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Chemical Information Sources/Molecular Visualization Tools and Sites

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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
[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 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
[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
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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
[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 Language
Almost 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 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
[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 for
customizing 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 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
[14]
Chemical Information Sources/Molecular Visualization Tools and Sites
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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
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Article Sources and Contributors
Chemical Information Sources/Molecular Visualization Tools and Sites Source: http://en.wikibooks.org/w/index.php?oldid=2204152 Contributors: Adrignola, Emily W., Gary Dorman
Wiggins, QuiteUnusual, 1 anonymous edits
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