I have been running Avogadro on Mac for few months and this issue has been a great headache for me. This issue do arise when you try opening 2-3 PDBs (one at a time) or a big molecule with 780 atoms. Please attached image. Could it be that it’s just a MACOSx issue?
Thanks @ghutchis. I have tried opening the PDB (with 780 atoms) with Avogadro2 and was unsuccessful because the software closed immediately. I got the same result with Avogadro (1.20). Meanwhile, I tried opening the same PDB with two windows computer and was successful. Only the strong PC (with 16GB RAM) has all its Avogadro’s GUI functions working appropriately while the other has only it’s Zoom In/Out function active but the navigation tool (F9) button is unresponsive.