For reason that I did not understand Avogadro has been phased out of Ubuntu 20.x and the available package Avogadro2 is instead another branch of the package, which unfortunately does not cover all the features. As it appears impossible to install that older but more powerful version of Avogadro on last Ubuntu, does anyone know if it is still possible to delete selected atoms? I am really surprised such a basic feature has been "lost".

Basically, you can click and select atoms (although they do not appear selected for any displaying style but "ball and stick"), but then if you press CANCEL the whole model is deleted (all atoms). I was using this feature a lot to manipulate structures via GUI and now I just can't proceed unless I use my older Ubuntu distribution.

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    $\begingroup$ An answer to an earlier question about using Avogadro2 input generators mentions a method for getting the original Avogadro installed on Ubuntu. I haven't tried it on my Ubuntu version, but on the Windows version of Avogadro2, I can just right click an atom/bond to delete it if I'm in "Draw" mode (the pencil in the toolbar). $\endgroup$
    – Tyberius
    Commented Dec 23, 2020 at 15:08
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    $\begingroup$ thanks @Tyberius ... I have seen that but I was hoping to avoid to install a Window version via wine ... :-S $\endgroup$
    – gluuke
    Commented Dec 23, 2020 at 15:15
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    $\begingroup$ in the meantime I have also asked on avogadro forum: discuss.avogadro.cc/t/… $\endgroup$
    – gluuke
    Commented Dec 23, 2020 at 15:16
  • $\begingroup$ also: please note that similar issues have been risen few times already on avogadro forum and also here for example: reddit.com/r/Ubuntu/comments/gb55uo/… $\endgroup$
    – gluuke
    Commented Dec 23, 2020 at 15:19
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    $\begingroup$ The main problem was that the selection tool and particularly 'rubber band' selections were only added recently, so there are still a few features missing. Help, is always welcome. :-) $\endgroup$ Commented Dec 24, 2020 at 19:29

2 Answers 2


Yes, I saw your post on the forum - not sure why that commit didn't make it in, but I have a pull-request now.

The long and short is that while the main "guts" of Avogadro 2 are finished, there's a lot of small pieces that need to be done (case in point). Help is always welcome - there are plenty of tasks that can be done in a few hours for anyone interested.


In the meantime I have found a couple of solutions and I am listing them here for other users, as frankly not many packages allow to easily (via mouse) select atoms and delete them.

  1. you can use chimera as it offers the same feature via CTRL+mouse: https://www.cgl.ucsf.edu/chimera/data/downloads/1.15/linux_x86_64.html and then menu Actions -> Atoms/Bonds -> delete.

  2. if you still want to use avogadro2 on Linux you can actually delete atoms one-by-one by using right-click in "Draw" mode: https://discuss.avogadro.cc/t/delete-some-atoms-in-a-supercell/341/2


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