{"id":5312,"date":"2011-10-31T13:23:58","date_gmt":"2011-10-31T13:23:58","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=5312"},"modified":"2011-10-31T14:25:18","modified_gmt":"2011-10-31T14:25:18","slug":"blogbooks-e-books-and-future-proofing-chemical-diagrams","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5312","title":{"rendered":"Blogbooks, e-books and future proofing chemical diagrams."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"5312\">\n<p>Most of the chemical structure diagrams in this blog originate from Chemdraw, which seems to have been around since the dawn of personal computers! I have tended to use this program to produce JPG bitmaps for the blog, writing them out in 4x magnification, so that they can be scaled down for display whilst retaining some measure of higher resolution if needed for other purposes. These other purposes might be for\u00a0<em>e.g.<\/em> the production of e-books (using <a href=\"http:\/\/calibre-ebook.com\/\" target=\"_blank\">Calibre<\/a>), the interesting Blog(e)book format offered as a service by <a href=\"http:\/\/www.feedfabrik.com\/\" target=\"_blank\">Feedfabrik<\/a>, or display on mobile tablets where the touch-zoom metaphor to magnify works particularly well. But bitmap images are not really well future proofed for such new uses. Here I explore one solution to this issue.<\/p>\n<p><a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/taxol-page001.svg\"><img decoding=\"async\" class=\"aligncenter size-full wp-image-5314\" title=\"taxol\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/taxol-page001.svg\" alt=\"\" \/><\/a><\/p>\n<p>I have\u00a0<a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=5218\" target=\"_blank\">previously mentioned<\/a>\u00a0scalable vector graphics (SVG) as an alternative, and fortunately the production of such has become routine.<sup>3<\/sup> The diagram above<sup>2<\/sup> is indeed SVG (and if you cannot see it, then try a modern SVG-capable browser<sup>1<\/sup>). It was produced thus:<\/p>\n<ol>\n<li>Drawn in Chemdraw<\/li>\n<li>Exported as Encapsulated postscript<\/li>\n<li>Imported into <a href=\"http:\/\/www.scribus.net\/canvas\/Scribus\" target=\"_blank\">\u00a0Scribus<\/a>, an Open Source desktop publishing program (where it can be annotated\/edited if need be)\n<ul>\n<li>This program will also need Ghostscript installed to handle the EPS<\/li>\n<\/ul>\n<\/li>\n<li>and exported from Scribus to SVG.<\/li>\n<li>Notice how the diagram above automatically scales to fill the width of the page. If you click on it, you get the diagram on its own. If you zoom the browser window, it should scale perfectly.<\/li>\n<li>I note that these SVG diagrams work well in e-books or blogbooks.<\/li>\n<\/ol>\n<div>There seem to be many other (open) programs out there which support SVG, so the above combination is not necessary the only one, or indeed the best.\u00a0There is one other aspect which might be mentioned. The old GIF or JPG bitmap formats do have good meta-data support, such as <a href=\"http:\/\/en.wikipedia.org\/wiki\/Exchangeable_image_file_format\" target=\"_blank\">\u00a0EXIF<\/a>, <a href=\"http:\/\/en.wikipedia.org\/wiki\/GPS\" target=\"_blank\">GPS<\/a>\u00a0or <a href=\"http:\/\/en.wikipedia.org\/wiki\/Extensible_Metadata_Platform\" target=\"_blank\">XMP<\/a>. These invisible data have often been used to embed a molecular connection table into a GIF or JPG file, such that the original molecular data can be reconstituted from the image file. Unfortunately, there are no real standards for doing this, and so round-tripping the data is probably a closed process within a specific software environment. However, because SVG is an XML format, it can be readily made to carry such information in a fully inter-operable manner. For example, one could easily embed a CML description of the molecule into its own container (namespace) in the SVG file. For the purposes of rendering an on-screen image, this extra information is of course ignored.<\/div>\n<hr \/>\n<p><sup>1<\/sup> I notice that Internet Explorer\u00a09 (both 32- and 64-bit versions) will display (and save) the above diagram if you click on it, but it cannot (yet) be inlined into the post, although the <a href=\"http:\/\/msdn.microsoft.com\/en-us\/ie\/hh410107.aspx\" target=\"_blank\">documentation<\/a> implies it should.<br \/>\n<sup>2<\/sup>\u00a0The version below is the conventional JPG form (click on it to see the original 4x version).<\/p>\n<div id=\"attachment_5334\" style=\"width: 424px\" class=\"wp-caption aligncenter\"><a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/taxol.jpg\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-5334\" class=\"size-full wp-image-5334   \" title=\"taxol\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/taxol.jpg\" alt=\"\" width=\"414\" height=\"154\" \/><\/a><p id=\"caption-attachment-5334\" class=\"wp-caption-text\">Diagram displayed using JPG.<\/p><\/div>\n<p><sup>3<\/sup>. Historical note. Peter Murray-Rust and I have been promoting SVG for use in chemistry for 11+ years now. For one ancient page,<a href=\"http:\/\/www.ch.ic.ac.uk\/svg\/\" target=\"_blank\"> see here<\/a>. The syntax has decayed somewhat, but some of the diagrams still work!<\/p>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 5312 -->","protected":false},"excerpt":{"rendered":"<p>Most of the chemical structure diagrams in this blog originate from Chemdraw, which seems to have been around since the dawn of personal computers! I have tended to use this program to produce JPG bitmaps for the blog, writing them out in 4x magnification, so that they can be scaled down for display whilst retaining [&hellip;]<\/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":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[2,1],"tags":[320,728,726,521,730,725,724,727,31,729,705],"ppma_author":[2661],"class_list":["post-5312","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-general","tag-chemical-diagrams","tag-chemical-structure-diagrams","tag-desktop-publishing","tag-e-books","tag-feedfabrik","tag-gif","tag-gps","tag-internet-explorer","tag-peter-murray-rust","tag-software-environment","tag-vector-graphics"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Blogbooks, e-books and future proofing chemical diagrams. - Henry Rzepa&#039;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=5312\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Blogbooks, e-books and future proofing chemical diagrams. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"Most of the chemical structure diagrams in this blog originate from Chemdraw, which seems to have been around since the dawn of personal computers! I have tended to use this program to produce JPG bitmaps for the blog, writing them out in 4x magnification, so that they can be scaled down for display whilst retaining [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5312\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2011-10-31T13:23:58+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2011-10-31T14:25:18+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/taxol-page001.svg\" \/>\n<meta name=\"author\" content=\"Henry Rzepa\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Henry Rzepa\" \/>\n\t<meta name=\"twitter:label2\" content=\"Estimated reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"3 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Blogbooks, e-books and future proofing chemical diagrams. - Henry Rzepa&#039;s Blog","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5312","og_locale":"en_GB","og_type":"article","og_title":"Blogbooks, e-books and future proofing chemical diagrams. - Henry Rzepa&#039;s Blog","og_description":"Most of the chemical structure diagrams in this blog originate from Chemdraw, which seems to have been around since the dawn of personal computers! 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We could acquire a computer which could be used to draw chemical structures in one application, and via a mysterious and mostly invisible entity called the clipboard, paste it into a word processor (it was\u2026","rel":"","context":"In &quot;Chemical IT&quot;","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":11735,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11735","url_meta":{"origin":5312,"position":1},"title":"Chemistry data round-tripping. Has there been  ANY progress?","author":"Henry Rzepa","date":"December 2, 2013","format":false,"excerpt":"This is one of those topics that seems to crop up every three years or so. Since then, new versions of operating systems, new versions of programs, mobile devices and perhaps some progress?\u00a0 Right, I will briefly recapitulate. Chemical structure diagrams are special; they contain chemical semantics (what an atom\u2026","rel":"","context":"In &quot;Chemical IT&quot;","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":5011,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5011","url_meta":{"origin":5312,"position":2},"title":"Steve Jobs and chemistry: a personal recollection.","author":"Henry Rzepa","date":"October 9, 2011","format":false,"excerpt":"Steve Jobs death on October 5th 2011 was followed by a remarkable number of tributes and reflections on the impact the company he founded has had on the world. Many of these tributes summarise the effect as a visionary disruption. Here I describe from my own perspective some of the\u2026","rel":"","context":"In &quot;Chemical IT&quot;","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/jobs1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":2962,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2962","url_meta":{"origin":5312,"position":3},"title":"Data-round-tripping: wherein the future?","author":"Henry Rzepa","date":"December 7, 2010","format":false,"excerpt":"Moving (chemical) data around in a manner which allows its (automated) use in whichever context it finds itself must be a holy grail for all scientists and chemists. I posted earlier on the fragile nature of molecular diagrams making the journey between the editing program used to create them (say\u2026","rel":"","context":"In &quot;Chemical IT&quot;","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":83,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=83","url_meta":{"origin":5312,"position":4},"title":"On the importance of  Digital repositories in Chemistry","author":"Henry Rzepa","date":"April 3, 2009","format":false,"excerpt":"The preceeding blog entries contain stories about chemical behaviour. If you have clicked on the diagrams, you may even have gotten a Jmol view of the relevant molecules popping up. But if you are truly curious, you may even have the urge to acquire the relevant 3D information about the\u2026","rel":"","context":"In &quot;Chemical IT&quot;","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"blog11","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/04\/blog11.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":5218,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5218","url_meta":{"origin":5312,"position":5},"title":"Science publishers (and authors) please take note.","author":"Henry Rzepa","date":"October 24, 2011","format":false,"excerpt":"I have for perhaps the last 25 years been urging publishers to recognise how science publishing could and should change. My latest thoughts are published in an article entitled \"The past, present and future of Scientific discourse\" (DOI: 10.1186\/1758-2946-3-46). Here I take two articles, one published 58 years ago and\u2026","rel":"","context":"In &quot;Chemical IT&quot;","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":[]}],"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\/5312","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=5312"}],"version-history":[{"count":0,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/5312\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=5312"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=5312"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=5312"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=5312"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}