pdbfixer

[brianlross]

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'

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[martin-steinegger]

Do you have an input to reproduce the issue?

[vinbl]

I am having the same issue when I select use_amber. Have you found a solution?