[chimerax-users] AlphaFold July 2022 update to PAE json file - cannot open PAE file with ChimeraX.

[Brandon Payliss]

Hi there,

I’m having some issues loading the PAE JSON file from a recent AlphaFold multimer prediction into ChimeraX, generated using a Colab notebook. The warning message is as follows:

JSON file "./predicted_aligned_error.json" is not AlphaFold predicted aligned error data, expected a dictionary with keys "residue1", "residue2" and "distance"

It appears that AlphaFold reduced their JSON file size by 4X on July 28th 2022 (https://alphafold.ebi.ac.uk/faq) and it no longer uses “distances”, “residue 1” and “residue 2” keys.

Just curious, will there be an update coming to ChimeraX to support the new JSON file format from AlphaFold?

Thanks for your time!

Best,
Brandon


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