id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project
15214 AlphaFold3 with ligands PAE json file: number of structure residues does not match matrix size rob.klose@… Tom Goddard "{{{
To whom it may concern:
When I load new alphafold3 predictions into chimera x and try to load the json files to look at PAE data I get the following error:
Structure fold_2024_05_09_15_13_cfp1_with_h3k4me3nuclesome_model_0.cif #1 does not match PAE matrix size 2020.The structure has 1998 polymer residues and 0 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.
It seems to only occur when I have post translational modifications in the prediction. Is there a fix for this?
Best wishes
Rob
Rob Klose
Professor of Genetics
Department of Biochemistry and Keble College
University of Oxford
www.kloselab.co.uk
PA:
Sarah-jane Scard
Sarah-jane.scard@bioch.ox.ac.uk
Tel: 01865 613212
}}}
" defect closed normal Structure Prediction duplicate all ChimeraX