Chemical Information Sources/Molecular Visualization Tools and Sites

HTML (Hypertext Markup Language)Edit

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 add-ons 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.

Some File Formats on the InternetEdit
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
WAVE format audio file    
and many, many others
Molecular Formats and MIMEEdit

Peter Murray-Rust and Henry Rzepa pioneered the development of the Chemical MIME (Multipurpose Internet Mail Extensions) protocol to attach special files to electronic mail messages or embed them in HTML documents. Dr. Murray-Rust has been partcularly active in developing CML, the Chemical Markup Language.

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 accelrys Draw
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.

Molecular Visualization SoftwareEdit

The Structural Biology Software Database is maintained by the Theoretical and Computational Biophysics Group at University of Illinois at Urbana-Champaign. As of November, 2011, it contains 367 Applications in 24 Categories, including 63 applications in the category of molecular visualization.

  • PyMOL: products include PyMOL (rendering and animating 3D structures), AxPyMOL (plug-in for embedding 3D images and animations into PowerPoint presentations), and JyMOL (software package for customizing 3D visualizations)
  • JMol: an open-source Java viewer for chemical structures in 3D
  • VMD (Visual Molecular Dynamics): free software from UIUC displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.


Molecular visualization software and coding systems for use on the Web are revolutionizing the way chemical structures and data about chemicals are being utilized today. The chemical publishing industry has been somewhat slow to adopt some of these innovations, but under user pressure, they are gradually changing the way chemical images and data are incorporated into the formal publication process.

SIRCh Link for Molecular Visualization Tools and Sites

Problem Set for this topic

Last modified on 31 October 2011, at 19:56