Hi Tony, If you used ChimeraX's AlphaFold predict, there should be a results directory (click Options button on AlphaFold tool to see default location) including both your PDB files and associated other outputs including those with the PAE values. I don't have such results handy but they would probably be named similarly to the PDB files except ending in .json or .npy and you could try opening them with the "open" command, as mentioned briefly here: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#pae> My faint memory was that if you used Alphafold predict in ChimeraX it would automatically "know" which PAE goes with the structures that are automatically opened when the prediction is done, but maybe that is not the case. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 1, 2025, at 2:41 AM, Anthony Newcombe via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello I have a commercial license of ChimeraX, I have a question you may be able to help with I have used Structure prediction > Alphafold to predict structures and interactions between 2 proteins and this returned the best_model.pdb But I would like to identify contacts within 8 angstroms, as shown in the Youtube video: https://www.youtube.com/watch?v=TMcjEecFHaI&list=WL&index=26 I’m typing the command: alphafold contacts /A to /B distance 8 But receive the error: ‘Structure best_model.pdb #1 does not have PAE data opened’ Do I need to open something? If you can help that would be much appreciated Many thanks
Tony Anthony Newcombe PhD Applied Biopharm Consulting Ltd Cork, Ireland www.appliedbiopharm.com IE: +353 (0)87 3634486<image001.png>
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