Maybe I am doing something wrong, but this is what I need to do:

1. Open the Molecule
2. Select the Molecule (see Bug #442)
3. Open Animation->Per Molecule Settings
4. Select Vibration as Animation Mode
5. Close Animation Preferences
6. Hit "Start Animation" in the toolbar
7. Open Animation->Per Molecule Settings again
8. Select Vibration Tab
9. Select/Deselect desired vibration

Overall very complicated.

Steps 5./6./7. seem to be necessary because the Animation Preferences window is modal(?), i.e. I cannot click the main toolbar while it's open, at least not on my system (Gnome-2.22, metacity as window manager)

Overall, it would be much more intuitive if just selecting a particular vibration (i.e. checking the box beside it) would start the frequency animation, no matter what other settings. The skip forward/backward toolbar buttons do not apply to vibrations anyway.

Maybe it would be best to split up vibrations and trajectories?

PS: Sorry for not submitting bugs 442,443 and 444 under my name, I forgot I had a bioinformatics.org account.