Chemical Information Structure Viewers
Helper applications, or Viewers, are needed to visualize the structural records made available through these pages. Structures are in the MOL format developed by MDL Information Systems, Inc., and Web Browsers such as Mosaic, Internet Explorer, and Netscape can't read this without a helper application. The main Chemical Structure Server uses a the MDL Chime plugin. In order to display a structure, a structure drawing program or WWW viewer must be used. Your Browser must be configured to expect the appropriate Chemical MIME value used by the server to send this data. In our case this is "chemical/x-mdl-molfile". Following are several sites where a user may obtain such a program.
CambridgeSoft offers several chemical drawing and searching packages in their ChemOffice and ChemOffice Pro software. The CS ChemOffice Net 5.0 version of the software can display the MDL MOL format, although printing and saving is allowed only the ChemOffice Pro versions. There are Mac and PC versions.
MDL Information Systems, Inc. A special Web version of their ISIS/Draw program has been made available by this company. The name of the product is ISIS/Draw, and is available at their WWW site. It is free for personal use by academic users. There are Mac and PC versions. A product called Chemscape Chime is available as a Netscape Plugin. It will display structures in the MDL Molfile format our server delivers (plus others), and render them in several 2D and 3D formats. It can also be used as input to our structure search system.
Molecular Simulations, Inc.(Accelrys) offers WebLab, a free structure viewer. It offers a variety of viewing options, will accept molfile input and will convert to 3D display if this is requested. Editing structures is not offered in the free version.
RasMol is a viewer which can create 2d or 3d images from mol files. You must add the expression "-mdl" to the command line in setup for your browser. This viewer shows line drawing or ball and stick representations, and separate commands must be given to label atom and bond types.
The NIH Guide to Molecular Modeling gives an excellent summary of chemical structure software for various computer types.
How to set up a Viewer
To set up the ISIS/Draw software as a viewer following are the steps needed:
- For Netscape 4, invoke the "Edit", and "Preferences" menus, then the "Navigator" and "Applications"
tab
- Choose "New", then
- Type "Mol Files" in the "Description" box
- Type "chemical/x-mdl-molfile" in the "MIME Type" box
- Type ".mol" in the "File Extensions" box
- Set the "Action" radio button to "Application" for the program, e.g. "c:\isis214\isisdraw.exe" (if this is your directory). If using RASMOL, you should add the string "-mdl" and any other RASMOL startup values after "isisdraw.exe".
- Choose OK to save these settings, and the viewer should be available immediately.
If the viewer is set up correctly, any structure data from our server with the .MOL extension will invoke the viewer program. In many cases Netscape will prompt you for some of these values the first time it encounters this data. If you are using MDL Chime, structure display will take place in the Netscape window..