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

[Tom Goddard]

Hi Brandon,

  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.

	Tom


> On Sep 20, 2022, at 12:47 PM, Brandon Payliss via ChimeraX-users <chimerax-users at 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 28th 2022 (https://alphafold.ebi.ac.uk/faq <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
>  
>  
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20220921/66a62f2c/attachment.html>