Technical FAQ

Do you provide a User Guide?

Yes, please download a pdf copy here

I can't read old models into Berkeley Madonna 9.1 on Mac.

We use a new file format to store models, and the converter has not yet been incorporated into the  macOS version. You have two options:
  1. If you have access to Windows, download the latest Java version and open your old file. It will automatically be converted to the new format and saved in the same directory. You can then use the converted model on macOS.
  2. Send your model to MadonnaExec@gmail.com with the subject "Please Convert", and we will do it for you. This may take 2-3 days.

I can't read old models into Berkeley Madonna 9.1 on Windows.

There are a few reasons why this might be the case:

  1. You may have blank spaces in your file name or the pathway pointing to your file name. Our convertor cannot interpret these spaces, so please change the storage location and name of the old Madonna file so that it does not include any blank spaces.
  2. If your old model uses the Chemical Reactions Module, it cannot be opened with Berkeley Madonna 9.1. The Chemical Reaction module works in Berkeley Madonna 9.1, but you will still have to recreate the old model, or email it to MadonnaExec@gmail.com with the subject "Please Convert", and we will do it for you. This may take 2-3 days.

    I have the latest Java - why doesn't Berkeley Madonna 9.1 work?

    Berkeley Madonna 9.1 currently requires Java 6 for macOS. Berkeley Madonna will take you to the appropriate download page at Apple, or you can download it now from here.

    For Windows, please visit the Oracle Java 8 download page here, and download a 32 bit Java installer with a file name ending in windows-i586.exe, for example: jre-8u171-windows-i586.exe. Berkeley Madonna will not work with the 64 bit versions (*-windows-x64.exe) at this time. 

    Please note that on both macOS and Windows, the above java versions will not interfere with other Java installations. If you install a 64 bit Java 9 or later, either before or after installing one of the above versions, then all programs capable of using the 64 bit version will do so. In the future we expect to release a version which can always use the latest Java version.

    I get the Java VM out of memory error.

    On Windows: Open BerkeleyMadonna.ini in Notepad, and add the following text to the end of the file on a new line: vmarg.1=-Xmx1024m This tells Java to use at most 1024 MB of memory. You may experiment with this number to suit your needs. 2048 MB may be the maximum available at this time. To see your current maximum available memory, select "About..." in the Help menu, select "Memory", and hit the "Information" button.


    On macOS: Using a text editor, open the file /Applications/BerkeleyMadonna.app/Contents/Info.plist Find the line that says: <string>-d32 -Xmx1024m</string> and change 1024m to suit your needs. To see your current maximum available memory, select "About Berkeley Madonna" in the main menu, select "Memory", and then hit the "Information" button.

    The Chemical Reactions Module gives an error at start up on Windows 8.3.18.

    Unfortunately, due to increased security on Windows 10, the reaction module no longer functions. Please install Berkeley Madonna on an older version of Windows, or use the Java-based Madonna 9.1 or higher.

    Where did some of the features from the 9.0 beta version go?

    Unfortunately, due to increased security on Windows 10, the reaction module no longer functions. Please install Berkeley Madonna on an older version of Windows, or use the Java-based Madonna 9.1 or higher.