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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