AlphaFold3 PAE plot for phospho-protein not working

[Stephane.Mouilleron@…]

Hi,
Thank you so much for quickly enabling the visualisation of PAE plot from AF3 in the new version of Chimera. 👍

I can now open the PAE plot for prediction containing DNA, ATP, Ions but it doesn’t seems to work for phosphor-residues.

I attached an example of an AF3 prediction that I can’t open.

Here is the error message I get in ChimeraX:

alphafold pae<help:user/commands/alphafold.html#pae> #1 file "/Users/mouills/Downloads/fold_pp1_neurabin_4ebp1_70pt (1)/fold_pp1_neurabin_4ebp1_70pt_full_data_0.json"
Structure fold_pp1_neurabin_4ebp1_70pt_model_0.cif #1 does not match PAE matrix size 601.The structure has 589 polymer residues and 2 non-polymer atoms

This can happen if chains or atoms were deleted from the AlphaFold model or if the PAE data was applied to a structure that was not the one predicted by AlphaFold. Use the full-length AlphaFold model to show predicted aligned error.

Many thanks

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fold_pp1_neurabin_4ebp1_70pt_full_data_0.json​

fold_pp1_neurabin_4ebp1_70pt_summary_confidences_0.json​

fold_pp1_neurabin_4ebp1_70pt_model_0.cif​

[Stephane.Mouilleron@…]

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[Tom Goddard]

Modified residues are the one case I didn't test. I'll look into it today. I tested glycosylation and it worked and I guessed incorrectly that modified residues would work the same way. Hope to fix it for tonight's ChimeraX daily builds.

[Tom Goddard]

Fixed in May 16 daily build or 1.8 release candidate.

AlphaFold 3 modified residues were not handled correctly by the ChimeraX PAE code. They are polymer residues but with atom-level PAE values. Made the pae plot and alphafold contacts command use atom-level PAE values for those.