Web Publishing with ChemOffice Plugins


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ChemNews.Com VOL 6 NO 4

Web Publishing with ChemOffice Plugins
Bruce R. Gelin, PH.D.

Publishing your chemical drawings, reaction diagrams, and three-dimensional structures on the World Wide Web couldn't be easier! Just as ChemDraw and Chem3D revolutionized publishing your work in print, the ChemDraw and Chem3D Plugins are the future for Web publishing. Your colleagues anywhere on the Internet can view your structures and models, and even copy and use them in other applications, while maintaining all the chemical information content. In this article, we'll get you started with the basics of Web publishing.

First, you don't need to be a Web wizard to publish your chemical information. When I started to write this article, I had encountered the ChemDraw Plugin on the search results pages of CambridgeSoft's ChemFinder WebServer. I saw that I could copy structures and use them in other applications, but I had no idea how it all worked; and I had never used the Chem3D Plugin. In terms of Web programming, I've built simple HTML pages for a personal Web site, but I am certainly no HTML expert. In short, with just a beginner's introduction to HTML, you can produce useful Web pages to publish your chemical information.

The basic idea is simple: plugins are programs that add specific capabilities to your Web browser. To invoke them in your Web page, you use the embed HTML statement. When viewers access your page with their plugin-equipped Web browsers, they see the structure or model you have specified. They can view it, or copy it complete with all its chemical information to use in their programs. For example, you might publish a ChemDraw sketch of a molecule you think would be of interest to your research group. Researchers reading your Web page could copy the structure and paste it into ChemDraw, Chem3D, or other programs that read ChemDraw files. (By the way, the ChemDraw Plugin handles reaction diagrams too.)

Adding the ChemDraw plugin to a Web page is as simple as adding the following statement to the HTML for the page:

< embed src=struct1.cdx width="480" height="300" >

A structure displayed by the ChemDraw Plugin, with the standard ChemDraw tool bar

Here struct1.cdx is the ChemDraw structure you want to publish, and the rest of the statement tells the dimensions (in pixels) of the box that the Plugin uses on the screen. If struct1.cdx isn't in the same directory or folder as your HTML code, be sure to include the file specification, e.g.:

< embed src="D:\bruce\project3\struct1.cdx" width="480" height="300" >

You could center your box on the page with just a few more keystrokes:

< embed src=struct1.cdx width="360" height="200" >

ChemDraw and Chem3D Plugins are the future for web publishing.

The embed statement actually has a few more fields, which revert to default values in the above examples. These statements give an editable structure in a drawing area bounded by a pair of scroll bars on its bottom and right sides. The ChemDraw toolbar appears on the screen and can be moved like any other window. When the mouse is in the drawing area, a right-click (or control-click for Mac) will bring up all traditional menus (File, Edit, etc.) that usually appear across the top of the ChemDraw window.

If you don't want people to be able to edit your work, you just add the viewonly=true qualifier (the default is that your picture is editable):

< embed src=struct1.cdx width="360" height="200" viewonly=true >

With this statement your structure appears without scroll bars, and the ChemDraw toolbar does not appear. This is what you would use to publish a paper-you want your colleagues to read your work, not change it! Of course, they can still copy your structures and use them in their own work.

Before leaving the ChemDraw Plugin for now, we point out that in addition to ChemDraw structures, you can also publish structures in MDL molfile and SMILES formats. These require extra keywords in the embed statement. To read the full story about the ChemDraw Plugin and its syntax, point your browser to doc.camsoft.com and choose the ChemDraw Plugin selection from the menu.

The basic idea of the Chem3D Plugin is exactly the same, and the simplest example of its embed statement is just as easy:

< embed SRC="D:\bruce\C3Dmodel.c3d" width=500 height=500 >

When a Web browser equipped with the Chem3D plugin encounters this statement, the page image it produces shows your molecule, with no box or border. When the user moves the cursor over the image, it turns into the familiar hand icon. The model can be rotated by pressing down and dragging, exactly as in Chem3D.

A Chem3D model displayed by the Chem3D Plugin. The model can be rotated by moving the pointer over the structure, then pressing and dragging.

Two useful qualifiers for the embed command determine the control icons that surround your model. The statement

< embed SRC="D:\bruce\C3Dmodel.c3d" width=500 height=500 rotationbars="true" >

produces the normal Chem3D rotation bar borders, allowing precise rotations about the Cartesian axes. The reader of your Web page can also select atoms or bonds and do internal rotations.

A Chem3D model shown with rotation bars

The statement:

< embed SRC="D:\bruce\C3Dmodel.c3d" width=500 height=500 moviecontroller="true" >

produces the Chem3D control bar that lets the reader of your Web page replay a molecular dynamics trajectory. Of course, this is useful only if your model file actually contains one-just as you first draw a structure or calculate a model, you must calculate the dynamics, then save it, for your Web page viewer to use it.

The Chem3D Plugin can also display a dynamics trajectory.

The various qualifiers can be combined, e.g.,

< embed SRC="D:\bruce\C3Dmodel.c3d" width=500 height=500 moviecontroller="true" rotationbars="true" >

If you omit the qualifiers, they revert to their default values of "false." You should also keep in mind that the reader of your Web page sees whatever you saved in your model: if you saved a protein model with a ribbon rendering, that's what they'll see. If you saved a molecular electrostatic potential surface, that's what will show up when someone accesses your Web page.

A fine point for advanced users: The Chem3D Plugin can also view models in file formats other than Chem3D (*.c3d), and your readers will be able to see whatever display information is supported by the format. Popular formats include certain Gaussian and MOPAC files, and interchange standards such as the Protein Data Bank PDB format. For a complete list, see the documentation page on doc.camsoft.com.

To wrap up, the ChemDraw and Chem3D Plugins bring "live"chemical structures to Web pages. Readers anywhere on the Internet can view and manipulate structures and models that you place in your Web pages, provided their Web browsers have the Plugins. With the ChemDraw and Chem3D Plugins now available, the era of electronic chemical publishing is here!