Dear Bob,
I have succeeded in getting FirstGlance to load 1d66 in JSmol 14.0.3.
All the main buttons and views work. YAY! VERY EXCITING! PERFORMANCE
IS IMPRESSIVE!. I adapted what you helped me to do when we met at the
Gordon Conference in RI months ago, having taken a careful look at
simpleOpt.htm etc. in 14.0.3. It is not yet on a server, but I can
put it on tomorrow if that will help you debug the signed Java
applet, or just put a zip or tar.gz file of the whole system where
you can download it.
FirstGlance in JSmol works in Safari and Firefox (on OS 10.6.8,
running from local files).
I cannot get the JSmol menu to pop up in either browser. I do have
JSmol occupying about 60% of the window width and going up against
the right edge of the browser window.
This will be a lifesaver in the course I'm teaching next week if
Oracle releases a new Java and the applet stops working. As you know,
Proteopedia already offers JSmol.
What I did NOT succeed with is getting it to run in SIGNED Jmol
14.0.3. This is with Java 1.6.0_65 on OS 10.6.8. I have not yet tried
the files in Windows 7 with Java 1.7 but I can do that tomorrow.
I have tried changing use: to "SIGNED" from "HTML5". In Safari, the
applet begins loading (pink background displays but no frank), I
approve the Integrated Graphics signature, then I get an "Error:"
message in the upper left of the Jmol rectangle. See the report below.
In Firefox, the molecule (nor the frank) never appear on the blank
pink background, but the text report gets completed, showing all
details for 1d66, hence Jmol must be working enough to report the
molecular details to javascript, even tho no molecule is displayed.
The same version of FirstGlance works fine with signed or unsigned
Jmol 13.0.15 (Java 1.6.0_65).
----------------------
My main file contains:
var JmolPath = "jsmol/java/";
<script type="text/javascript" src="jsmol/JSmol.min.js"></script>
<script type="text/javascript" src="jsmol/js/Jmol2.js"></script><
(The old Jmol.js is no longer loaded.)
<script language='javascript'>
Jmol.Info = //jz
{
use: "HTML5", // HTML5 or SIGNED or JAVA (JAVA means unsigned)
// width: "",
// height: "",
debug: false, // alerts full Info before JSmol displays
color: "0xffd0d0",
j2sPath: "jsmol/j2s",
jarPath: "jsmol/java",
jarFile: "JmolAppletSigned0.jar",
isSigned: "true",
disableJ2SLoadMonitor: false, // brown and yellow progress
banners at lower
disableInitialConsole: true, // startup text in JSmol rectangle
addSelectionOptions: false, // puts load slot/menu below JSmol
serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php";,
readyFunction: null, // or define one
// script: "set zoomLarge false; load $caffeine"
pickCallback: "jmolPickCallback",
messageCallback: "jmolMessageCallback",
loadStructCallback: "jmolLoadStructCallback"
}
------------------
Elsewhere I do:
jmolInitialize(JmolPath); // have also tried with (JmolPath, true);
jmolApplet("100%", makeJmolScript());
--------------------
Here is what appears in the Java Console for Safari:
Java Plug-in 1.6.0_65
Using JRE version 1.6.0_65-b14-462-10M4609 Java HotSpot(TM) 64-Bit Server VM
User home directory = /Users/emartz
----------------------------------------------------
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
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>
----------------------------------------------------
java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
at
sun.plugin2.applet.Plugin2ClassLoader.defineClassHelper(Plugin2ClassLoader.java:1097)
at
sun.plugin2.applet.Plugin2ClassLoader.access$100(Plugin2ClassLoader.java:64)
at
sun.plugin2.applet.Plugin2ClassLoader$2.run(Plugin2ClassLoader.java:1055)
at java.security.AccessController.doPrivileged(Native Method)
at
sun.plugin2.applet.Plugin2ClassLoader.findClassHelper(Plugin2ClassLoader.java:1019)
at
sun.plugin2.applet.Applet2ClassLoader.findClass(Applet2ClassLoader.java:130)
at
sun.plugin2.applet.Plugin2ClassLoader.loadClass0(Plugin2ClassLoader.java:259)
at
sun.plugin2.applet.Plugin2ClassLoader.loadClass(Plugin2ClassLoader.java:189)
at
sun.plugin2.applet.Plugin2ClassLoader.loadClass(Plugin2ClassLoader.java:170)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at
sun.plugin2.applet.Plugin2ClassLoader.loadCode(Plugin2ClassLoader.java:721)
at
sun.plugin2.applet.Plugin2Manager.createApplet(Plugin2Manager.java:3148)
at
sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Plugin2Manager.java:1536)
at java.lang.Thread.run(Thread.java:695)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at
sun.plugin2.applet.Plugin2ClassLoader.defineClassHelper(Plugin2ClassLoader.java:1078)
... 13 more
Caused by: java.lang.NullPointerException
at
sun.plugin2.applet.Plugin2ClassLoader.loadAllowedCodebases(Plugin2ClassLoader.java:462)
at
sun.plugin2.applet.Plugin2ClassLoader.getPermissions(Plugin2ClassLoader.java:452)
at
sun.plugin2.applet.Applet2ClassLoader.getPermissions(Applet2ClassLoader.java:680)
at
java.security.SecureClassLoader.getProtectionDomain(SecureClassLoader.java:235)
at
java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:217)
... 18 more
Exception: java.lang.RuntimeException:
java.lang.reflect.InvocationTargetException
-------------
No error messages jump out at me in the Java Console using Firefox,
but it is a very long log.
-------------
Thanks, Eric
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