Add pLDDT scores to structures predicted by the AlphaFold2

alphafold_plddt2pdb.py

import prody
import dill  # or pickle

# Read AF2 output
with open('result_model_1.pkl', 'rb') as f:
    af = dill.load(f)

# Parse PDB structure
pdb = prody.parsePDB('relaxed_model_1.pdb')

# Assign per-residue pLDDT scores as B-factors
for r in pdb.iterResidues():
    r.setBetas(af['plddt'][r.getResnum() - 1])

# Save output PDB file
prody.writePDB('relaxed_model_1_plddt.pdb', pdb)

# To color structure in PyMOL in the AF colorscheme use command
# spectrum b, rainbow_rev