I got the console to show up!! Here's the entire output copied and pasted here:
Java Plug-in 1.5.0_11 Using JRE version 1.5.0_11 Java HotSpot(TM) Client VM User home directory = C:\Documents and Settings\emily ---------------------------------------------------- c: clear console window f: finalize objects on finalization queue g: garbage collect h: display this help message l: dump classloader list m: print memory usage o: trigger logging p: reload proxy configuration q: hide console r: reload policy configuration s: dump system and deployment properties t: dump thread list v: dump thread stack x: clear classloader cache 0-5: set trace level to <n> ---------------------------------------------------- ClassPreloader - javax.vecmath.Point3f+ ClassPreloader - javax.vecmath.Vector3f+ ClassPreloader - javax.vecmath.Matrix3f+ ClassPreloader - javax.vecmath.Point3i+ ClassPreloader - org.jmol.g3d.Graphics3D ClassPreloader - org.jmol.g3d.Sphere3D urlImage=jar:http://idm6.burnham.org:3000/javascripts/jmol-11.2.14/JmolApple t0.jar!/jmol75x29x8.gif ClassPreloader - org.jmol.g3d.Line3D ClassPreloader - org.jmol.g3d.Cylinder3D ClassPreloader - org.jmol.g3d.Colix3D ClassPreloader - org.jmol.g3d.Shade3D ClassPreloader - org.jmol.adapter.smarter.SmarterJmolAdapter ClassPreloader - org.jmol.adapter.smarter.Atom ClassPreloader - org.jmol.adapter.smarter.Bond ClassPreloader - org.jmol.adapter.smarter.AtomSetCollection Init jmol language=en_US Jmol applet jmolApplet0 ClassPreloader - org.jmol.adapter.smarter.AtomSetCollectionReader ClassPreloader - org.jmol.adapter.smarter.Resolver AppletRegistry.checkIn(jmolApplet0) ClassPreloader - org.jmol.popup.JmolPopup viewer.setIntProperty(_version,1102014) - integer variable defined (C) 2007 Jmol Development Jmol Version 11.2.14 2007-08-31 15:35 java.vendor:Sun Microsystems Inc. java.version:1.5.0_11 os.name:Windows XP memory:2.5/3.0 appletId:jmolApplet0 appletDocumentBase=http://idm6.burnham.org:3000/maths/jmolDisplayTest/pmap.0 0017 FileManager.openFile(http://idm6.burnham.org:3000/static/images/pdbFiles/1G6 5) //http://idm6.burnham.org:3000/static/images/pdbFiles/1G65 FileManager opening http://idm6.burnham.org:3000/static/images/pdbFiles/1G65 The Resolver thinks Xml Exception in thread "Thread-16" java.lang.NoClassDefFoundError: IllegalName: <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" at java.lang.ClassLoader.preDefineClass(Unknown Source) at java.lang.ClassLoader.defineClass(Unknown Source) at java.security.SecureClassLoader.defineClass(Unknown Source) at sun.applet.AppletClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at sun.applet.AppletClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at javax.xml.parsers.FactoryFinder.newInstance(Unknown Source) at javax.xml.parsers.FactoryFinder.findJarServiceProvider(Unknown Source) at javax.xml.parsers.FactoryFinder.find(Unknown Source) at javax.xml.parsers.SAXParserFactory.newInstance(Unknown Source) at org.jmol.adapter.readers.xml.XmlReader.allocateXmlReader14(Unknown Source) at org.jmol.adapter.readers.xml.XmlReader.getXmlReader(Unknown Source) at org.jmol.adapter.readers.xml.XmlReader.readAtomSetCollection(Unknown Source) at org.jmol.adapter.smarter.Resolver.resolve(Unknown Source) at org.jmol.adapter.smarter.SmarterJmolAdapter.openBufferedReader(Unknown Source) at org.jmol.viewer.FileManager$FileOpenThread.openBufferedReader(Unknown Source) at org.jmol.viewer.FileManager$FileOpenThread.run(Unknown Source) at org.jmol.viewer.FileManager.openFile(Unknown Source) at org.jmol.viewer.Viewer.openFile(Unknown Source) at org.jmol.viewer.Eval.load(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) at org.jmol.viewer.Eval.runEval(Unknown Source) at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source) at org.jmol.viewer.ScriptManager.runScript(Unknown Source) at org.jmol.viewer.ScriptManager.runNextScript(Unknown Source) at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source) at java.lang.Thread.run(Unknown Source) -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Angel Herraez Sent: Saturday, December 22, 2007 12:31 AM To: [email protected] Subject: Re: [Jmol-developers] Switching from 10.00 to 11.2.14 On 21 Dec 2007 at 13:11, Emily Heureux wrote: > The jmol looks like it is starting. I see the purple "Jmol" at the top, and > at the bottom of the browser, it says, "Applet jmolApplet0 started". It > stays that way, so there is an empty black box on the screen. If I > right-click to use the jmol menu, at the top it says "No atoms loaded", > which I believe is not correct. So Jmol is loaded correctly. It looks like a problem with not finding the pdb file, but in that case the error should be shown inside Jmol as Bob says. Of course, there should be no difference among versions for that, so it's extrange. Yes, v11 has a single "Console" entry in the popup menu instead of v10's "Open/Close". That's right, but the Jmol console should open. Try to locate the Java console, where error reports may help. If you have a Java cup icon on the lower right of your screen (the taskbar), right-click on it and choose "open console". See what shows up there. Also, if you can provide a URL so we can test your setup, that will be easier. ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
