Journals Using Jmol - Revision history

Rzepa at 10:14, 12 August 2022

2022-08-12T10:14:55Z

Rzepa at 10:13, 12 August 2022

2022-08-12T10:13:58Z

AngelHerraez: ACS Inorganic Chemistry

2022-08-12T08:56:55Z

ACS Inorganic Chemistry

AngelHerraez: Elsevier journals using Jmol applet

2012-10-12T22:24:05Z

Elsevier journals using Jmol applet

AngelHerraez: adding Elsevier

2012-09-10T17:45:01Z

adding Elsevier

EricMartz at 14:16, 13 September 2010

2010-09-13T14:16:14Z

EricMartz: /* Interactive Usage */

2010-09-13T14:10:58Z

‎Interactive Usage

Rhuehne: /* Interactive Figures */

2010-02-17T14:48:24Z

‎Interactive Figures

Rhuehne at 14:45, 17 February 2010

2010-02-17T14:45:46Z

Rhuehne at 14:36, 17 February 2010

2010-02-17T14:36:55Z

@@ Line 3: / Line 3: @@
 === 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].
-* '''[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 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.
+* '''[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://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://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].

@@ Line 3: / Line 3: @@
 === 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].
-* '''[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 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 to examine the material as it was originally designed.
+* '''[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 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://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://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].

@@ Line 3: / Line 3: @@
 === 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].
 * '''[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://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].

@@ Line 5: / Line 5: @@
 * '''[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://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].
-* '''Elsevier''' uses Jmol to display structures along the articles in several journals ([[Journals_Using_Jmol/Elsevier|list of journals]]).
+* '''Elsevier''' uses Jmol to display structures along the articles in [[Journals_Using_Jmol/Elsevier|several journals]].
 * '''[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/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.

@@ Line 2: / Line 2: @@
 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 ===
-* [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://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).
+* '''[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://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://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.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.
+* '''Elsevier''' uses Jmol to display structures along the articles in several journals ([[Journals_Using_Jmol/Elsevier|list of journals]]).
-* [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://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/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/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://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://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://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.
+* '''[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.
 :* 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 ===
 * [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.

← Older revision		Revision as of 14:36, 17 February 2010
Line 10:		Line 10:
	* [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.		* [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 Generated with Jmol ===
		+	* [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.