecule is displayed. The scripting language is fairly straightforward, and the vocabulary is manageable in size. Users who are familiar with other chemical scripting languages should have no trouble scripting this program.

Ability to Import and Export in Different File Formats

WebLab ViewerPro has its own default file type (MSV), which combines atomic coordinates with display, position, and lighting information. In addition, it can output a variety of file formats, including GIF and JPEG for use on the Internet; PDB, ENT, and MOL for use in other molecular modeling/visualization programs such as Chime and Deep View; XYZ animation files; POV for ray-tracing programs, SMI, BMP, and more. WebLab ViewerPro can import all of the file types it can export, as well as files from Insight (CAR) and Quanta (MSF), various crystallographic file types (CIF, CSD), and more.

Useful or Unusual Features

The key feature of WebLab ViewerPro is its ability to combine effectively a high degree of visualization with helpful sketching/modeling tools and a wide variety of output formats, and to package them all in an intuitive and stylish interface. It neatly fills the niche between free programs, which often lack support and documentation and can be difficult to learn, and hard-core modeling software with prohibitive price tags and extensive training requirements. Another excellent feature of WebLab ViewerPro is the ability to easily create 3-D molecules from scratch (sketching), with on-the-fly energy minimization and structure cleanup. In addition, WebLab ViewerPro molecules can be embedded directly into various third-party programs, including popular word-processing and presentation software. MSI also distributes WebLab ViewerLite, a cross-platform, free version of the program available at its Web site, so users do not need the full version just to view molecules in 3-D.

Selecting and modifying parts of a molecule is extremely easy. The program offers a wide variety of colors and display styles which, combined with the high-resolution output, make WebLab ViewerPro a powerful molecular-graphics program. The status line across the bottom shows helpful hints for the current tool and reports the current selection (which is also colored bright yellow in the structure itself).

WebLab ViewerPro offers it all in a single program. As an example, I opened the structure of a peptide-bound MHC molecule (a protein that displays antigenic peptides on the surface of immune cells). I wanted to know how much I could change the sequence of the bound natural peptide without explicitly disturbing its fit inside the MHC binding cleft. I used the molecule editing and sketching tools to modify side-chain atoms one at a time or entire amino acids, minimizing energy with each change. Utilizing several of WebLab ViewerPro's monitors, I could see the regions of steric hindrance and possible hydrogen-bond interaction form as I altered the peptide. I replaced several nonpolar side chains with similar-sized polar groups, added labels, and exported it as a GIF file for display on the Internet. I also changed the stereochemistry of one amino acid in the peptide to investigate stereospecificity of the MHC molecule at a key position. Then I rendered the binding-cleft region as a solvent-accessible surface and the peptide as space fill, with the altered residue labeled with its new stereochemistry and colored for emphasis. I saved this in MSV format (WebLab ViewerPro's default) and sent it to an immunologist colleague who had downloaded WebLab ViewerLite (free). At no time did I need to launch another program or enter any scripting commands.

Limitations

The program is limited to systems running Windows 95 or later. Under most circumstances, the molecule snaps to a thin wire-frame view during rotation, translation, or zoom, and loses all three dimensionality. This was especially true with large molecules; the program handled rotation of small molecules without trouble. (In this sense, RasMol and Chime are still unparalleled.) The command to synch molecules in multiple windows did not work well on my system. Energy minimization is performed by an admittedly simple calculation, which I could not evaluate for accuracy. In several places, the tutorial did not accurately reflect what was happening in the program, especially the section that explored hydrogen bonding. In addition, I could find no explanation for how hydrogen bonds are determined or what rules are followed when adding hydrogen atoms to a structure.

One feature that WebLab ViewerPro appears to lack is the ability to toggle quickly through the rotate, translate, and zoom tools; this is unfortunate because these tools see the most use.

Comparisons with Similar Software

WebLab ViewerPro is better than most free software because it successfully integrates so many useful features. It is slightly less flexible than Chime and RasMol for customizing the display of a molecule, but offers much better output options, a more intuitive interface, the ability to load multiple molecules, and sketching and energy-minimization features. It does not offer true molecular-modeling features as Deep View does, but it is much more flexible in displaying molecules.

Technical Support and Documentation

Online documentation is limited to a tour of the features and a short FAQ, although MSI does provide an email address for WebLab ViewerPro technical support. I did not evaluate response time or effectiveness of the email support. The CD-ROM contains many helpful extras, including the Getting Started tutorial, sample molecules, and a list of scripting commands, and the program's Help section was good.

Target Users

WebLab ViewerPro is most useful for the user who lies somewhere between a total novice and a structural biologist.