Note: We really recommend that you use Java Web Start to get the Control Panel working with BioCoRE. It is quite a bit nicer and instructions on doing this are available.

For using the NAMD Configuration File Generator (and for more convenient Control Panel interactions, although we recommend Java Web Start for that), you will need to have Swing installed.

You don't seem to have Java enabled. Please enable it and reload this page.

Can you see "You're Ready For BioCoRE" in a grey box right above this line? If so, you are ready to access BioCoRE!

If you didn't see the line above (in the grey box), we need you to do a little bit of work with your browser. Note: If you try this a few times and don't get it working, PLEASE contact us and let us know. We really want you to be able to use BioCoRE to its fullest.

If you are a Unix or Windows user, we are assuming that you are running version 4+ of your web browser. If you are running anything older than that, please upgrade. For MacOS, you'll need Internet Explorer (tested on IE 5) or iCab (tested on version Pre 2.1)

If you are running Windows, our best suggestion is to install Netscape 6.1 or higher (or equivalent, such as Mozilla) with the Sun java plugin. If you do this, you automatically get Swing. If you don't want to do that, read on.

All of the methods below start with downloading Swing.

If you are on Windows, download this zip file (1.6M). (right click and select "Save link as") The zip file contains a single file, swing.jar. Use an unzip program ( Winzip (shareware) or Aladdin Expander (freeware) work nicely) to unzip the swing.jar file somewhere that you will remember the location of. (A note for those that care: If you download swing.jar directly (without it being in a zip file) Windows tries to be intelligent and modifies the swing.jar file (adding about 7,000 bytes to it) causing it to not work. It is possible that this happens on operating systems other than Windows. (We haven't noticed it, though) If you download Swing directly and can't get it working, try downloading this version and unzipping it)

If you are on Unix, you can download the jar file directly swing.jar (1.8M) (right click and select "Save link as") and save it somewhere where you remember the location of it.

Let's assume you put the file in C:\path\to\swing.jar (or, on Unix /path/to/swing.jar) (A note for those that care: This swing.jar file is very similar to the swing.jar file available from Sun with one noticeable exception: Our swing.jar file loads about 3 times faster than the one from Sun.)

In addition, all of the steps below assume that you aren't running a web browser when you perform them. If you are, you will need to completely exit the web browser and restart it to have the changes take effect. Also, please note that the following instructions are only useful for Netscape version 4.x (support for Netscape 4 was dropped June 2004 for BioCoRE) and below. Netscape 6.x and above comes with the Java Plug-In installed, so it should be detected.

Internet Explorer on Windows XP, NT, and 2000
Internet Explorer on Windows9x
Netscape 4.x on Windows XP, NT, and 2000
Netscape 4.x on Windows9x
Netscape 4.x on Unix/Linux
Internet Explorer or iCab on MacOS 8-9



Internet Explorer on Windows XP, NT, and 2000

Please note that Internet Explorer now has the option to use Sun's Java instead of the built in java. If you are using Sun's version of Java (and this is what we recommend), you don't need to do the following.
  1. From the Windows Control Panel, double-click on the System icon.
  2. From System Properties, select the Environment tab.
  3. If you have Administrative access, click in the "System Variables" box, and type "CLASSPATH" in the "Variable" field. If you do not have Administrative access, click in the "User variables for username" box, choose the CLASSPATH variable and type "CLASSPATH" in the "Variable" field.
  4. In the "Value" field, add the path, including the filename, of swing.jar. For example...

    %CLASSPATH%;C:\swing.jar

  5. Click the Set button to apply the changes. If you had Administrative access, you should see the update in the "System variables" box. This will enable swing for all users on the machine. Otherwise, you should see the update in the "User variables for username" box. This will enable swing only for your account.
  6. Restart your computer to activate the changes.

Internet Explorer on Windows95/98

Please note that Internet Explorer now has the option to use Sun's Java instead of the built in java. If you are using Sun's version of Java, this doesn't apply. For Internet Explorer to work properly with BioCoRE it needs to be using the built in Java with Swing applied to it.

  1. Open your computers AUTOEXEC.BAT file in a text editor.
  2. Add the path, including the filename, of swing.jar to the CLASSPATH environment variable.

    set CLASSPATH=%CLASSPATH%;\path\to\swing.jar;

  3. Restart your computer to activate the changes.


For Windows XP, NT, and 2000

For Windows NT, you may need administrative privileges to place the swing.jar file in the necessary directory. If you are experiencing problems doing this, please let your system administrator do the installation.

  1. Put the swing.jar file in

    C:\Program Files\Netscape\Communicator\Program\java\classes

If you do not have administrative access, you may not have permission to write to that file. You may wish to try the following:
  1. Put swing.jar in

    C:\JAVA\CLASSES

  2. Click on Start. Go to "Settings", then "Control Panel".
  3. Double click on "System".
  4. Click on the "System Properties - Environment" tab.
  5. Highlight any one of the current entries in the top box. ("System Variables:")
  6. In the top entry field, replace the text displayed with the word "CLASSPATH" and replace the path with "swing.jar".
  7. Click on the "Set" button.
  8. Click on the "OK" button.
  9. Exit your browser now, and start it up again. You should be swing-enabled. If it is not, it may be necessary to restart your computer for changes to take effect.
If you do not have permission to complete the above procedure, please ask your system administrator to do the installation.


Netscape 4.x on Windows95/98/NT/2000/ME

If you are installing on WindowsNT, and you want it to automatically work for all of the users on your machine, you need to have Administrator permission.

For Windows95/98

  1. Find the Netscape directory. This defaults to: C:\Program Files\Netscape\

    Put the swing.jar file in:

    C:\Program Files\Netscape\Communicator\Program\java\classes

Netscape 4.x on Unix/Linux

    If you want it to automatically work for all of the users on your system, you need to have root permission and do the following:
    1. Find your netscape installation. Common places to look include:

      /usr/lib/netscape
      /var/netscape/communicator
      /usr/local/netscape
      /usr/netscape
      

    2. There should be a directory structure under that location of java/classes There will be a bunch of font.properties files and jar files in that directory. Put swing.jar there and make sure it is readable by everyone.
    3. This method requires you to repeat this if you upgrade versions of netscape. (The new version of netscape will overwrite the directories)

      - OR -

    4. If you don't have root access, you will need to create/change your CLASSPATH environment variable to point to your copy of swing.jar. (We suggest that you put this in your startup files so that you are set up each time you log in)

      csh/tcsh:

      To create:
      setenv CLASSPATH /path/to/swing.jar

      To change:
      setenv CLASSPATH /path/to/swing.jar:$CLASSPATH

      sh:

      To create:
      CLASSPATH=/path/to/swing.jar

      To change:
      CLASSPATH=/path/to/swing.jar:$CLASSPATH

    If the above method just doesn't seem to work when you come back to this page (after restarting your browser), check the following: Do you (or did you ever) have two copies of netscape installed? Check to see if you have the environment variable MOZILLA_HOME set (Slackware Linux, for one, sets this variable in its startup scripts). If you do have a MOZILLA_HOME variable set, and it doesn't point to the netscape directory where you installed swing.jar, it won't work (and has potentially been causing other netscape problems for quite some time on your machine). The fix: set MOZILLA_HOME so that it points to the proper netscape directory.




Internet Explorer or iCab on MacOS 8-9

Please note that Internet Explorer now has the option to use Sun's Java instead of the built in java. If you are using Sun's version of Java, this doesn't apply.
If you have write permission to your System Folder, installation is simple. Find the System Folder on your startup disk. Put the swing.jar file into the ĘSystem Folder:Extensions:MRJ Libraries:MRJ Classes" folder.

If you are a Multiple Users restricted user, or for some other reason cannot modify your system folder, you can use the following procedure with Internet Explorer:

  1. Put swing.jar in any convenient folder
  2. In IE, go to Preferences and select Web Browser/Java
  3. Add swing.jar the the Class Paths box using the Add... button

I cannot find a similar procedure for iCab, so there you will have to use the System Folder method.


Feedback

The BioCoRE team welcomes any comments, questions, or suggestions that you might have concerning our software! Please email us or fill out our feedback form.