Yes, the latest EBI AlphaFold database release changed the format of the PAE json files on July 28 to reduce their size so the last ChimeraX release (1.4) which came out before that change in June does not know how to read them. But the ChimeraX daily build since July 29 reads them correctly. So get the daily build on the ChimeraX download page.

On Sep 20, 2022, at 12:47 PM, Brandon Payliss via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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 28^th 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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