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Atom selection and Energy minimization in Avogadro 1.93.0 (Avogadro 2)

Dear All,
I have previously used an older version of Avogadro where I can select an atom (using the black arrow) and delete that particular atom. In that version there is also an option for energy minimization of an atomic structure.

However, recently I have installed (as I have rebooted my PC) the latest version of Avogadro (from linux terminal using the command
sudo apt update
sudo apt install avogadro)

The version installed is 1.93.0 (Avogadro2). But in this version I could not find the option for deleting a particular atom nor the option of energy minimization.

Could anybody please help me with this?


Deleting atoms:

  • Use edit tool and right click on the atom
  • Use the select tool and Edit => Clear to remove the atom
    (I will admit, I’ve been using the development version for 1.94 and number 2 might need that.)


  • The “auto optimize” tool is gone - it will be a menu command, but it’s not yet finished (debugging that feature takes time)
  • Extensions => Open Babel => Optimize Geometry