Difference between revisions of "Journals Using Jmol"

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Please, feel free to add here a link to any journal that uses Jmol for publishing molecular structures (e.g. as supplementary materials for articles). The history of interactive 3D molecular visualization in scientific journals is summarized in articles in [http://proteopedia.org Proteopedia.Org], namely [http://proteopedia.org/wiki/index.php/Kinemages%2C_Mage_and_KiNG Kinemages, Mage and KiNG] and [http://proteopedia.org/wiki/index.php/Jmol Jmol].
 
Please, feel free to add here a link to any journal that uses Jmol for publishing molecular structures (e.g. as supplementary materials for articles). The history of interactive 3D molecular visualization in scientific journals is summarized in articles in [http://proteopedia.org Proteopedia.Org], namely [http://proteopedia.org/wiki/index.php/Kinemages%2C_Mage_and_KiNG Kinemages, Mage and KiNG] and [http://proteopedia.org/wiki/index.php/Jmol Jmol].
 
=== Interactive Usage ===
 
=== Interactive Usage ===
* [http://pubs.acs.org/journals/acbcct/ ACS Chemical Biology], from the American Chemical Society (USA), is providing interactive Jmol renderings of structures matching figures in articles (look for ''enhanced objects'' link). Examples are linked to [http://moleculesinmotion.com MoleculesInMotion.Com].
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* '''[http://pubs.acs.org/journals/acbcct/ ACS Chemical Biology]''', from the American Chemical Society (USA), is providing interactive Jmol renderings of structures matching figures in articles (look for ''enhanced objects'' link). Examples are linked to [http://moleculesinmotion.com MoleculesInMotion.Com].
* [http://www.biochemj.org./bj/ Biochemical Journal] is including interactive Jmol renderings of structures matching figures in articles (look for ''3D interactive structure'' link). First article with this feature (27 June 2007) is "Structures and metal-ion-binding properties of the Ca<sup>2+</sup>-binding helix-loop-helix EF-hand motifs"; [http://www.biochemj.org./bj/405/bj4050199.htm abstract and citation]; [http://www.biochemj.org./bj/405/0199/bj4050199add.htm 3D model] (access is restricted to subscribers).
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* '''[https://pubs.acs.org/ic ACS Inorganic Chemistry]''', as far back as 2005, supported Electronic Supplements that used interactive Jmol renderings of structures that expanded the contents of articles. [https://doi.org/10.1021/ic0519988 Here is an example]; although the link to the supplemental material has now disappeared from the publisher's page, a [https://doi.org/10.14469/hpc/10849 backup copy] has been hosted by the authors and converted from old Jmol syntax (<code>applet</code> tags) to current JSmol syntax, allowing one to examine the material as it was originally designed. The journal has been contacted to update their page.
* [http://journals.iucr.org/ Crystallography Journals Online], the web site for journals of  the International Union of Crystallography (IUCr), is using Jmol to visualize published crystal structures: click on any ''3d view'' button on a journal table of contents page, ''e.g.'' [http://journals.iucr.org/c/issues/2007/01/00/issconts.html ''Acta Crystallographica Section C'' (2007) Part 1].
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* '''[http://www.biochemj.org./bj/ Biochemical Journal]''' is including interactive Jmol renderings of structures matching figures in articles (look for ''3D interactive structure'' link). First article with this feature (27 June 2007) is "Structures and metal-ion-binding properties of the Ca<sup>2+</sup>-binding helix-loop-helix EF-hand motifs"; [http://www.biochemj.org./bj/405/bj4050199.htm abstract and citation]; [http://www.biochemj.org./bj/405/0199/bj4050199add.htm 3D model] (access is restricted to subscribers).
* [http://www.rsc.org/Publishing/Journals/MB/ Molecular BioSystems], from the Royal Society of Chemistry (UK), provides 3D visualisation of macromolecules in articles, by using [http://firstglance.jmol.org FirstGlance in Jmol] to show the associated PDB file. Links to the 3D images can be found on the ''Electronic Supplementary Information'' (ESI) page of the online article.
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* '''[http://journals.iucr.org/ Crystallography Journals Online]''', the web site for journals of  the International Union of Crystallography (IUCr), is using Jmol to visualize published crystal structures: click on any ''3d view'' button on a journal table of contents page, ''e.g.'' [http://journals.iucr.org/c/issues/2007/01/00/issconts.html ''Acta Crystallographica Section C'' (2007) Part 1].
* [http://www.nature.com/nature Nature] offers ''3D View'' links for every new molecular structure. These use [http://firstglance.jmol.org FirstGlance in Jmol]. The debut was November 30, 2007. Consistent with FirstGlance in Jmol being free and open source, structure viewing at this journal is free (the ''3D View'' links are accessible to non-subscribers). ''Nature'' is a strong supporter of open-source software, as evidenced by their [http://connotea.org Connotea] project.
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* '''Elsevier''' uses Jmol to display structures along the articles in [[Journals_Using_Jmol/Elsevier|several journals]].
* [http://www.nature.com/nchembio/ Nature Chemical Biology] and [http://www.nature.com/nchem/ Nature Chemistry] use Jmol to display chemical compounds related to articles, in the ''compound data index page'' for a paper. Examples: [http://www.nature.com/nchembio/journal/v3/n4/compound/nchembio867_comp12_3d.html NCB] and [http://www.nature.com/nchem/journal/v1/n1/compound/nchem.100_comp7_3d.html NC].
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* '''[http://www.rsc.org/Publishing/Journals/MB/ Molecular BioSystems]''', from the Royal Society of Chemistry (UK), provides 3D visualisation of macromolecules in articles, by using [http://firstglance.jmol.org FirstGlance in Jmol] to show the associated PDB file. Links to the 3D images can be found on the ''Electronic Supplementary Information'' (ESI) page of the online article.
* [http://www.nature.com/nsmb/ Nature Structural & Molecular Biology] displays new protein structures in [http://firstglance.jmol.org FirstGlance in Jmol]. The debut was February, 2006. See [http://www.nature.com/nsmb/journal/v13/n2/index.html We're Living in a 3D World]. Structure viewing at this journal is free, via ''3D View'' links visible to non-subscribers. ''Nature'' is a strong supporter of open-source, as evidenced by their [http://connotea.org Connotea] project.
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* '''[http://www.nature.com/nature Nature]''' offers ''3D View'' links for every new molecular structure. These use [http://firstglance.jmol.org FirstGlance in Jmol]. The debut was November 30, 2007. Consistent with FirstGlance in Jmol being free and open source, structure viewing at this journal is free (the ''3D View'' links are accessible to non-subscribers). ''Nature'' is a strong supporter of open-source software, as evidenced by their [http://connotea.org Connotea] project.
* [http://proteinscience.org Protein Science] announced the adoption of FirstGlance in Jmol, and interactive figures in Jmol, in late 2009. See [http://www.proteinscience.org/view/0/editorMessage.html Interactive graphics return to Protein Science]. Protein Science was the first journal to offer interactive computer graphics of protein structure figures, in the form of [http://proteopedia.org/wiki/index.php/Kinemages%2C_Mage_and_KiNG Kinemages] on floppy disks in the 1990's.
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* '''[http://www.nature.com/nchembio/ Nature Chemical Biology]''' and '''[http://www.nature.com/nchem/ Nature Chemistry]''' use Jmol to display chemical compounds related to articles, in the ''compound data index page'' for a paper. Examples: [http://www.nature.com/nchembio/journal/v3/n4/compound/nchembio867_comp12_3d.html NCB] and [http://www.nature.com/nchem/journal/v1/n1/compound/nchem.100_comp7_3d.html NC].
 +
* '''[http://www.nature.com/nsmb/ Nature Structural & Molecular Biology]''' displays new protein structures in [http://firstglance.jmol.org FirstGlance in Jmol]. The debut was February, 2006. See [http://www.nature.com/nsmb/journal/v13/n2/index.html We're Living in a 3D World]. Structure viewing at this journal is free, via ''3D View'' links visible to non-subscribers. ''Nature'' is a strong supporter of open-source, as evidenced by their [http://connotea.org Connotea] project.
 +
* '''[http://proteinscience.org Protein Science]''' announced the adoption of FirstGlance in Jmol, and interactive figures in Jmol, in late 2009. See [http://www.proteinscience.org/view/0/editorMessage.html Interactive graphics return to Protein Science]. Protein Science was the first journal to offer interactive computer graphics of protein structure figures, in the form of [http://proteopedia.org/wiki/index.php/Kinemages%2C_Mage_and_KiNG Kinemages] on floppy disks in the 1990's.
 
:* Example of Jmol interactive figures: [http://jmol.wiley.com/details/jmol/148775/OSR1_figure1.html fig. 1], [http://jmol.wiley.com/details/jmol/148576/OSR1_figure2.html fig. 2] of Li and Palmer's article, DOI 10.1002/pro.98
 
:* Example of Jmol interactive figures: [http://jmol.wiley.com/details/jmol/148775/OSR1_figure1.html fig. 1], [http://jmol.wiley.com/details/jmol/148576/OSR1_figure2.html fig. 2] of Li and Palmer's article, DOI 10.1002/pro.98
  
 
=== Cover Images ===
 
=== Cover Images ===
 
* [http://rnajournal.cshlp.org/content/16/2.cover-expansion RNA Issue Feb 2010] - cover image of PDB entry 3CW1 generated with the Jmol-based [http://jena3d.fli-leibniz.de Jena3D] viewer.
 
* [http://rnajournal.cshlp.org/content/16/2.cover-expansion RNA Issue Feb 2010] - cover image of PDB entry 3CW1 generated with the Jmol-based [http://jena3d.fli-leibniz.de Jena3D] viewer.

Latest revision as of 10:14, 12 August 2022

Jmol / JSmol Applications

Please, feel free to add here a link to any journal that uses Jmol for publishing molecular structures (e.g. as supplementary materials for articles). The history of interactive 3D molecular visualization in scientific journals is summarized in articles in Proteopedia.Org, namely Kinemages, Mage and KiNG and Jmol.

Interactive Usage

  • ACS Chemical Biology, from the American Chemical Society (USA), is providing interactive Jmol renderings of structures matching figures in articles (look for enhanced objects link). Examples are linked to MoleculesInMotion.Com.
  • ACS Inorganic Chemistry, as far back as 2005, supported Electronic Supplements that used interactive Jmol renderings of structures that expanded the contents of articles. Here is an example; although the link to the supplemental material has now disappeared from the publisher's page, a backup copy has been hosted by the authors and converted from old Jmol syntax (applet tags) to current JSmol syntax, allowing one to examine the material as it was originally designed. The journal has been contacted to update their page.
  • Biochemical Journal is including interactive Jmol renderings of structures matching figures in articles (look for 3D interactive structure link). First article with this feature (27 June 2007) is "Structures and metal-ion-binding properties of the Ca2+-binding helix-loop-helix EF-hand motifs"; abstract and citation; 3D model (access is restricted to subscribers).
  • Crystallography Journals Online, the web site for journals of the International Union of Crystallography (IUCr), is using Jmol to visualize published crystal structures: click on any 3d view button on a journal table of contents page, e.g. Acta Crystallographica Section C (2007) Part 1.
  • Elsevier uses Jmol to display structures along the articles in several journals.
  • Molecular BioSystems, from the Royal Society of Chemistry (UK), provides 3D visualisation of macromolecules in articles, by using FirstGlance in Jmol to show the associated PDB file. Links to the 3D images can be found on the Electronic Supplementary Information (ESI) page of the online article.
  • Nature offers 3D View links for every new molecular structure. These use FirstGlance in Jmol. The debut was November 30, 2007. Consistent with FirstGlance in Jmol being free and open source, structure viewing at this journal is free (the 3D View links are accessible to non-subscribers). Nature is a strong supporter of open-source software, as evidenced by their Connotea project.
  • Nature Chemical Biology and Nature Chemistry use Jmol to display chemical compounds related to articles, in the compound data index page for a paper. Examples: NCB and NC.
  • Nature Structural & Molecular Biology displays new protein structures in FirstGlance in Jmol. The debut was February, 2006. See We're Living in a 3D World. Structure viewing at this journal is free, via 3D View links visible to non-subscribers. Nature is a strong supporter of open-source, as evidenced by their Connotea project.
  • Protein Science announced the adoption of FirstGlance in Jmol, and interactive figures in Jmol, in late 2009. See Interactive graphics return to Protein Science. Protein Science was the first journal to offer interactive computer graphics of protein structure figures, in the form of Kinemages on floppy disks in the 1990's.
  • Example of Jmol interactive figures: fig. 1, fig. 2 of Li and Palmer's article, DOI 10.1002/pro.98

Cover Images