Thanks for reporting the problem. Google Colab updated from the Python numpy library from version 1 to version 2 which has broken Colabfold that ChimeraX is trying to run. Colabfold reinstalls numpy version 1 over the default numpy 2, but Python does not get restarted and so it continues to use numpy 2 and fails with the error you saw. I am looking into how to fix this.

On Mar 17, 2025, at 12:46 PM, Charity Conlin via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I am trying to use ChimeraX to predict the interaction of 2 proteins using alphafold: Beta-Lactoglobulin and Lactoferrin. I have plugged the 2 protein sequences into the alphafold tool to try to predict the interaction, but I get a failure code in google colab. I am wondering how I can get around this? I think it is because the wrong versions of numpy and colab are installed during the program.

Thanks,

Charity

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