Molecular Visualization Tools and Sites

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HTML (Hypertext Markup Language)

By now, most people are savvy users of the Web, but some may not know the nitty-gritty of how browsers really work. It is important to understand that there is chemistry helper and plugin software that extends the visualization capabilities of the standard Web browsers. Every personal and laboratory computer used by chemists, as well as the computers in science libraries, should be equipped with suitable chemistry visualization and the free Adobe Acrobat Reader.

Formatting of an HTML document is done by the browser, so a document may have a different look on different browsers. Some popular browsers are:

Other media (images, sounds, animation) can be imported in a browser. HTML permits:

  • Links (anchors) to other documents or text within the same document or to other points on the Internet via a URL (Uniform Resource Locator): an address of the item you want to retrieve. URLs exist for WWW files, FTP, Gopher, UseNet, Telnet, etc.
  • Absolute reference -- contains the complete address: host name, directory path, and file name
  • Relative reference -- assumes that the previous machine and directory path are being used: just the file name (or possibly a subdirectory and file name) is specified

Helpers and Plug-in software extend the capabilities of the browser. There are both general and specialized helpers/browsers.

File Formats on the Internet
Some General File Formats
Format Description Helper/Plugin
.gif CompuServe Graphics Interchange Format browser
.jpg JPEG (Joint Photographic Experts Group) graphics format browser
.pdf Adobe's Portable Document Format Acrobat Reader
.tif TIFF graphics format (Group IV fax)
.mid MIDI music format file
.mpg MPEG movie format
.mov QuickTime movie format file
.wav    
WAVE format audio file    
and many, many others
Molecular Formats and MIME

Peter Murray-Rust and Henry Rzepa pioneered the development of Chemical MIME (Multipurpose Internet Mail Extensions) - protocol to attach special files to electronic mail messages or embed them in HTML documents.

Chemical MIME Formats (chemical/x- )
Extension MIME Subtype Use Helper/Plugin
kin x-kinemage Kinemage file for macromolecules MAGE
pdb x-pdb Protein Data Bank format Rasmol, Chime
jdx x-jcamp-dx Spectra format: infrared, NMR, Mass JCAMP-DX
mol x-mdl-molfile MDL's Molecular File Format MDL Chime
chm x-chemdraw CambridgeSoft's ChemDraw format CHEMDRAW
and others

Some other formats in common use include:

  • .cif Crystallographic data
  • netCDF For chromatography, infrared and mass spectrometry
  • andi/MS ANalytical Data Interchange for Mass Spectrometry
  • CML and XML Chemical Mark-up Language and Extensible Mark-up Language

Almost all modern e-mail software understands the MIME format codes nowadays.


Internet Sites for Further Information

Link to supplemental readings

Link to Internet Sources for Molecular Visualization Tools and Sites

This wiki page was originally created by Gary Wiggins. If you have a legitimate desire to contribute to its contents, please request an account from the sysop, Dr. David J. Wild, by e-mailing him at djwild @ indiana.edu

Retrieved from "http://cheminfo.informatics.indiana.edu/cicc/cis/index.php/Molecular_Visualization_Tools_and_Sites"
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