Overview

Chemscape Chime from MDL Information Systems is a plug-in for the Internet Explorer and Netscape Navigator Web browsers that allows integrated viewing of three-dimensional chemical structures and associated data from within the browser. The plug-in extends the capabilities found in Roger Sayle's RasMol, using the same 3-D rendering and scripting code, with a few extensions added to allow the viewing of different file formats. The plug-in works hand in hand with two other programs from the MDLI stable, ISIS/Draw and SCULPT, allowing a full range of further options to be explored for any structure of interest.

Figure 1

The molecules in the Web page are not static pictures, but chemical structures that can be rotated, reformatted, and saved in various file formats for use in modeling or database software. Anyone with knowledge of HTML can add structures to any Web page. In addition, one can use RasMol or CSML scripting to preset highlighted views of a molecule's features. Combining scripting with a text explanation of the main features of the structure make Chime ideal for tutorial applications (figure 1).

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

For anyone who is comfortable with a Web browser and with using the right as well as left mouse buttons (or holding down the one button on a Macintosh), learning the basics of structure manipulation takes only minutes. To use Chime for inserting structures into Web pages, the user really needs to already be conversant with the basics of HTML. More advanced uses of the plug-in, such as RasMol scripting, require more experience with both HTML coding and RasMol itself.

Product Quality

Customizability

Figure 2

Visitors to a Web page containing dynamic Chime structures can customize their view of the molecule easily with the click of a mouse button. The plug-in can't be forced to load all molecules with user-defined default views, except if these are specified on the individual Web page being visited. The Web designer can customize features of the program by the use of embedded tags; a full explanation of the different tags is available in the Chime support section. An impressive yet simple tag allows the molecule to start rotating automatically upon loading, which may encourage the visitor to explore further (figure 2).

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

The use of the RasMol scripting language within Chime gives the Web designer an enormous amount of control in specifying what a structure first looks like when loaded. A step-by-step progression highlighting different parts of a molecule is relatively easy to create with a script. Depending on the way the scripting is utilized, the visitor to a page can move between views in either a linear or a nonlinear fashion. Many tutorials developed using Chime and RasMol scripting are available through the links page on the Chime support section. These are good places to start if you wish to add tutorials to your Web pages; further information on the scripting commands is available on MDLI's site.

Figure 3

The widespread availability and use of Chime have led to its use as a building block for Web- and Java-based programs that extend its features. Among the programs using Chime as a base is the STING program (from Goran Neshich and Barry Honig), which provides a clickable amino acid sequence and highlights the positions of selected residues in a user-loaded 3-D structure. Eric Martz's Protein Explorer and Noncovalent Bond Finder (NCBF) are examples of possible future development directions for Chime; each has many useful features incorporated while still retaining Chime's ease of use (figure 3).

Ability to Import and Export in Different File Formats

Chime understands the following input formats:

Chime can also save files in their original formats for viewing offline.

Useful or Unusual Features

Chime is really a must-have plug-in even if you only occasionally view structures over the Web. If your requirements for structural information analysis are greater than that, integration with ISIS/Draw and SCULPT gives it an added dimension of usefulness. Transferring structures of small molecules directly into ISIS/Draw makes life simple if you need some quick diagrams for a presentation or want to work on a reaction mechanism.

Figure 4

Transferring the structure to SCULPT opens the full range of possibilities for exploring the molecule of interest. Extra structural information becomes available, different conformations can be examined, and structures can be aligned with other molecules - for substrate-binding simulations, for instance. Some of the power of SCULPT is also available directly from menus within Chime itself. Simply switching to "Sculpt Mode" allows for bond rotation and torsioning and interactions calculated (figure 4) - although, since I am not a SCULPT user, I must admit to being a little lost over how to make best use of some of this.

Figure 5

The easy creation of a molecular surface, including lipophilic and electrostatic potential, is a great tool for examining proteins properties (figure 5).

The feature I found most useful compared to those of other 3-D-visualization software I've used was the excellent "Select" menu. As well as being able to select groups of atoms, such as "basic amino acids," the user can add or subtract items from a selection as well as define mutually exclusive selections. If this menu dragged into a floating toolbar with its own selection history, it would be ideal.

Limitations

Completely hassle-free use of Chime is restricted to those running later versions of Netscape only. Internet Explorer lacks the full implementation of the Java standard from which Chime originated (according to Eric Martz's site). Chime is also capable of utilizing the LiveConnect support found in Netscape (and not Internet Explorer). For general structure viewing, I found Internet Explorer 5.0 worked equally well, although I'd guess that also depends on the rest of the coding on the Web pages being viewed. For example, HTML pages that contain an "executeScript" command will produce a plug-in error message in Internet Explorer. I did experience some problems with the plug-in causing the Web browser to "freeze" while performing image manipulations. Extended use of "Chimed" pages caused a gradual memory leak and crashed my computer, but I had been using it for quite a few hours without a break… There have also been reported problems in printing Web pages containing Chime structures, mainly with earlier versions of Internet Explorer (4.0 and below).

Since it originates from the same code, it is no surprise that Chime shares the excellent rendering and impressive speed of RasMol. Due to the equally excellent design of Chime by Tim Maffett and Bryan van Vliet of MDL Information Systems, none of these qualities were sacrificed in Chime, and many enhancements were added. The fact that Chime works as a plug-in as well as its added features, particularly the "Select" menu, make it the better option for many applications. Chime versions 2.0 and above offers improved compatibility with different source file types, including a JCAMP-DX reader and viewer for spectral data. Chime's ability to generate and display molecular surfaces is also a big plus. Chime is faster, offers more features, and seems easier to use than any other 3-D visualization plug-in I've come across.

Technical Support and Documentation

All support for the plug-in is available via MDLI's Chime support section, which includes the FAQ, tutorials on incorporating Chime structures into Web pages, and a support email address. The site also offers a list of sites that have implemented Chime - many well worth a look. For webmasters wanting to include a Chime structure on their own Web sites, the list of available HTML tags is also well worth exploring.

Target Users

Anyone who has a need to visualize chemical structures on a computer, which these days covers researchers in most areas of the life sciences.

Comments

If you don't already have it, get Chime for your Web browser now. Even if you do have Chime installed on your computer, it's worth checking that you have the latest version (and probably worth checking that you have the latest version of Netscape, while you're at it). I'm sure most users are not yet aware of the great features added in the latest version of this free software.