import error in AF_cluster colab notebook

[palvinaveen]

Hi,
while executing the colab notebook following error is coming
ImportError: cannot import name 'SCOPData' from 'Bio.Data' (/usr/local/lib/python3.10/dist-packages/Bio/Data/init.py)
could you help me out why it cannot import SCOPData in colab notebook.

ImportError Traceback (most recent call last)
in <cell line: 17>()
15
16 from alphafold.model import model, config, data
---> 17 from alphafold.data import parsers, pipeline
18 from alphafold.common import protein
19

2 frames
/content/alphafold/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)

Thank you
Best
Naveen

[hiyata]

Hi @palvinaveen the package is depreciated, but I was able to solve this by uninstalling biopython and reinstalling an older version. I made two cells.

First:

!pip uninstall biopython

Next:

!pip install http://biopython.org/DIST/biopython-1.81.tar.gz

Restart the runtime when prompted and then the cell should run!

[AhmedHassanin-IPB]

I did the same with older version of biopython==1.78, and now is working.