Managing Java Security

Managing typical Java security issues
with the interactive 3D structure viewer


pocketZebra implements JavaScript and Java-based openAstex plugin for on-site visualization of the results. In order to enable this feature you will have to approve execution of the Java plugin. Two typical problems are discussed below.

While pocketZebra output is primarily web-based and viewable on the website, the off-line version of the output is also available. Therefore, if you do not want to use the plugin you can still use pocketZebra and download the results to your computer for off-line use.

Problem 1: running an unsigned application
Problem 2: application blocked by security settings

Problem 1: running an unsigned application
When opening the result page or accessing our example pages you can be prompted to run an unsigned application from http://biokinet.belozersky.msu.ru/. To enable the on-site visualization feature press "Run" (or "Proceed") button.

In Windows:


(The exact appearance of this dialog window will depend on your operating system and Java distribution)

In Linux:


(The exact appearance of this dialog window will depend on your operating system and Java distribution)



Problem 2: application blocked by security settings
If security setting of your Java distribution are set to "High" or "Very High" the on-site visualization feature may be disabled. In this case, opening the result page or accessing our example pages will invoke a dialog window stating that the application has been blocked:


(The exact appearance of this dialog window will depend on your operating system and Java distribution)


If you decide to use the on-site visualization feature you have two options to overcome this limitation:
I. Change Java security settings to "Medium"
OR
II. Add http://biokinet.belozersky.msu.ru to the "Exception Site List"

Solution I. Change Java security settings to "Medium"

1. Open Java Console. In Windows press "Start" > "Programs" > "Java" > "Configure Java". In Linux execute /usr/bin/jcontrol or /usr/java/latest/bin/jcontrol depending on the path to the Java distribution actually used by your browser.
2. Under the "Security" tab set the security level to "Medium".


(The exact appearance of this dialog window will depend on your operating system and Java distribution)


3. Press "OK". Close your browser and start it again. This step is absolutely required to reset Java setting.


Solution II. Add http://biokinet.belozersky.msu.ru to the "Exception Site List"

Note: you may need to update to the latest release of Java in order to have this feature available to you

1. Open Java Console. In Windows press "Start" > "Programs" > "Java" > "Configure Java". In Linux execute /usr/bin/jcontrol or /usr/java/latest/bin/jcontrol depending on the path to the Java distribution used by your browser.
2. Under the "Security" tab press "Edit Site List" button.
3. Add http://biokinet.belozersky.msu.ru to the list and press "Add"


(The exact appearance of this dialog window will depend on your operating system and Java distribution)

4. Confirm


(The exact appearance of this dialog window will depend on your operating system and Java distribution)

5. You can now see http://biokinet.belozersky.msu.ru in the "Exception Site List" and may increase the security level to "High".


(The exact appearance of this dialog window will depend on your operating system and Java distribution)

6. Press "OK". Close your browser and start it again. This step is absolutely required to reset Java setting.
7. When opening the result page or accessing our example pages you will need to approve execution of the Java visualization plugin.


(The exact appearance of this dialog window will depend on your operating system and Java distribution)