pKa plugin has stopped working

User 870ab5b546

08-11-2013 14:25:47

If I go to http://epoch.uky.edu/ace/public/pKa.jsp, draw CC=O, and choose Tools -> Protonation -> pKa, absolutely nothing happens.  This is a new development, and I can't figure out what has changed between Wednesday and today.  The last time I tried this, I was told that I did not have a valid license, so it would run in evaluation mode.  Other tools seem to be working.


The same problem occurs if I use Marvin 6.1.3 instead.


Any ideas what could be wrong?  The Java console shows this exception:


Exception in thread "Thread-19" java.lang.NullPointerException
at chemaxon.marvin.plugin.PluginFactory.b(Unknown Source)
at chemaxon.marvin.plugin.PluginFactory.createDefaultParameterPanel(Unknown Source)
at chemaxon.marvin.plugin.PluginFactory.createDefaultParameterPanel(Unknown Source)
at chemaxon.marvin.plugin.PluginFactory$PluginRecord.a(Unknown Source)
at chemaxon.marvin.plugin.PluginFactory$PluginRecord.b(Unknown Source)
at chemaxon.marvin.plugin.PluginFactory$PluginRecord.getOptionsPane(Unknown Source)
at chemaxon.marvin.plugin.PluginFactory.getOptionsPane(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPluginManager.a(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPluginManager.callback(Unknown Source)
at chemaxon.marvin.plugin.PluginManager.callback(Unknown Source)
at chemaxon.marvin.common.swing.MolPanel$5.run(Unknown Source)

With Marvin 6.1.3, I see a similar error in the console:


Exception in thread "Thread-19" java.lang.NullPointerException
at chemaxon.marvin.plugin.PluginFactory.readUserProperties(Unknown Source)
at chemaxon.marvin.plugin.PluginFactory.createDefaultParameterPanel(Unknown Source)
at chemaxon.marvin.plugin.PluginFactory.createDefaultParameterPanel(Unknown Source)
at chemaxon.marvin.plugin.PluginFactory$PluginRecord.a(Unknown Source)
at chemaxon.marvin.plugin.PluginFactory$PluginRecord.b(Unknown Source)
at chemaxon.marvin.plugin.PluginFactory$PluginRecord.getOptionsPane(Unknown Source)
at chemaxon.marvin.plugin.PluginFactory.getOptionsPane(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPluginManager.a(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPluginManager.callback(Unknown Source)
at chemaxon.marvin.plugin.PluginManager.callback(Unknown Source)
at chemaxon.marvin.common.swing.MolPanel$6.run(Unknown Source)

User 870ab5b546

12-11-2013 00:51:40

One other piece of information: on my computer at home, which is still running Safari 5.0.6 on MacOS 10.5, the pKa plugin *works* in Marvin 5.4.1.1 delivered from the same Web page as below.  So maybe there's a bug in one of the new versions of Java or Safari.

ChemAxon d51151248d

12-11-2013 12:39:05

Dear Bob, 


we run your tests, but unfortunately didn't manage to reproduce the bugs. In order to be able to do more detailed testing, could you give us the detailed configuration of your machine (OS and Java version and Marvin used) ? We suspect there might be a problem with Java on your system.


Best wishes, 


Daniel 


 

User 870ab5b546

12-11-2013 13:38:35

cp339mac:~ Bob$ java -version
java version "1.7.0_25"
Java(TM) SE Runtime Environment (build 1.7.0_25-b15)
Java HotSpot(TM) 64-Bit Server VM (build 23.25-b01, mixed mode)

Mac mini


Processor  2.3 GHz Intel Core i5 


Memory  8 GB 1333 MHz DDR3


Graphics  Intel HD Graphics 3000 512 MB


Software  Mac OS X Lion 10.7.5 (11G63)

ChemAxon 5fc3e8d7d0

14-11-2013 10:47:27

Dear Bob,

The new Safari blocks the Applet to read/write the file system. Probably this new feature could cause the described problems.
Please see the following post: https://www.chemaxon.com/forum/viewpost53092.html#53092 />
Let us know if the new settings does not solve your problem.

Best regards,
Laszlo

User 870ab5b546

14-11-2013 14:57:53

Thanks, that solved the problem!  You guys are the best.