Hmm, definitely an odd message. Right, Jmol is now recognizing it as a
known file format, probably Pdb. My guess is that you somehow have some bad
JAR files there. Perhaps two JAR files from two different Jmol versions, or
a JAR file that was improperly put on the server (using ASCII transfer
instead of BIN, for example) or something like that. Jmol is attempting to
open the reader for the PDB file, and to do that it has to use the
PdbReader class for the first time. It is finding the class, but the class
Maybe try changing your jmolInitialize command to
jmolInitialize(".","JmolApplet.jar")
and make sure you have in that HTML directory the file JmolApplet.jar.
It's a very odd error. Actually, more likely is that you do not have all
the JmolApplet0... jar files on your server, and the server is responding
to the Jar file request using an HTML 404 error message instead. So do try
the above, and make sure the JAR files are really all there.
Bob
On Fri, 28 Dec 2007 11:35:59 -0800, "Emily Heureux" <[EMAIL PROTECTED]>
wrote:
> Ok, I changed the filename to 1G65.txt, and got a different but similar
> error in the java console (at least it thinks it is a pdb file, right?):
>
> 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>
> ----------------------------------------------------
> Exception in thread "Thread-211" java.lang.ClassFormatError: Incompatible
> magic value 1008813135 in class file
> org/jmol/adapter/readers/cifpdb/PdbReader
> at java.lang.ClassLoader.defineClass1(Native Method)
> 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 java.lang.ClassLoader.loadClassInternal(Unknown Source)
> at java.lang.Class.forName0(Native Method)
> at java.lang.Class.forName(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)
> Init Jmol
> language=en_US
> Jmol applet jmolApplet0[9517808398840184]
> AppletRegistry.checkIn(jmolApplet0[9517808398840184])
> (C) 2007 Jmol Development
> Jmol Version 11.3.65 2007-12-20 06:37
> java.vendor:Sun Microsystems Inc.
> java.version:1.5.0_11
> os.name:Windows XP
> memory:14.1/29.4
> appletId:jmolApplet0
>
appletDocumentBase=http://idm6.burnham.org:3000/maths/jmolDisplayTest/pmap.0
> 0017
> appletCodeBase=http://idm6.burnham.org:3000/javascripts/jmol-11.3.65/
>
urlImage=jar:http://idm6.burnham.org:3000/javascripts/jmol-11.3.65/JmolApple
> t0.jar!/jmol75x29x8.gif
>
> FileManager.openFile(http://idm6.burnham.org:3000/static/images/1G65.txt)
> //http://idm6.burnham.org:3000/static/images/1G65.txt
> FileManager opening http://idm6.burnham.org:3000/static/images/1G65.txt
> The Resolver thinks Pdb
>
> -----Original Message-----
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of
Robert
> Hanson
> Sent: Thursday, December 27, 2007 6:22 PM
> To: [email protected]
> Subject: Re: [Jmol-developers] Switching from 10.00 to 11.2.14
>
> OK, this explains the change. Jmol 11.2.14 thinks this is an XML file,
> which it is not. Please send me off-line the SOURCE of the url at
> http://idm6.burnham.org:3000/static/images/pdbFiles/1G65
>
> (Not the file, but a copy of the file you get with your browser when you
> click that link and then "view source" -- Something your server is doing
> makes Jjmol think that this is an XML file.
>
> If this is an XML file, then it's also possible that Jmol 11.2.14 does
> have
> a bug that makes it not possible to read XML files -- looks like it isn't
> finding the XML reader in the JAR files.
>
> Please try again with 11.3.65 and report if the same issue arises.
>
> Thanks,
>
> Bob Hanson
>
>> 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)
>
>
>
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