Avogadro quit unexpectedly

Hello admin,

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?

It’s hard to know more without the text of the report, which might indicate what exactly is crashing.

Depending on what features you use, you might want to try a nightly build of Avogadro2: https://two.avogadro.cc/ which is what I use on my MacBook.

I can definitely attest that it’ll read 2-3 PDBs or thousands of atoms without breaking a sweat.

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.

Can you please send me the file or a link to the file?

Here it is


Thanks! I’m curious what program created that PDB file. Avogadro should never crash, but it’s very much non-standard which is why there were problems.

There’s a fix for Avo2 here:

In about an 60-90 minutes there should be a link to a Mac build for you added as a comment on that GitHub link.

Thanks @ghutchis. The PDB was created with python using a monomeric unit (created in Avogadro). I will watch out for the fix. See attached error message for Avogadro 1.20 and Avogadro2. Thanks!

Avogadro 1.20 error report

Avogadro2 error report

If a Python program you wrote, I’d suggest a few minor tweaks for compatibility beyond Avogadro:

Thanks @ghutchis. I will follow your advice. Super appreciate it

The Mac build is here:

You should also be able to use a “nightly build” from https://two.avogadro.cc/ fairly soon since the fix has been merged into the main code.