pdbfixer

When trying to run Colabfold from the AlphaFold2.ipynb notebook, after installing the dependcies, I got an error that the module pdbfixer couldn't be found. I tried installing it with !pip and with !apt, but it didn't work. Any thoughts?

47f2ac9d9492616b97fef7051e70caf3289d9fa7
2021-11-28 09:19:27,715 Running colabfold 1.2.0 (47f2ac9d9492616b97fef7051e70caf3289d9fa7)
2021-11-28 09:19:27,719 Found 8 citations for tools or databases
2021-11-28 09:19:36,641 Query 1/1: NGF_daniorerio_cea14 (length 450)
2021-11-28 09:19:52,881 Running model_1
2021-11-28 09:30:30,508 model_1 took 0.0s with pLDDT 91.1

ModuleNotFoundError Traceback (most recent call last)
in ()
34 rank_mode="auto",
35 pair_mode="unpaired+paired",
---> 36 stop_at_score=float(100),
37 )

4 frames
/usr/local/lib/python3.7/dist-packages/alphafold/relax/cleanup.py in ()
20 import io
21
---> 22 import pdbfixer
23 from simtk.openmm import app
24 from simtk.openmm.app import element

ModuleNotFoundError: No module named 'pdbfixer'

Open AlphaFold2.ipynb and review the dependency-installation cells alongside the traceback from alphafold/relax/cleanup.py. Reproduce the missing pdbfixer import in the notebook environment, then verify that the notebook proceeds past the relaxation step without ModuleNotFoundError.