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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.

Any idea?

Pymol: http://apt.ubuntu.com/p/pymol

(Python games only showing python icon, but not game icon: https://bugs.launchpad.net/ubuntu/+source/unity/+bug/777417 )

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2 Answers 2

As of 2011-07-06, this has been fixed.

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It doesn't seem that this fix was implemented in Pymol (I am running version 1.4.1). –  Alkalyzer Dec 29 '11 at 19:14
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I tried today to create a proper Pymol launcher in Unity (under Oneiric) and modified the pymol.desktop file in (/usr/share/applications) as followed :

[Desktop Entry]
Version=1.0
Name=PyMOL Molecular Graphics System
GenericName=Molecular Modeller
Comment=Model molecular structures and produce high-quality images of them
Type=Application
Exec=pymol
Icon=pymol
MimeType=chemical/x-pdb
Categories=Education;Science;Chemistry;
StartupNotify=false
StartupWMClass=Tk

The most important part is the "StartupWMClass=Tk". While doing so, the Tk control panel of Pymol is always linked to the Pymol icon in the Unity launcher.

Basically, this "StartupWMClass" explains to Unity what should be the name of the windows that would appear after clicking on the launcher. (I figured out what was the name of the Tk control panel while running xprop|grep X11_WM_CLASS in a terminal)

But this only solves half of the problem because the main graphical window is still linked to an icon referred by a question mark which appears after invoking the program and I couldn't guess under which name refers to this main window.

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