{"id":8,"date":"2008-04-12T17:15:17","date_gmt":"2008-04-12T16:15:17","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8"},"modified":"2021-07-08T12:21:02","modified_gmt":"2021-07-08T11:21:02","slug":"loading-3d-molecular-orbitals-and-other-isosurfaces-into-a-blog","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8","title":{"rendered":"Jmol and WordPress: Loading 3D molecular models, molecular isosurfaces and molecular vibrations into a blog"},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"8\">\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2021\/07\/a80.jpg\" alt=\"\" width=\"292\" height=\"354\"  onclick=\"jmolApplet([500,500],'load wp-content\/uploads\/2021\/07\/a73.xyz;isosurface wp-content\/uploads\/2021\/07\/a73.jvxl;isosurface append wp-content\/uploads\/2021\/07\/a80.jvxl translucent;','c1');\"   alt=\"A lemniscular molecular orbital\" \/><\/p>\n<p>Click on the static image to get an active model. The code used to obtain the above was:<\/p>\n<ol>\n<li>\n<pre>&lt;script src=\"..\/Jmol\/Jmol.js\" type=\"text\/javascript\" \/&gt;<\/pre>\n<\/li>\n<li>\n<p>This line is best added to the theme header by editing the file \/wp-content\/themes\/default\/header.php to add the following line in the header:<\/p>\n<p><code>&lt;script src=\"..\/Jmol\/Jmol.js\" type=\"text\/javascript\"&gt;&lt;\/script&gt;<\/code><\/p>\n<\/li>\n<li>\n<p><small>&lt;img onclick=&#8221;jmolInitialize(&#8216;..\/Jmol\/&#8217;,&#8217;JmolAppletSigned.jar&#8217;);jmolSetAppletColor(&#8216;yellow&#8217;); <br \/>\n jmolApplet([450,450],&#8217;load wp-content\/uploads\/2009\/08\/HV2-62.jvxl;isosurface translucent;zoom 5;moveto 4 0 2 0 90 70;&#8217;);&#8221; \u00a0alt=&#8221;A lemniscular molecular orbital&#8221; src=&#8221;http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2008\/04\/14-knot.jpg&#8221; \/&gt;<\/small><\/p>\n<p>where of course the uploads directory needs to be modified to correspond to your own content, and the file and script following it also correspond to the effect you wish to achieve.<\/p>\n<\/li>\n<\/ol>\n<p>The path <strong>wp-content\/uploads\/2009\/08\/<\/strong> is that created by the built-in editor using the <strong>Add media file upload<\/strong> mechanism. The Jmol directory is located at the level above that of the blog itself. The JVXL file is created from either the corresponding (Gaussian) output file, or a CUB file created using a program such as Gaussview. Any suitable surface can be displayed using JVXL. In addition to MOs, we have also displayed ELF (Electron localization function) isosurfaces and molecular vibrations. For the latter, use a script of the form<\/p>\n<p><code>'load wp-content\/uploads\/2008\/04\/vibration.log; frame 9; vectors on;vectors 4;vectors scale 5.0; color vectors green; vibration 10;animation mode loop;'<\/code><\/p>\n<p>where the vibration you want is contained in e.g. frame 9.<\/p>\n<p>There does appear to be a display bug with the above; the Jmol model replaces the window rather than being inlined in it. Once the model is displayed, just refresh the page to return to the blog entry.<\/p>\n<p>A recent addition is the display of non-covalent-interaction (NCI) surfaces, which are colour coded by using the values in one cube of points to colorize a second cube.<\/p>\n<p><code>'load wp-content\/uploads\/2011\/05\/isobornyl1.xyz;isosurface wp-content\/uploads\/2011\/05\/isobornyl1.jvxl colorscheme translucent bgyor;'<\/code><\/p>\n<hr \/>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 8 -->","protected":false},"excerpt":{"rendered":"<p>Click on the static image to get an active model. The code used to obtain the above was: &lt;script src=&#8221;..\/Jmol\/Jmol.js&#8221; type=&#8221;text\/javascript&#8221; \/&gt; This line is best added to the theme header by editing the file \/wp-content\/themes\/default\/header.php to add the following line in the header: &lt;script src=&#8221;..\/Jmol\/Jmol.js&#8221; type=&#8221;text\/javascript&#8221;&gt;&lt;\/script&gt; &lt;img onclick=&#8221;jmolInitialize(&#8216;..\/Jmol\/&#8217;,&#8217;JmolAppletSigned.jar&#8217;);jmolSetAppletColor(&#8216;yellow&#8217;); jmolApplet([450,450],&#8217;load wp-content\/uploads\/2009\/08\/HV2-62.jvxl;isosurface translucent;zoom 5;moveto 4 0 [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_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},"jetpack_post_was_ever_published":false},"categories":[2,4],"tags":[152,2647,988,217,2648,6,789,373,989],"ppma_author":[2661],"class_list":["post-8","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-interesting-chemistry","tag-animation","tag-chemical-it","tag-editor","tag-http","tag-interesting-chemistry","tag-jmol","tag-php","tag-tutorial-material","tag-www-ch-imperial-ac-ukrzepablogwp-contentuploads20080414-knot-jpg"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.6 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Jmol and WordPress: Loading 3D molecular models, molecular isosurfaces and molecular vibrations into a blog - 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=8\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Jmol and WordPress: Loading 3D molecular models, molecular isosurfaces and molecular vibrations into a blog - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"Click on the static image to get an active model. The code used to obtain the above was: &lt;script src=&quot;..\/Jmol\/Jmol.js&quot; type=&quot;text\/javascript&quot; \/&gt; This line is best added to the theme header by editing the file \/wp-content\/themes\/default\/header.php to add the following line in the header: &lt;script src=&quot;..\/Jmol\/Jmol.js&quot; type=&quot;text\/javascript&quot;&gt;&lt;\/script&gt; &lt;img onclick=&#8221;jmolInitialize(&#8216;..\/Jmol\/&#8217;,&#8217;JmolAppletSigned.jar&#8217;);jmolSetAppletColor(&#8216;yellow&#8217;); jmolApplet([450,450],&#8217;load wp-content\/uploads\/2009\/08\/HV2-62.jvxl;isosurface translucent;zoom 5;moveto 4 0 [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2008-04-12T16:15:17+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2021-07-08T11:21:02+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2021\/07\/a80.jpg\" \/>\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=\"2 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Jmol and WordPress: Loading 3D molecular models, molecular isosurfaces and molecular vibrations into a blog - 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=8","og_locale":"en_GB","og_type":"article","og_title":"Jmol and WordPress: Loading 3D molecular models, molecular isosurfaces and molecular vibrations into a blog - Henry Rzepa&#039;s Blog","og_description":"Click on the static image to get an active model. The code used to obtain the above was: &lt;script src=\"..\/Jmol\/Jmol.js\" type=\"text\/javascript\" \/&gt; This line is best added to the theme header by editing the file \/wp-content\/themes\/default\/header.php to add the following line in the header: &lt;script src=\"..\/Jmol\/Jmol.js\" type=\"text\/javascript\"&gt;&lt;\/script&gt; &lt;img onclick=&#8221;jmolInitialize(&#8216;..\/Jmol\/&#8217;,&#8217;JmolAppletSigned.jar&#8217;);jmolSetAppletColor(&#8216;yellow&#8217;); jmolApplet([450,450],&#8217;load wp-content\/uploads\/2009\/08\/HV2-62.jvxl;isosurface translucent;zoom 5;moveto 4 0 [&hellip;]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8","og_site_name":"Henry Rzepa&#039;s Blog","article_published_time":"2008-04-12T16:15:17+00:00","article_modified_time":"2021-07-08T11:21:02+00:00","og_image":[{"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2021\/07\/a80.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Jmol and WordPress: Loading 3D molecular models, molecular isosurfaces and molecular vibrations into a blog","datePublished":"2008-04-12T16:15:17+00:00","dateModified":"2021-07-08T11:21:02+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8"},"wordCount":295,"commentCount":8,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8#primaryimage"},"thumbnailUrl":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2021\/07\/a80.jpg","keywords":["animation","Chemical IT","editor","http","Interesting chemistry","jmol","php","Tutorial material","www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2008\/04\/14-knot.jpg"],"articleSection":["Chemical IT","Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8","name":"Jmol and WordPress: Loading 3D molecular models, molecular isosurfaces and molecular vibrations into a blog - 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Many of my subsequent efforts have indeed invoked Jmol. I thought I might review progress since then, with a particular focus on using\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":19697,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19697","url_meta":{"origin":8,"position":1},"title":"Ten years on: Jmol and WordPress.","author":"Henry Rzepa","date":"May 16, 2018","format":false,"excerpt":"Ten years are a long time when it comes to (recent) technologies. The first post on this blog was on the topic of how to present chemistry with three intact dimensions. I had in mind molecular models, molecular isosurfaces and molecular vibrations (arguably a further dimension). Here I reflect on\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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":25452,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25452","url_meta":{"origin":8,"position":2},"title":"Four stages in the evolution of interactive ESI as part of articles in chemistry journals.","author":"Henry Rzepa","date":"August 25, 2022","format":false,"excerpt":"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\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":12607,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12607","url_meta":{"origin":8,"position":3},"title":"Test of JSmol in WordPress: the background story.","author":"Henry Rzepa","date":"June 8, 2014","format":false,"excerpt":"A word of explanation about this test page for experimenting with JSmol. Many moons ago I posted about how to include a generated 3D molecular model in a blog post, and have used that method on many posts here ever since. It relied on Java as the underlying software (first\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":25369,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25369","url_meta":{"origin":8,"position":4},"title":"Web page decay and Journals: How an interactive  &#8220;ESI&#8221; from 2006 was rescued.","author":"Henry Rzepa","date":"August 12, 2022","format":false,"excerpt":"In 2006 we published an article illustrating various types of pseudorotations in small molecules. It's been cited 20 times since then, so reasonable interest! We described rotations known as Lever and Turnstile as well as the better known Berry mode. Because the differences between these rotations are quite subtle, we\u2026","rel":"","context":"With 10 comments","block_context":{"text":"With 10 comments","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25369#comments"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":11895,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11895","url_meta":{"origin":8,"position":5},"title":"3D-rendered molecular models on this blog: an update.","author":"Henry Rzepa","date":"January 16, 2014","format":false,"excerpt":"So much to do, so little time to do it. That is my excuse at least. Right from my first post on this blog in 2008\u00a0I have tried to enhance it using Jmol, a Java-based applet (normally indicated with the caption Click for 3D). This has been pretty stable for\u2026","rel":"","context":"In &quot;General&quot;","block_context":{"text":"General","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1"},"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\/8","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=8"}],"version-history":[{"count":85,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/8\/revisions"}],"predecessor-version":[{"id":24026,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/8\/revisions\/24026"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=8"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=8"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=8"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=8"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}