Hello,

I am an undergraduate doing research involving protein protein interactions in C. elegans, and I have recently been having some issues with the alphafold contacts command when measuring buried area in protein-protein interfaces. I am running the same batch of dimers that was measured a few years ago with AF2 data, and now with current AF3 data I am seeing vastly different results with the same maxPae, distance values. The main change I noticed with ChimeraX is that the argument in the alphafold contacts command has been changed from “toResidues” to “toAtoms” - is there any reason why this change took place, and would it cause the amount of interacting residues to be measured differently?
Thank you,

Rowan Cain