Error in using alphafold by ChimeraX
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) --------------------------------------------------------------------------- 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
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)
---------------------------------------------------------------------------
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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ChimeraX AlphaFold prediction is fixed now. You do not need to update ChimeraX since the fix was in the script loaded by ChimeraX from Github to run AlphaFold. The problem was that ColabFold was using the latest Biopython and BioPython updated to a new version 1.82 that removed a feature required by AlphaFold. I made it use the previous Biopython 1.81 instead. Thanks for reporting the problem. Tom
On Dec 25, 2023, at 6:13 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)
---------------------------------------------------------------------------
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
-
Ping-Hung Chen 陳炳宏 -
Todd Minehardt -
Tom Goddard