pair_chains_iptm score returned when folding a single chain

[avaektefaie]

When I run Boltz with a single protein subunit (no multiple chains) and a ligand I still get a pair_chains_iptm score and other scores associated with chain interaction. Why is this the case when I'm only using one protein chain?

[gcorso]

You can have an ipTM score even across non-polymer entities. This is computed by constructing frames for atoms in the molecule. You can take a look at the AlphaFold3 supplementary material for more information about how these are constructed.