Hi Catrin, 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 K560_dimer_MAP7_Fragment_581_783_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb and the predicted aligned error file for that structure is named K560_dimer_MAP7_Fragment_581_783_scores_rank_001_alphafold2_multimer_model_3_seed_000.json 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

<K560_dimer_MAP7_Fragment_581_783_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb><K560_dimer_MAP7_Fragment_581_783_predicted_aligned_error_v1.json>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/