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sokrypton / ColabFold

Making Protein folding accessible to all!
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AF2 with MMseqs2 ColabFold crash: unable to find SCOPdata #540

Open jfbazan opened 10 months ago

jfbazan commented 10 months ago

This is fairly new, having run ColabFold 1.5.3 (the workhorse AF2 w/ MMseqs version) quite well last night, but the first job this morning crashed at the "Run Prediction" stage with the following error message––that centers on the inability to load SCOPdata, an interesting dependency that I wasn't aware of! Just in case, I restarted and ran clean ColabFolds twice, and the error recurred exactly as the first time. Thx in advance for your kind help!

ImportError Traceback (most recent call last) in <cell line: 12>() 10 from colabfold.download import download_alphafold_params, default_data_dir 11 from colabfold.utils import setup_logging ---> 12 from colabfold.batch import get_queries, run, set_model_type 13 from colabfold.plot import plot_msa_v2 14

5 frames /content/alphafold/data/mmcif_parsing.py in 22 from absl import logging 23 from Bio import PDB ---> 24 from Bio.Data import SCOPData 25 26 # Type aliases:

ImportError: cannot import name 'SCOPData' from 'Bio.Data' (/usr/local/lib/python3.10/dist-packages/Bio/Data/init.py)

milot-mirdita commented 10 months ago

We are fixing the issue by downgrading biopython. Will deploy a real fix soon afterwards!

jfbazan commented 10 months ago

Patch seems to work! Many thanks, Milot!

pdeepakb commented 10 months ago

Hi @jfbazan,

How did you patch the issue? It would be helpful to know.

Thanks, Deepak

sokrypton commented 10 months ago

@pdeepakb Make sure you are using the latest notebook.

pdeepakb commented 10 months ago

@sokrypton Hi,

I'm using this one https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb

can you point me to the newer version?

Thanks, Deepak

KevinZhang97 commented 10 months ago

I have met the same question, and I find the reason. From file of biopython , I found this: 

Bio.Data.SCOPData
Declared obsolete in release 1.80, and removed in release 1.82. Please use Bio.Data.PDBData instead.

So I downgraded biopython (to 1.79) in Conda. And it works.