{"id":25452,"date":"2022-08-25T09:42:17","date_gmt":"2022-08-25T08:42:17","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=25452"},"modified":"2022-09-11T06:15:32","modified_gmt":"2022-09-11T05:15:32","slug":"four-stages-in-the-evolution-of-interactive-esi-as-part-of-articles-in-chemistry-journals","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25452","title":{"rendered":"Four stages in the evolution of interactive ESI as part of articles in chemistry journals."},"content":{"rendered":"
\n

A previous post<\/a> was triggered by Peter alerting me that interactive electronic supporting information (IESI<\/strong>) we had submitted to a journal in 2005[1]<\/a><\/span> appeared to be strangely missing from the article landing page. This set me off recollecting our journey, which had started around 1998, and to explore what the current state of these ancient IESI<\/strong>s were in 2022. I have now reached 2014 in this journey, which is being recorded as it happens in the comments page<\/a> of the post. I discovered there were four distinct stages in that evolution of IESI<\/strong> which I thought it would be of interest to record here.<\/p>\n

    \n
  1. From around 1998 to 2004, our efforts at IESI centred around a browser plugin called Chime, which was itself derived from stand-alone code called Rasmol and a collaboration between the company that implemented this (MDL) and Netscape, who happened to have offices in San Francisco close to each other. Chime came in two versions, free to use and a commercial version that added further functionality such as access to MDL databases etc. An example from 1998[2]<\/a><\/span> can be seen at https:\/\/www.rsc.org\/suppdata\/perkin2\/1998\/2695\/<\/a> and the code is shown below:\n
    <EMBED border=0 src=\"geom+vib\/12e-dft.gau\" name=\"12e-dft\"\r\nalign=center width=150 height=150 spiny=36 startspin=true\r\ndisplay3D=sticks PLUGINSPAGE=\"http:\/\/www.ch.ic.ac.uk\/cgi-bin\/plugin.cgi\"\r\nscript=\"zoom 175;\"><\/EMBED><\/small><\/small><\/pre>\n
    I have to say that access to the data underpinning this IESI is still good; but the interactive component itself has long gone, along with Chime itself.<\/li>\n
  2. By 2005, Jmol had emerged as a more general open-source browser plugin replacing Chime. This so-called Java “run time library” had to be installed by the user into their browser instance (and hence required admin rights). The interactivity in the first article where we deployed it[3]<\/a><\/span> was invoked as per below.\n
    <applet height=\"300\" archive=\"JmolApplet.jar\"\r\nwidth=\"300\" code=\"JmolApplet\" name=\"TS2\"\r\nmayscript=\"true\" id=\"TS2\">\r\n<param name=\"progressbar\" value=\"true\" \/>\r\n<param name=\"progresscolor\" value=\"blue\" \/>\r\n<param name=\"boxmessage\"\r\nvalue=\"starting JmolApplet ...\" \/>\r\n<param name=\"emulate\" value=\"chime\" \/>\r\n<param name=\"boxbgcolor\" value=\"black\" \/>\r\n<param name=\"load\" value=\"RRSS_fm-5-ts2-49.xyz\" \/>\r\n<\/applet><\/small><\/pre>\n
    It is this invocation where the interactivity was rescued by Angel as described in the earlier post comments page<\/a> in the form of an adaptor library that converts the syntax above to modern form.<\/p>\n<\/li>\n
  3. By 2007, this applet syntax had gone, to be replaced by a JavaScript version invoking the same Java-based Jmol.[4]<\/a><\/span>\n
    <script type=\"text\/javascript\" src=\"JSmol.min.js\"><\/script>\r\n<script type=\"text\/javascript\" src=\"js\/Jmol2.js\"><\/script>\r\n<!-- The second command is modern, to convert to using  JSmol --><\/small><\/small><\/pre>\n
    and then to invoke a molecule:<\/p>\n
    <script type=\"text\/javascript\">\r\njmolApplet(300,\"load GaL3.mol; select all; spacefill 0.25; \r\nwireframe 0.1; center atomno=1\")<\/script><\/small><\/pre>\n
    Here again an adapter library to update this syntax is available as Jmol2.js<\/strong>.<\/li>\n
  4. Around 2012, the development of a Java replacement of Jmol by the script-based JSmol had started (ten years ago almost to the day!). Our first deployment was in 2014[5]<\/a><\/span> where you can see an example in operation at DOI: https:\/\/doi.org\/10.14469\/hpc\/11017<\/a> You will notice that bets were being hedged and the viewer was given a choice of using either Jmol (Java) or JSmol (Javascript). The reason was that in terms of speed, Jmol was perhaps 15 times faster than JSmol and so more complex rendered objects such as orbital isosurfaces, or proteins, could be very slow in JSmol. As computers themselves have got faster, and Javascript implementations in browsers similarly so, the need for Java has largely faded other than some specialist applications. Now only\n
    <script type=\"text\/javascript\" src=\"JSmol.min.js\"><\/script><\/small><\/pre>\n
    is needed to set things up, whilst the molecule call is illustrated by eg<\/p>\n
     <a href=\"javascript:Jmol.script(jmolApplet0, \r\n'load 24880.log<\/strong>',%20';frame 13;spin 3;')\">log<\/a><\/small><\/pre>\n<\/li>\n<\/ol>\n
    Now, ten years on from the genesis of JSmol, the functionality and capability of this program have continued to increase by leaps and bounds, but the general form has remained stable.<\/p>\n
    One other change in our usage did also occur in 2014. Previously the content being viewed came from a local file installed on the web server,\u00a0as per eg 24480.log<\/b> above. However we were now starting to source such files directly from a data repository, being a specialist resource to host such content. All that would be needed was the\u00a0DOI<\/strong> of the repository collection where the data was being hosted, along with the Media type of the desired file. But that comes with its own issues and this is another story that will be told elsewhere.<\/p>\n
    References<\/h2>\n    
    1. H.S. Rzepa, and M.E. Cass, \"A Computational Study of the Nondissociative Mechanisms that Interchange Apical and Equatorial Atoms in Square Pyramidal Molecules\", Inorganic Chemistry<\/i>, vol. 45, pp. 3958-3963, 2006. https:\/\/doi.org\/10.1021\/ic0519988<\/a>\n\n<\/li>\n
    2. C. Conesa, and H.S. Rzepa, \"Re-engineering potential energy surfaces: trapezoidally distorted \u03c02s\u2005+\u2005\u03c02s thermal cycloaddition\/elimination reactions\", Journal of the Chemical Society, Perkin Transactions 2<\/i>, pp. 2695-2698, 1998. https:\/\/doi.org\/10.1039\/a805668d<\/a>\n\n<\/li>\n
    3. E.L. Marshall, V.C. Gibson, and H.S. Rzepa, \"A Computational Analysis of the Ring-Opening Polymerization of <i>r<\/i><i>ac<\/i>-Lactide Initiated by Single-Site \u03b2-Diketiminate Metal Complexes:\u2009 Defining the Mechanistic Pathway and the Origin of Stereocontrol\", Journal of the American Chemical Society<\/i>, vol. 127, pp. 6048-6051, 2005. https:\/\/doi.org\/10.1021\/ja043819b<\/a>\n\n<\/li>\n
    4. H.S. Rzepa, and M.E. Cass, \"In Search of the Bailar and R\u00e2y\u2212Dutt Twist Mechanisms That Racemize Chiral Trischelates:\u2009 A Computational Study of Sc<sup>III<\/sup>, Ti<sup>IV<\/sup>, Co<sup>III<\/sup>, Zn<sup>II<\/sup>, Ga<sup>III<\/sup>, and Ge<sup>IV<\/sup> Complexes of a Ligand Analogue of Acetylacetonate\", Inorganic Chemistry<\/i>, vol. 46, pp. 8024-8031, 2007. https:\/\/doi.org\/10.1021\/ic062473y<\/a>\n\n<\/li>\n
    5. A. Armstrong, R.A. Boto, P. Dingwall, J. Contreras-Garc\u00eda, M.J. Harvey, N.J. Mason, and H.S. Rzepa, \"The Houk\u2013List transition states for organocatalytic mechanisms revisited\", Chem. Sci.<\/i>, vol. 5, pp. 2057-2071, 2014. https:\/\/doi.org\/10.1039\/c3sc53416b<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"
      A previous post was triggered by Peter alerting me that interactive electronic supporting information (IESI) we had submitted to a journal in 2005 appeared to be strangely missing from the article landing page. This set me off recollecting our journey, which had started around 1998, and to explore what the current state of these ancient […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":5,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[],"tags":[],"ppma_author":[2661],"class_list":["post-25452","post","type-post","status-publish","format-standard","hentry"],"yoast_head":"\nFour stages in the evolution of interactive ESI as part of articles in chemistry journals. - Henry Rzepa's Blog<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25452\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Four stages in the evolution of interactive ESI as part of articles in chemistry journals. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"A previous post was triggered by Peter alerting me that interactive electronic supporting information (IESI) we had submitted to a journal in 2005 appeared to be strangely missing from the article landing page. 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Part 2: a possible 3D Model  for Calicheamicin revealing the non-covalent-interactions (NCI) present.","author":"Henry Rzepa","date":"August 26, 2024","format":false,"excerpt":"Calicheamicin is a natural product with antitumour properties discovered in the 1980s, with the structure shown below. As noted elsewhere, this structure has many weird properties, including amongst other features an unusual \"enedidyne\" motif and the presence of an iodo group on an aromatic ring. Its\u00a0isolated 3D structure is quite\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":15313,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15313","url_meta":{"origin":25452,"position":1},"title":"Some examples of open access publications citing managed research data (RDM).","author":"Henry Rzepa","date":"January 5, 2016","format":false,"excerpt":"In May 2015, the EPSRC funding council in the UK required researchers to publish the outcomes of the funded work to include an OA (open access) version of the narrative and to cite the managed research data used to support the research with\u00a0a DOI (digital object identifier). I was discussing\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":10998,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10998","url_meta":{"origin":25452,"position":2},"title":"A two-publisher model for the scientific article: narrative+shared data.","author":"Henry Rzepa","date":"September 15, 2013","format":false,"excerpt":"I do go on rather a lot about enabling or\u00a0hyper-activating data. So do others. Why is sharing data important? Reproducibility is a cornerstone in science, To achieve this, it is important that scientific research be\u00a0open and transparent. Openly available research data is central to achieving this. It is estimated that\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":29429,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29429","url_meta":{"origin":25452,"position":3},"title":"The even more mysterious N\u2261N triple bond in a nitric oxide dimer.","author":"Henry Rzepa","date":"August 18, 2025","format":false,"excerpt":"Previously, I pondered about the strange N=N double bond in nitrosobenzene dimer as a follow up to commenting on the curly arrow mechanism of the dimerisation. By the same curly arrow method, one can produce the below, showing how the simpler nitric oxide radical could potentially dimerise to a species\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":26941,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26941","url_meta":{"origin":25452,"position":4},"title":"Internet Archeology:  reviving a 2001 article published in the Internet Journal of Chemistry.","author":"Henry Rzepa","date":"March 21, 2024","format":false,"excerpt":"In the mid to late 1990s as the Web developed, it was becoming more obvious that one area it would revolutionise was of scholarly journal publishing. Since the days of the very first scientific journals in the 1650s, the medium had been firmly rooted in paper. Even printed colour only\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/03\/Screenshot-297-1024x698.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":10611,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10611","url_meta":{"origin":25452,"position":5},"title":"Another Woodward pericyclic example dissected: all is not what it seems.","author":"Henry Rzepa","date":"May 22, 2013","format":false,"excerpt":"Here is another example gleaned from that Woodward essay of 1967 (Chem. Soc. Special Publications (Aromaticity), 1967, 21, 217-249), where all might not be what it seems. Woodward notes that the reaction between the (highly reactive) 1 does not occur. This is attributed to it being a disallowed \u03c06 +\u2026","rel":"","context":"In \"free energy barrier\"","block_context":{"text":"free energy barrier","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=free-energy-barrier"},"img":{"alt_text":"w2+2+2","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/05\/w2%2B2%2B2.gif?resize=350%2C200","width":350,"height":200},"classes":[]}],"jetpack_likes_enabled":false,"authors":[{"term_id":2661,"user_id":1,"is_guest":0,"slug":"admin","display_name":"Henry Rzepa","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/25452","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=25452"}],"version-history":[{"count":19,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/25452\/revisions"}],"predecessor-version":[{"id":25471,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/25452\/revisions\/25471"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=25452"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=25452"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=25452"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=25452"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}