How to generate predicted frame?

[andrewliu2001]

I understand the ground truth frame is generated by taking the two nearest neighbors of each atom. How is the predicted frame generated? Do you perform two nearest neighbors on the predicted coords?

[amorehead]

Please see:

alphafold3-pytorch/alphafold3_pytorch/alphafold3.py

Line 5861 in e54c050

pred_frames, _ = self.rigid_from_three_points(pred_three_atoms)

In short, for polymer (protein, DNA, and RNA) residues, their three residue-specific atom indices are predefined according to each residue's canonical backbone structure. You can read what these predefined indices represented in the AF3 supplement. For ligands, for each heavy atom, first and second nearest neighbors are used to determine the remaining two atom indices to construct a frame. For single-atom ligands such as ions, frames can only be constructed if multiple ions exist in the same chain (asym_id). Otherwise, those ions can't be associated with a frame and won't be trained on w.r.t. PAE.