{
  "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/2006/03/11/classpath-090-makes-jmol-application.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/ef1pm-6g994",
      "url": "https://chem-bla-ics.linkedchemistry.info/2006/03/11/classpath-090-makes-jmol-application.html",
      "title": "Classpath 0.90 makes the Jmol application run",
      "content_html": "<p>A few days back, <a href=\"http://www.gnu.org/software/classpath/announce/20060306.html\">Classpath 0.90</a> was released, the first release after the 0.20 release. Earlier Classpath releases\n<a href=\"/blog/2005/11/27/open-source-swing-jmol-renderer-runs.html\">could run the rendering engine <i class=\"fa-solid fa-recycle fa-xs\"></i></a>,\nbut <a href=\"/blog/2005/11/18/goal-live-chemblaics-cd.html\">running the application failed so far <i class=\"fa-solid fa-recycle fa-xs\"></i></a>.</p>\n\n<p>Today it hit Debian unstable, so upgrade my sid32 chroot and had <a href=\"http://www.cacaojvm.org/\">Cacao</a> run Jmol.\nI had some memory issues opening a small molecule (4-methyl-2-pentyne),\nand the rendering speed was a factor 100 or so slower than Sun’s JVM, but it runs!</p>\n\n<p>Using the command <code class=\"language-plaintext highlighter-rouge\">cacao -Xmx512M -jar Jmol.jar triplebond.mol</code> I got results.</p>\n\n<p>Note the exceptions copied to the console. Many thanx to the Classpath team!</p>\n\n<p>The stacktrace:</p>\n\n<div class=\"language-shell highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code>The full stack trace:\n\njava.lang.IllegalArgumentException: width&lt;<span class=\"o\">=</span>0 height&lt;<span class=\"o\">=</span>0\nat java.awt.image.SampleModel.&lt;init&gt; <span class=\"o\">(</span>SampleModel.java:63<span class=\"o\">)</span>\nat java.awt.image.SinglePixelPackedSampleModel.&lt;init&gt; <span class=\"o\">(</span>SinglePixelPackedSampleModel.java:61<span class=\"o\">)</span>\nat java.awt.image.SinglePixelPackedSampleModel.&lt;init&gt; <span class=\"o\">(</span>SinglePixelPackedSampleModel.java:55<span class=\"o\">)</span>\nat org.jmol.g3d.Swing3D.allocateImage <span class=\"o\">(</span>Swing3D.java:65<span class=\"o\">)</span>\nat org.jmol.g3d.Platform3D.allocateBuffers <span class=\"o\">(</span>Platform3D.java:102<span class=\"o\">)</span>\nat org.jmol.g3d.Graphics3D.beginRendering <span class=\"o\">(</span>Graphics3D.java:697<span class=\"o\">)</span>\nat org.jmol.viewer.Viewer.render1 <span class=\"o\">(</span>Viewer.java:1840<span class=\"o\">)</span>\nat org.jmol.viewer.Viewer.renderScreenImage <span class=\"o\">(</span>Viewer.java:1798<span class=\"o\">)</span>\nat org.openscience.jmol.app.DisplayPanel.paint <span class=\"o\">(</span>DisplayPanel.java:100<span class=\"o\">)</span>\nat javax.swing.JComponent.paintChildren <span class=\"o\">(</span>JComponent.java:1659<span class=\"o\">)</span>\nat javax.swing.JComponent.paint <span class=\"o\">(</span>JComponent.java:1564<span class=\"o\">)</span>\nat javax.swing.JComponent.paintChildren <span class=\"o\">(</span>JComponent.java:1659<span class=\"o\">)</span>\nat javax.swing.JComponent.paint <span class=\"o\">(</span>JComponent.java:1564<span class=\"o\">)</span>\nat javax.swing.JComponent.paintChildren <span class=\"o\">(</span>JComponent.java:1659<span class=\"o\">)</span>\nat javax.swing.JComponent.paint <span class=\"o\">(</span>JComponent.java:1564<span class=\"o\">)</span>\nat javax.swing.JComponent.paintChildren <span class=\"o\">(</span>JComponent.java:1659<span class=\"o\">)</span>\nat javax.swing.JComponent.paint <span class=\"o\">(</span>JComponent.java:1564<span class=\"o\">)</span>\nat javax.swing.JComponent.paintChildren <span class=\"o\">(</span>JComponent.java:1659<span class=\"o\">)</span>\nat javax.swing.JComponent.paint <span class=\"o\">(</span>JComponent.java:1564<span class=\"o\">)</span>\nat javax.swing.JLayeredPane.paint <span class=\"o\">(</span>JLayeredPane.java:647<span class=\"o\">)</span>\nat javax.swing.JComponent.paintChildren <span class=\"o\">(</span>JComponent.java:1659<span class=\"o\">)</span>\nat javax.swing.JComponent.paint <span class=\"o\">(</span>JComponent.java:1564<span class=\"o\">)</span>\nat javax.swing.JComponent.paintDoubleBuffered <span class=\"o\">(</span>JComponent.java:1782<span class=\"o\">)</span>\nat javax.swing.JComponent.paint <span class=\"o\">(</span>JComponent.java:1555<span class=\"o\">)</span>\nat java.awt.Container<span class=\"nv\">$GfxPaintVisitor</span>.visit <span class=\"o\">(</span>Container.java:1888<span class=\"o\">)</span>\nat java.awt.Container.visitChild <span class=\"o\">(</span>Container.java:1703<span class=\"o\">)</span>\nat java.awt.Container.visitChildren <span class=\"o\">(</span>Container.java:1674<span class=\"o\">)</span>\nat java.awt.Container.paint <span class=\"o\">(</span>Container.java:770<span class=\"o\">)</span>\nat gnu.java.awt.peer.gtk.GtkWindowPeer.handleEvent <span class=\"o\">(</span>GtkWindowPeer.java:268<span class=\"o\">)</span>\nat java.awt.Component.dispatchEventImpl <span class=\"o\">(</span>Component.java:4968<span class=\"o\">)</span>\nat java.awt.Container.dispatchEventImpl <span class=\"o\">(</span>Container.java:1723<span class=\"o\">)</span>\nat java.awt.Window.dispatchEventImpl <span class=\"o\">(</span>Window.java:626<span class=\"o\">)</span>\nat java.awt.Component.dispatchEvent <span class=\"o\">(</span>Component.java:2320<span class=\"o\">)</span>\nat java.awt.EventQueue.dispatchEvent <span class=\"o\">(</span>EventQueue.java:474<span class=\"o\">)</span>\nat java.awt.EventDispatchThread.run <span class=\"o\">(</span>EventDispatchThread.java:60<span class=\"o\">)</span>\nat java.lang.VMThread.run <span class=\"o\">(</span>VMThread.java:121<span class=\"o\">)</span>\n</code></pre></div></div>",
      "summary": "A few days back, Classpath 0.90 was released, the first release after the 0.20 release. Earlier Classpath releases could run the rendering engine , but running the application failed so far .",
      
      "date_published": "2006-03-11T00:00:00+00:00",
      "date_modified": "2023-09-24T00:00:00+00:00",
      "tags": ["jmol"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}