Release candidate

A 1.3 release candidate is available for download. You are encouraged to use this version if possible. Note that below are the links for the old version as well.

Full archive

The msms binary instillation is as simple as unpacking a zip file for all supported platforms. The same archive works for all platforms, and the manual is included.


 11.0 MB

Just unpack the archive to your favorite applications directory and you are ready to roll. You may wish to add the msms/bin directory to your path. Alternatively on Unix systems (OSX and Linux) you can symlink msms/bin/msms.

Pure jar file

This is just the compiled class files in jar and is the smallest download. It can be run with the following command:
java -jar msms3.2rc-b163.jar


 1.7 MB

Manual and Cheat Sheet

The manual provides the primary user reference for this program. It is included in all standard downloads. However, it is provided here as a separate download for convenience.


 189 kB


 53 kB


 17.5 kB


You need to have java 6 (sometimes called java 1.6) installed on your computer. If you don't have java 6/1.6 installed download it from sun.

If you are a OSX user you will need the latest java updates that provide java 6. However this does not change the default java. To change the default go to Applications->Utilities->Java Preferences. Ensure that java SE 6 or higher is ticked, and drag it to the top of each list.