Avogadro unable to open very big molecule files (8700 something atoms)

Hi, I am wondering if this issue is concerning just my computer or if other people have experienced it before. I am trying to open a molecule under the PBD code name 2hyy which is around 9 thousand molecules large. It renders in other programs like UCSF Chimera but I want to edit it in Avogadro. Every time I open it, Avogadro unexpectedly crashes and it outputs this error message.

Termination Reason: Namespace SIGNAL, Code 10 Bus error: 10
Terminating Process: exc handler [20379]

I have the latest version of Avogadro and the file isn’t corrupted so I was wondering if there was an issue with the memory because of how large the file is.

It would be really helpful to know what OS you’re using (and version) and what specific version of Avogadro you’re using.

Also, are you trying to load 2hyy from a file? If so can you post a link to it? Or are you using the “Download from PDB” feature?

There’s absolutely no problem loading a few thousand atoms. (Unless you really mean 9000 molecules, in which case I’m unclear on what you’re trying to do.)

Hi, thank you for replying, I am using macOS Sonoma 14.5. I downloaded the lastest version – Avogadro 1.2.0 and I am downloading from the button on the PDB website says “Download from PDB” I want to view and edit this protein for research purposes, but every time I open it, the Avogadro app just terminates.

Try a nightly build of Avogadro 1.99:

Thank you so much, it rendered! I have to ask though, is there a way to translate the app from Spanish to English?

If you’re seeing it in Spanish, you have set your system language with Spanish, but it’s possible to override the localization in 1.99:

Extensions ⇒ User Interface Language…

Thank you so much, I really do appreciate your help on this matter and I will now be able to successfully complete my research tasks! Again, I appreciate your time!

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