Jmol: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Wayne Decatur, Jaime Prilusky, Angel Herraez, Joel L. Sussman

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-'''Interactive 3D figures.''' Following the lead set by [[Kinemages, Mage and KiNG|Protein Science with Kinemages in the early 1990's]], figures in scientific journal articles have been implemented in Jmol so they can be rotated, etc. This involves manual implementation of each figure, a laborious task requiring a person knowledgeable in Jmol programming. Probably the first instance was in November, 2006, in [http://pubs.acs.org/journal/acbcct ACS Chemical Biology], and subsequently in June, 2007, in [http://biochemj.org Biochemical Journal] with interactive 3D figures in Jmol implemented by Frieda Reichsman. Authoring of these interactive 3D figures remains time consuming, and only about a dozen articles have been so illustrated as of early 2010  (listed at Reichsman's site [http://moleculesinmotion.com MoleculesInMotion.Com]). In 2008, the International Union of Crystallography developed a toolkit to facilitate the authoring of interactive figures in Jmol in their journals<ref>PMID: 19461848</ref>. In  2009, [http://www.proteinscience.org/view/0/editorMessage.html Protein Science began using this technology]<ref>A. G. Palmer and B. W. Matthews, [http://www.proteinscience.org/details/journalArticle/174315/Interactive_graphics_return_to_protein_science.html Interactive graphics return to protein science], Protein Science 18:677 (2009).</ref>.
+'''Interactive 3D figures.''' Following the lead set by [[Kinemages, Mage and KiNG|Protein Science with Kinemages in the early 1990's]], figures in scientific journal articles have been implemented in Jmol so they can be rotated, etc. This involves manual implementation of each figure, a laborious task requiring a person knowledgeable in Jmol programming. Probably the first instance was in November, 2006, in [http://pubs.acs.org/journal/acbcct ACS Chemical Biology], and subsequently in June, 2007, in [http://biochemj.org Biochemical Journal] with interactive 3D figures in Jmol implemented by Frieda Reichsman. Authoring of these interactive 3D figures remains time consuming, and only about a dozen articles have been so illustrated as of early 2010  (listed at Reichsman's site [http://moleculesinmotion.com MoleculesInMotion.Com]). In 2008, the International Union of Crystallography developed a toolkit to facilitate the authoring of interactive figures in Jmol in their journals<ref>PMID: 19461848</ref>. Outstanding examples are in the 2010 article by Robert M. Hanson (principal author of Jmol after 2005) <i>Jmol – a paradigm shift in crystallographic visualization</i><ref>Hanson, R. M. Jmol – a paradigm shift in crystallographic visualization. <i>J. Appl. Crystallography</i> 43 (2010). Open Access doi:10.1107/S0021889810030256</ref>. In  2009, [http://www.proteinscience.org/view/0/editorMessage.html Protein Science began using this technology]<ref>A. G. Palmer and B. W. Matthews, [http://www.proteinscience.org/details/journalArticle/174315/Interactive_graphics_return_to_protein_science.html Interactive graphics return to protein science], Protein Science 18:677 (2009).</ref>.
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