Chemical Information Sources/Molecular Visualization Tools and Sites 1

Chemical Information Sources/MolecularVisualization Tools and SitesHTML (Hypertext Markup Language)

By now, most people are savvy users of the Web, but some may not know the nitty-gritty of how browsers reallywork. It is important to understand that there is chemistry helper and plugin software that extends the visualizationcapabilities of the standard Web browsers. Every personal and laboratory computer used by chemists, as well as thecomputers in science libraries, should be equipped with suitable chemistry visualization add-ons and the free AdobeAcrobat Reader.Formatting of an HTML document is done by the browser, so a document may have a different look on differentbrowsers. Some popular browsers are:• Google Chrome [1]

• Firefox [2]

• Microsoft Internet Explorer [3]

• Opera [4]

• mozilla Firefox [5]

• Safari [6]

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 specifiedHelpers and Plug-in software extend the capabilities of the browser. There are both general and specializedhelpers/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 [7]

.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

Chemical Information Sources/Molecular Visualization Tools and Sites 2

Molecular Formats and MIME

Peter Murray-Rust and Henry Rzepa pioneered the development of the Chemical MIME (Multipurpose InternetMail 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 [8], 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 [9]

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

Molecular Visualization Software

The Structural Biology Software Database [10] is maintained by the Theoretical and Computational BiophysicsGroup at University of Illinois at Urbana-Champaign. As of November, 2011, it contains 367 Applications in 24Categories, including 63 applications in the category of molecular visualization.• PyMOL [11]: products include PyMOL (rendering and animating 3D structures), AxPyMOL (plug-in for

embedding 3D images and animations into PowerPoint presentations), and JyMOL (software package forcustomizing 3D visualizations)

• JMol [12]: an open-source Java viewer for chemical structures in 3D• VMD [13] (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 chemicalstructures and data about chemicals are being utilized today. The chemical publishing industry has been somewhatslow to adopt some of these innovations, but under user pressure, they are gradually changing the way chemicalimages and data are incorporated into the formal publication process.SIRCh Link for Molecular Visualization Tools and SitesProblem Set for this topic [14]

Chemical Information Sources/Molecular Visualization Tools and Sites 3

References[1] http:/ / www. google. com/ chrome[2] http:/ / www. mozilla. com/ en-US/ firefox/ ?from=getfirefox[3] http:/ / www. microsoft. com/ windows/ internet-explorer/ default. aspx[4] http:/ / www. opera. com/[5] http:/ / www. mozilla. org/[6] http:/ / www. apple. com/ safari/[7] http:/ / www. adobe. com[8] http:/ / cml. sourceforge. net/[9] http:/ / accelrys. com/ products/ informatics/ cheminformatics/ draw/ index. html[10] http:/ / www. ks. uiuc. edu/ Development/ biosoftdb/ biosoft. cgi[11] http:/ / www. pymol. org/[12] http:/ / jmol. sourceforge. net/[13] http:/ / www. ks. uiuc. edu/ Research/ vmd/[14] http:/ / www. indiana. edu/ ~cheminfo/ C471/ 471ex2. html

Article Sources and Contributors 4

Article Sources and ContributorsChemical Information Sources/Molecular Visualization Tools and Sites  Source: http://en.wikibooks.org/w/index.php?oldid=2204152  Contributors: Adrignola, Emily W., Gary DormanWiggins, QuiteUnusual, 1 anonymous edits

LicenseCreative Commons Attribution-Share Alike 3.0 Unported//creativecommons.org/licenses/by-sa/3.0/