id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15225 AlphaFold3 PAE plot for phospho-protein not working Stephane.Mouilleron@… Tom Goddard "{{{ 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 #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 I frequently send e-mails outside of standard working hours. Please do not feel obliged to respond at times that are not within your working hours. ________________________ Dr Stephane Mouilleron Staff Scientist Structural Biology Science technology Platform The Francis Crick Institute 1 Midland Road London NW1 1AT ________________________ Email: stephane.mouilleron@crick.ac.uk Web: https://www.crick.ac.uk/research/find-a-researcher/stephane-mouilleron Twitter: https://twitter.com/StephCrystalLab LinkedIn: https://www.linkedin.com/feed/?trk=homepage-basic_sign-in-submit The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT }}} [attachment:""fold_pp1_neurabin_4ebp1_70pt_full_data_0.json""] [attachment:""fold_pp1_neurabin_4ebp1_70pt_summary_confidences_0.json""] [attachment:""fold_pp1_neurabin_4ebp1_70pt_model_0.cif""] " defect closed normal Structure Prediction fixed all ChimeraX