The file JSON predicted aligned error file you are trying to open is not the right file. This is confusing. Your predicted structure file is named
with the "unrelaxed" in the structure file replaced by "scores". Each of the 5 predicted structures has its own PAE file (rank_001, rank_002, ... rank_005 in the file name). If you use ChimeraX menu entry Tools / Structure Prediction / AlphaFold Error Plot it will find the correct PAE file for you.
The file you tried to open that failed
K560_dimer_MAP7_Fragment_581_783_predicted_aligned_error_v1.json
is actually a copy of the same same PAE data for the rank_001 prediction but using a slightly different file format (it uses a dictionary key "predicted_aligned_error" while the score files use the key "pae". I'm not sure why ColabFold decided to write this single rank_001 file in a different format. And I'm surprised I never noticed this problem before. I have made ChimeraX daily builds starting tomorrow accept this alternate format.
Tom
On Aug 30, 2024, at 4:15 AM, Catrin McHugh via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Good morning
Having successfully generated a PAE plot (and coloured the model accordingly) with data generated by AF3, I am getting an error message when I try to do the same using a JSON file generated by ColabFold for AF2. The error message is: 'is not AlphaFold predicted aligned error data, expected a top level list". I attach the JSON file, and the relevant structure PDB.
Many thanks in advance
Catrin
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