Thanks Gerardo! I have fixed the error reporting when no ModelCIF pairwise scores are found. You are right that the ChimeraX AlphaFold PAE plotting requires the pairwise score matrix to have rows for each non-polymer atoms. So ChimeraX won't currently plot pairwise scores for Model Archive structures with non-polymer residues. This could be fixed. But as you note the most important case to fix will be for AlphaFold 3 PAE values and currently ModelCIF does not have a table that can handle the mix of per-residue and per-atom PAE values that AlphaFold 3 reports. So let's wait until ModelCIF figures out how to handle AlphaFold 3 PAE scores then we can fix ChimeraX reading those from ModelCIF. I made a ChimeraX ticket for this issue https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16120 Tom
On Oct 11, 2024, at 9:30 AM, Gerardo Tauriello <gerardo.tauriello@unibas.ch> wrote:
Dear Tom,
Checking out the daily build, I noticed that files without local-pairwise values do not have a clean error handling anymore. E.g. "open ma-asfv-asfvg-001 from modelarchive pae true" is an example of a file without local-pairwise values and fails at "metric_id = met_ids[0] if met_ids else values[0][5]" because met_ids is empty in that case...
Also there is a caveat for files like ma-tbvar3d-15 which include a non-polymer. There I think that "alphafold pae" expects per-atom PAE values for the non-polymer and so we end up with a PAE JSON file with a wrongly sized matrix. That one is an edge case within ModelArchive and so it can be considered low priority until we properly handle AF3 PAE matrices in ModelCIF.
Regards, Gerardo