Huh. Those are built-in to Avogadro2, but none of the Open Babel formats are available.
If you Control-click the App you downloaded, thereās āShow Package Contentsā and you can see the paths inside the binary. It should look like this:
In Contents => MacOS there should also be an obabel binary.
Assuming all of that checks out (and it should - we downloaded the same package), Iād want you to run it from the Terminal to see what kind of error messages come up, something like:
I get an error message āzsh: permission deniedā. Sorry for the block-headed message, but Iām new at this. Do you have any suggestion for a workaround so that I can check the error messages you suggested?
Iāll guess that the various file formats were there under Contents => lib => openbabel as well?
Is that the path that you installed that build of Avogadro2?
Like if you left it in Downloads, it might be ~/Downloads/Avogadro2.app/Contents/MacOS/Avogadro
Put another way, you can save yourself some typing if zsh auto-completes the path for you. /App + [tab] => /Applications => Avogadro2 + [tab] = /Applications/Avogadro2.app/
If you can tab-complete the path, you should be able to run the program from the Terminal.
If that doesnāt work, letās find time to check this over Zoom. Iām really confused why itās not finding the Open Babel formats and itās kind of a problem (i.e., Avogadro2 will be missing a lot of features).
Looks like I can only upload images here, but feel free to email me (redacted) if youād like a readout of all of the messages, or I can post it here even though itās quite long.
I can verify that CIF files are an option in the file type list and I can open them in this build. Thanks for the prompt reply.
Now, off to figure out how to build some supercells.
One difference I see is that in v1.20, the Super Cell Builder function adds atoms with the bonds displayed. In v1.94 (Avogadro2) using the Build Supercell adds atoms without bonds (the only bonds showing are for the original unit cell). I can select Bond Atoms but, with the default parameters, unphysical bonds are added (e.g. Ti-Ti bonds in TiO2).