# Chemical Information Sources/Molecular Visualization Tools and Sites
##### 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 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:
* Google Chrome
* Firefox
* Microsoft Internet Explorer
* Opera
* mozilla Firefox
* Safari
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 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 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 Software

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.

##### Summary

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