Fig 3. Comparison of PF² fit with other software in synthesized EM fitting at 3Å.

A molecule is fitted into the synthetically generated EM map B with resolution 3Å(transparent green). The top-ranked result 𝓟₁ (red/yellow) is compared to the original PDB molecule 𝓟 (blue). (A) Top-ranked result using PF² fit —SE(3) with 8° uniform rotational sampling and 0.5Å translational step size. RMSD ≈ 0.88Å. (B) Top-ranked result using the Colores package; the ‘nopowell’ option is turned on. RMSD ≈ 3.2Å. (C) Top-ranked result using Colores with default options. RMSD ≈ 2.3Å. The fitted PDB 𝓟₁ is in yellow. (D) Top-ranked result using the ADP_EM package, with bandwidth L = 25. RMSD ≈ 0.94Å.