{
  "version": "https://jsonfeed.org/version/1.1",
  "title": "chem-bla-ics",
  "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.",
  "home_page_url": "https://chem-bla-ics.linkedchemistry.info/",
  "feed_url": "https://chem-bla-ics.linkedchemistry.info/2006/04/23/protein-support-in-bioclipse-using.json",
  "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png",
  "language": "en",
  "authors": [
    {
      "name": "Egon Willighagen",
      "url": "https://orcid.org/0000-0001-7542-0286",
      "_orcid": "0000-0001-7542-0286"
    }
  ],
  "items": [

    {
      "id": "https://doi.org/10.59350/23wn4-1nt07",
      "url": "https://chem-bla-ics.linkedchemistry.info/2006/04/23/protein-support-in-bioclipse-using.html",
      "title": "Protein support in Bioclipse using Jmol and the CDK",
      "content_html": "<p>I have not blogged for about a week now, and been too busy with other things, like finishing my PhD articles/manuscript,\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2006/03/25/cologne-university-bioinformatics.html\">my new job at the CUBIC <i class=\"fa-solid fa-recycle fa-xs\"></i></a> where I\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2006/04/10/getting-jmols-cartoon-on-to-work-in.html\">continued the work <i class=\"fa-solid fa-recycle fa-xs\"></i></a> on proper protein support in\n<a href=\"http://www.bioclipse.net/\">Bioclipse</a> using the <a href=\"http://cdk.sf.net/\">CDK</a> and\n<a href=\"http://www.jmol.org/\">Jmol</a>:</p>\n\n<p><img src=\"/assets/images/cdkpdbsupport800.png\" alt=\"Screenshot of Bioclipse with a protein visualized with Jmol in the middle.\" /></p>\n\n<p>The latter involves getting the <a href=\"https://sourceforge.net/p/bioclipse/code/11760/log/?path=/bioclipse/trunk/plugins/net.bioclipse.jmol/src/net/bioclipse/plugins/adapter/cdk/CdkJmolAdapter.java\">CdkJmolAdapter <i class=\"fa-solid fa-recycle fa-xs\"></i></a>,\nthe interface between the CDK and Jmol, <a href=\"https://web.archive.org/web/20060508024648/http://wiki.cubic.uni-koeln.de/cdkwiki/doku.php?id=cdknewsartjmolandcdk\">updated for changes <i class=\"fa-solid fa-box-archive fa-xs\"></i></a>\nsince the <a href=\"https://sourceforge.net/projects/cdk/files/CDK%20News/2_1/\">Jmol as 3D viewer for CDK <i class=\"fa-solid fa-recycle fa-xs\"></i></a>\narticle in <a href=\"https://sourceforge.net/projects/cdk/files/CDK%20News/\">CDK News <i class=\"fa-solid fa-recycle fa-xs\"></i></a>, the open access journal for CDK related projects.</p>\n\n<p>The screenshot is not showing the actual status: the <code class=\"language-plaintext highlighter-rouge\">CdkJmolAdapter</code> does not propagate all information to Jmol correctly; as you\ncan see in the screenshot in the <code class=\"language-plaintext highlighter-rouge\">BioPolymerTree</code> and <code class=\"language-plaintext highlighter-rouge\">Property</code> views, the CDK now reads the structure information from the PDB file,\nand I verified that Jmol really extracts this using the <code class=\"language-plaintext highlighter-rouge\">StructureIterator</code>, but the secundairy structure does not show up yet.\nI believe the problem is in the <code class=\"language-plaintext highlighter-rouge\">AtomIterator</code>: issueing the <code class=\"language-plaintext highlighter-rouge\">select protein</code> script, selects zero atoms.</p>\n\n<p>The above screenshot is using a workaround, and was made by using Jmol’s own IO instead of the <code class=\"language-plaintext highlighter-rouge\">CdkJmolAdapter</code>. But\nI’m very close and think I will be able to fix this soon.</p>",
      "summary": "I have not blogged for about a week now, and been too busy with other things, like finishing my PhD articles/manuscript, my new job at the CUBIC where I continued the work on proper protein support in Bioclipse using the CDK and Jmol:",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/cdkpdbsupport800.png",
      "date_published": "2006-04-23T00:00:00+00:00",
      "date_modified": "2025-02-15T00:00:00+00:00",
      "tags": ["bioclipse","jmol","cdk"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}