|Electronic Conference on|
|29 June - 24 July 1998|
The majority of web pages written by chemists also are restricted to this simple HTML approach. Web pages written like this offer little difference from documents printed on paper, with the notable exception of the hyperlink. These standard web pages offer static images of molecules and spectra.
But the web can offer much more. Web servers can deliver all types of files, not just HTML, text, and gif or jpeg. Instead of viewing a static image of a molecule, showing a single view from one direction, wouldn't the ability to visualize a three-dimensional structure, rotate it, zoom in a particular region, be a significant enhancement of the chemical content provided in the page? Instead of reporting an NMR spectra by simply listing the chemical shifts and the multiplicity, why not deliver the entire spectra which the reader can manipulate by enlarging a particular region, rescaling, etc.? Instead of providing one or two snaphots of a trajectory, wouldn't an animation of the entire process be much more valuable? These are some examples of an enhanced web page. This technology is available today and can be easily incorporated into any and all web pages for chemists.
|File type||MIME type||File name extension|
|jpeg image||image/jpeg||.jpeg, .jpg|
|mpeg movie||video/mpeg||.mpeg, .mpg|
|Quicktime movie||video/quicktime||.qt, .mov, .snm|
|portable data format (pdf)||application/pdf|
|Mac Binhex file||application/mac-binhex40||.hqx|
|Rich Text Format (RTF) file||application/rtf||.rtf|
When a file is sent by a server, the server attaches the appropriate MIME type to it. When the browser receives the file, it first examines the MIME type and decides what to do with the file. If the MIME indicates a file that the browser can handle by itself, such as an HTML file or a gif image, the browser will then process the file and deliver the contents to the screen. If it can't handle the file, the browser will examine its configuration file to see if an appropriate "helper application" is available. If there is a helper application available, the browser launches the application and directs the file as input into this new application. The file is then rendered to the screen in a separate window created and managed by the helper application. For example, if an MS-Word file is delivered, the browser will launch a local copy of MS-Word and the file will come up within the Word window ready for editing. If there is no helper available, the browser will offer to save the file to the local disk.
|File Types||MIME type||File extension|
|Brookhaven Protein Databank||chemical/x-pdb||.pdb|
|Crystalographic Information File||chemical/x-cif||.cif|
|Gaussian Input File||chemical/x-gaussian-input||.gau|
|IEMBL Nucleotide Format||chemical/x-embl-dl-nucleotide||.emb,.embl|
|Macromodel Input File||chemical/x-macromodel-input||.mmd, .mmod|
|MDL Transportable Graphics Format (tgf)||chemical/x-mdl-tgf||.tgf|
|Mopac Input File||chemical/x-mopac-input||.mop|
Browsers need also be configured by indicating the appropriate "helper application" that will properly handle each new MIME type. This is done using the browser settings itself.
For Netscape Navigator, you access this information through the Options Menu, General Preferences. In the General Preferences Window, select the Helpers tab. Displayed for your are all the built-in MIME types and the program that will handle each of them. Click on the New... button to add a chemical MIME type. In this window, make sure to enter the appropriate MIME type and suffix (file name extension) and then in the Handle By section you can select the appropriate application by browsing your disk. A similar procedure is followed using Internet Explorer.
|Accord Internet Chemistry Viewer||Mac and PowerMac,
Windows 3.1, 95 and NT
|http://www.synopsys.co.uk/accordiv.html||Accord's native format, MDL MOL, MDL Rxnfile, MDL Sketchfile, Daylight SMILES, and SMD|
|CS ChemOffice Net||Mac
|http://www.camsci.com/download.html||CS ChemDraw, CS Chem3D, MDL MOL, Brookhaven PDB|
|JCAMPDX.EXE||Windows 95 and NT||http://wwwchem.uwimona.edu.jm:1104/software/jcampdx.html||JCAMP|
|MDL Chime||Mac and PowerMac,
Windows 3.1, 95 and NT, SGI
|http://www.mdli.com/chemscape/chime/chime.html||MDL MOL, Brookhaven PDB, IEMBL Nucleotide Format, XMol XYZ, Gaussian Input, Rasmol Script, Mopac Input, Chemical Structure Markup Language, MDL Transportable Graphics, MDL RxnFile|
|MDL ISIS/Draw||Mac and PowerMac,
Windows 3.1, 95 and NT
|http://www.mdli.com/prod/ioffer.html||MDL MOL, MDL TGF, MDL RXN|
|MSI WebLab Viewer||PowerMac,
Windows 95 and NT
Version 1.1 for Mac and Windows 3.1
|http://www.msi.com/weblab/viewer/index.htm||Brookhaven PDB, MDL MOL, Insight II CAR and MDF, Cambridge CSD, Quanta MSF, Sybyl MOL2, Cerius2 MSI, Catalyst CPD, XMol XYZ, ISIS/Draw Sketch|
|RasMol||Mac and PowerMac,
Windows 3.1 and NT,
|http://www.glaxowellcome.co.uk/netscape/software/||XMol XYZ, Brookhaven PDB, MDL MOL, Alchemy, Charmm|
|XMol||UNIX X11||http://www.msc.edu/msc/docs/xmol/XMol.html||Alchemy, Chemlab, Gaussian Input, Gaussian Output, Molsim, Mopac (Archive, Cartesian Input, Internal Input), Mopac Output, PDB, and XMol XYZ|
Incorporation of molecular coordinates into documents that a reader can then manipulate has been termed a hyperactive molecule. The advantages of this approach are clear. Below is a 2-D representation and a static picture of the crystal structure of octamethyluranocene. The hydrogen atoms have been removed for clarity.
If this is the only image provided, the reader will be left with a number of unaswered questions, such as are the rings parallel to each other, are they eclipsed or staggered, do the methyl groups lie in the plane of the cyclooctatetryl rings or do they bend upwards or downwards? The author might provide a couple of more images to help answer these questions:
The above images have been provided simply as images using the
How can we turn this static representaion into an interactive tool? Instead of simply providing the picture, we must provide the coordinates of the molecule. Coordinates can be saved in a variety of file formats; each author should provide coordinates in a convenient form, but also one that has an established MIME type, such as any of the formats listed in the table above. In this example, the uranocene molecule has been saved in the xyz format. The web server has been properly configure to attach the chemical/x-xyz MIME type to the file.
A standard way to provide coordinates within a chemical document is to place a static image within the page, chosing the most appropriate orientation. Then make this image a hyperlink to the coordinate file. When a reader clicks on the image, the coordinate file is tramitted to the browser, and the browser will launch the appropriate molecular visualization program. The image below is actually a hyperlink to the molecular coordinates, and selecting it will start this whole process.
The HTML code used to create this image and link is:
In the next section, we discuss how to embed hyperactive molecules within a web page, thereby avoiding the use of an external helper application, using the plug-in module Chime.
On to Chime instructions