It's deprecated (see https://github.com/biopython/biopython/blob/master/DEPRECATED.rst): [image: image.png] Cheers, Todd On Mon, Dec 25, 2023 at 8:16 PM Ping-Hung Chen 陳炳宏 via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I tried to run Alphafold prediction by ChieraX, and it appears below Error.
Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. INFO:__main__:Starting prediction on 2023-12-26 UTC time INFO:__main__:Installing ColabFold on Google Colab virtual machine. --------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-8-1833a07b73e1> in <cell line: 329>() 327 remove_from_list(seq_list, 'prokaryote') # Obsolete "prokaryote" flag 328 --> 329 run_prediction(seq_list, use_templates = use_templates, energy_minimize = not dont_minimize)
7 frames /usr/local/lib/python3.10/dist-packages/alphafold/data/mmcif_parsing.py in <module> 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)
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Would you like to help me with it?
Thank you.
Sincerely,
PH Ping-Hung Chen, Ph.D., Assistant Professor Institute of Biochemistry and Molecular Biology College of Medicine, National Taiwan University Address: R913, No.1, Sec.1, Ren-Ai Rd., Zhongzheng Dist., Taipei 10051, Taiwan (R.O.C.) E-mail: pinghungchen@ntu.edu.tw; phcrose@gmail.com Phone: +886 2-23123456 Ext. 88864
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