Purpose of the Protein Explorer

by , January 1999

This document addresses the questions "Why do we need a Protein Explorer in Chime?" and "What does the Protein Explorer offer vs. RasMol for visual exploration of structure?"

The short answer is that indeed the Protein Explorer is a RasMol-like interface implemented in Chime, but that the Protein Explorer can offer much greater assistance and automation (see comparsion). Thus, the Protein Explorer can make visual exploration of protein structure much more accessible to novices, occasional users, or nonspecialists, as well as making it much more convenient than RasMol, even for experts.

Protein Explorer supports nearly* all RasMol commands, plus additional Chime-specific commands. However, Protein Explorer version is much easier to use, and considerably more powerful than RasMol. Much exploration can be accomplished without learning any of the command language common to RasMol and Chime. The main goal is for novices to be able to concentrate on the molecular structure, not on the software required to see it.

The remainder of this document expands upon some of these points, and summarizes key stages in the evolution of the uses of Chime (see also ).

*RasMol should still be used for saving files (other than ), such as GIF images and vector postscript images. These capabilities are disabled in Chime 1 and 2 so cannot be accomplished in the Protein Explorer.

RasMol vs. Chime

Both RasMol (Sayle & Milner-White, 1995) and Chime (MDLI) have superb graphic renderings and incredible speed, Chime having inherited these excellent qualities from Roger Sayle's RasMol. Beyond these qualities, RasMol offers a powerful and engaging interface for self-directed exploration of molecules. Due to the excellent design of Chime by Tim Maffett and Bryan van Vliet of MDL Information Systems, Inc., none of these qualities were sacrificed in Chime, and many enhancements were added.

Chime is much more effective than RasMol for presentations of chemical structure information (see ). In part this is because, by operating "on the paper" of a web document (as a Netscape plugin) Chime can be surrounded by explanatory text and color keys, in part because buttons in the text can control what Chime does (via javascript or LiveConnect), and in part because new and powerful features, which go beyond RasMol, have been added to Chime.

One of the most powerful interactive capabilities built directly into Chime 2.0 is the Select Menu (absent in Chime 1.0 and in RasMol). This frees the user from having to remember most of the command terminology for various categories of atoms, and offers many other conveniences as well. Chime continues to be actively developed by MDLI. RasMol's development by Roger Sayle ceased in 1996, but its development was resumed by a group of volunteers in 1999.

Linear Presentations

Most authors who created web sites using Chime 1.0 (1996-1998) focused on presenting a linear series of pre-selected images highlighting important structural features of a pre-selected molecule or molecules. These presentations of the authors' viewpoints were presaged by kinemages, which are remarkably similar in format, design, and function to most Chime presentations. Indeed, David Richardson's (Protein Science, 1992) was the first program which brought powerful visualization of macromolecular structures to personal computers. It did this in the form of kinemages: pre-programmed scripts which present author-selected viewpoints of author-selected molecules. MAGE remains a powerful presentation and visualization tool today, offering a number of specialized capabilities not found elsewhere.

Some of the earliest linear presentations were by Henry Rzepa and David Marcey, with the technical collaboration of Tim Maffett, principal architect of Chime (from MDLI). Marcey's presentation on DNA polymerase was one of the earliest (on the web in early 1996 but since revised) and is an outstanding example of the linear presentation approach.

Nonlinear Presentations

Chime has an extensive control interface and enormous flexibility, and is by no means limited to linear presentations. An early example (on the web November, 1996) is my , in which the results of each button depend on which buttons were pressed immediately preceding. The possibilities for nonlinear presentations on author-selected molecules remain largely unexplored at this time (January 1999).

Visual Analysis Tools for User-Selected Molecules

Another step in the evolution of Chime use is represented by Chime-based programs which allow the user to load any molecule of her choice, and then offer pre-scripted representations to show specific features. One example is STING by Goran Neshich and Barry Honig, which provides a clickable amino acid sequence and highlights the positions of selected residues in the 3D structure. Another is FirstGlance, which I built for the PDB Lite search interface, and which is now also offered at the Protein Data Bank.

A third example is the . This allows the user to load any molecule, select any target moiety within that structure, and it then finds and shows the atoms closest to the target structure. For example, the noncovalent interactions between a protein and a bound ligand can be identified visually. (I plan to integrate the Noncovalent Bond Finder into the Protein Explorer in a future version of the latter.)

The Protein Explorer represents the next logical step: a generalized visual analysis interface which allows any molecule to be loaded, and moreover places no restrictions on the kinds of analysis which can be done (except those inherent in Chime). In contrast, while allowing any user-selected molecule to be loaded, both STING and the Noncovalent Bond Finder are limited to specialized kinds of visual analysis. Such specialization, of course, comes with many conveniences and much automation.

The Protein Explorer: Accessibility for the General Scientific Public

Perhaps the most important reason for the Protein Explorer is to make it much easier for the general scientific public to explore 3D macromolecular structure. Despite RasMol's excellent design, most people who would benefit from using it never learn how. In my for college faculty, I find that it takes a full day of guided hands-on experience before people can begin to use RasMol effectively. Without the guidance of a workshop it would no doubt take several times longer. In part this is because one must become familiar with a "teletype style" command language to use RasMol fully. Protein Explorer's QuickViews menus allow novices to conduct more advanced exploration than RasMol's menus allow, and without learning any teletype-style commands.

Another portion of the time required for RasMol-beginners is to learn how to interpret the graphic images of macromolecules. Protein Explorer's FirstView explanation offers the information novices need to understand what the display means.

Finally, the control which javascript can exert over Chime enables automation of complex repetitive tasks. The is a good example. Nearly everything it offers can be done in RasMol, but doing it would take hundreds of carefully designed, expertly typed commands -- so many commands that during the process the user would likely lose track of the question! This is replaced with a single "Find" button, allowing the user to concentrate on the answers to the questions rather than the technology required to answer them. (The Noncovalent Bond Finder is accessible from within the Protein Explorer.) The Protein Explorer automates other useful tasks and provides many convenience "buttons".

The integration of Protein Explorer into the Protein Data Bank's Structure Explorer interface in late 1999 was an important step towards making 3D macromolecular structure more accessible to the general scientific public. Thanks to RCSB, Protein Explorer is now mirrored around the world.