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It seems Avogadro was phased out in Ubuntu 20.04 (Focal Fossa) and derivatives like Mint 20 (Ulyana). Now the version available in the repositories is Avogadro 2. If you had Avogadro installed in 18.04, and did a upgrade, it is replaced with Avogadro 2.

I faced a minor issue while trying to adapt my workflow to the new version. While drawing some molecules, I found the new location of the geometry optimization tool, under Extensions > Open Babel > Optimize geometry. The problem was, the relevant entry, together with others in the same location, were grayed out, and unselectable, as the image below shows:

enter image description here

It was a headscratcher, and I spent some time figuring out what was the problem, and opened this question afterwards to document the solution, to help other people that may face the same issue.

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    $\begingroup$ Maybe we can make the title more descriptive? This makes it sound like all menus are grayed out. $\endgroup$
    – Tristan Maxson
    Aug 31, 2020 at 23:57
  • $\begingroup$ Are you able to take a screenshot using Ubuntu's "shutter" or "screenshot" apps, or the "snipping tool" of Windows, or CMD+SHIFT+4 on Mac, or to just press "print screen" instead of taking a picture of your screen with a camera, which seems to be what you've done? $\endgroup$
    – Nike Dattani
    Sep 1, 2020 at 0:00
  • $\begingroup$ @NikeDattani, I tried to use printscreen at first, but it didn't work with the menu entry opened, so I took a photo as a workaround. $\endgroup$
    – ksousa
    Sep 1, 2020 at 0:04
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    $\begingroup$ With Ubuntu's screenshot app, you can delay the screenshot by 3 seconds. This gives you enough time to open the menu. What operating system are you using? $\endgroup$
    – Nike Dattani
    Sep 1, 2020 at 0:07
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    $\begingroup$ Is there any reason why avogadro has been phased out? the one available in ubuntu 20. has several missing feature, e.g.: I cannot make any selection by mouse. I am trying to install an older version of it instead ... $\endgroup$
    – gluuke
    Dec 23, 2020 at 10:59

2 Answers 2

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Solution: Install Open Babel

The underlying cause is that Open Babel was not installed by default as a dependency of Avogadro 2. I think this is odd, as basic features like geometry optimization depend on it. Anyway, just installing Open Babel separately fixed the problem. To install it, open the terminal and input the following command:

sudo apt install openbabel

When the installation is finished, and you restart Avogadro 2, now you can select Optimize geometry, and the other functions that rely on Open Babel:

enter image description here

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    $\begingroup$ In your case, you installed on Linux - it's up to the package maintainers to decide what dependencies should be optional. On Windows and Mac, Open Babel is bundled with the binaries. $\endgroup$
    – Geoff Hutchison
    Sep 9, 2020 at 19:56
  • $\begingroup$ Thank you @GeoffHutchison. Given its a platform-dependent issue, I changed the title to include information on the platform. $\endgroup$
    – ksousa
    Sep 9, 2020 at 23:13
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Geoff Hutchison might be able to provide a more up to date and authoritative answer, but I can at least point to some explanation of why OpenBabel isn't included by default with Avogadro 2: https://blog.kitware.com/avogadro-2-and-open-chemistry/

The important points of the article are:

  • The developers wanted to separate the Avogadro application from the various libraries/plugins that it used to have a more modular code.
  • To switch the license of the code from GPLv2+ to BSD, they had to change how they interfaced with OpenBabel. This improved some Avogadro features and made it easier to upgrade Avogadro and Open Babel independently of each other.
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    $\begingroup$ Case in point, while Open Babel 3 drastically changed the API, only minimal changes were needed in Avogadro. $\endgroup$
    – Geoff Hutchison
    Sep 9, 2020 at 19:55

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