Hello Haley, Our expert is away right now but I'll try to answer with what I observed when running a multimer prediction from within ChimeraX (today's daily build) just now:

(1) the JSON files in the ~/Downloads/ChimeraX/AlphaFold/prediction_N directories have ptm and iptm values, they appear to be at the very end of each file.

(2) the ColabFold results in the browser window include pTM and ipTM scores. See for example this screenshot of the end of my run

These appear to be evaluated repeatedly while the structures are being refined, and I would expect the final value for each structure to match what is given at the end of the corresponding JSON file. They did in the one case that I spot-checked in my results.

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 Mar 27, 2024, at 11:05 AM, Haley V Goodwin via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hello! I am using ChimeraX to use AlphaFold Multimer. I have read from a couple of places that AF provides pTM and ipTM scores to evaluate the quality of the models. I was wondering how I access these values from ChimeraX. I have looked through the results zip file, but can’t seem to find where these values may be stored.

Thank you so much for your help! Best, Haley Goodwin