pymol is started through a wrapper script. Once it runs I get two questionmarks in the Launcher. Pymol itself has an icon in the dash. But as 'pymol' is only the wrapper this icon is not used when the other two instances are running. I've had a look at the script at
/usr/bin/pymol but could not figure out how to continue. I guess I have to create .desktop files for each launched window then, but I don't know their name. Among the running process I can only see "python2.6". I think creating a .desktop-file for python2.6 would not really help if I want to use different icons for each window.
(Python games only showing python icon, but not game icon: https://bugs.launchpad.net/ubuntu/+source/unity/+bug/777417 )