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    News & Commentary - Message forums
    FirstGlance in Jmol adopted by Nature Structural & Mol. Biol.
    Submitted by Eric Martz; posted on Monday, February 06, 2006 (2 comments)

    Submitter
    FirstGlance in Jmol [1] is a new user interface to the Jmol java applet, for online interactive 3D viewing of protein and nucleic acid molecular structures. Today, it went live from Nature Structural and Molecular Biology [2], one of the top journals in the structural biology field. In the Feb. 2006 issue, where FirstGlance in Jmol debuts, an editorial [3] introduces new 3D View links in the online articles, crediting, among others, Bioinformatics.Org and J.W. Bizzaro for providing a home for this project. The Nature Publishing Group is active in open source projects, notably Ref. 4 (for collecting and sharing a personal scientific reference database), and Ref. 5 (an RSS aggregator).

    In 1996, MDL [6] offered the free Chime browser plugin for browser-based online 3D macromolecular visualization and structure communication. Based largely on the powerful and outstanding public domain code for the stand-alone program RasMol (by Roger Sayle), Chime has been widely used in biochemical research and education, and by pharmaceutical houses (see examples at Ref. 7). However, MDL stopped development of Chime several years ago, and declines to open its source code to the biochemical community.

    Recently, Jmol [8] has emerged as an open-source java applet powerful enough to replace Chime. This is largely due to years of expert, volunteer, nearly full-time effort by computer scientist Miguel Howard, building on an already-strong project started years earlier by others. In recent months, I was able to construct a simple user interface to Jmol, capable of loading and basic exploration of any on-line molecular structure data file. Newly published empirical macromolecular structures, freely available from the World Wide Protein Data Bank [9], can be displayed via links to the new interface, e.g. Ref. 10 (see the advance online publication by Losey et al. Feb 15, 2006 [11]).

    References:
    1. http://bioinformatics.org/firstglance/
    2. http://www.nature.com/nsmb/
    3. http://www.nature.com/doifinder/10.1038/nsmb0206-93
    4. http://connotea.org
    5. http://urchin.sourceforge.net
    6. http://www.mdl.com
    7. http://molvisindex.org
    8. http://jmol.sourceforge.net
    9. http://www.wwpdb.org
    10. http://firstglance.jmol.org/fg.htm?mol=2B3J
    11. http://www.nature.com/nsmb/journal/v13/n2/abs/nsmb1047.html
    Discussion forums: FirstGlance in Jmol adopted by Nature Structural & Mol. Biol.

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    Very very cool
    Submitted by Gary Van Domselaar; posted on Monday, February 06, 2006
    Submitter Nice Work, Eric and Jeff!
    insanly great.
    Submitted by Mark Luo; posted on Monday, February 06, 2006
    Submitter :)
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