Beginning yesterday, I have had repeated failure of alphafold2_multimer running through chimerax to generate models of two protein complexes (Ab H cand L chains, for instance). Individual chains work fine. The error from Colab AI says: The error is due to a bug in the ColabFold library. The kabsch function in the colabfold.py file is using the linalg.svd function to calculate the singular value decomposition of a matrix. However, the linalg.svd function is not guaranteed to converge, and in some cases it can fail to converge. This can cause the kabsch function to fail, and in turn cause the plot_protein_backbone function to fail. The bug has been fixed in the latest version of the ColabFold library, which is available on GitHub. To fix the error, you can upgrade to the latest version of the library. You can do this by running the following command in the Colab notebook: content_copy !pip install colabfold --upgrade Use code with caution<https://g.co/legal/generative-code> Once you have upgraded to the latest version of the library, you can run the code again and the error should be fixed. Can you advise? Thanks for your help. D David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bldg. 10; Room 11D12 10 Center Drive Bethesda, MD 20892-1892 Email: dmargulies@niaid.nih.gov<mailto:dmargulies@niaid.nih.gov>, dhm@nih.gov<mailto:dhm@nih.gov> Ph: 301-496-6429 Fax: 301-480-7352 Web: https://www.niaid.nih.gov/research/david-margulies-md-phd “Public service is a public trust, requiring employees to place loyalty to the Constitution, the laws, and ethical principles above private gain.” – executive order 12674, https://www.federalregister.gov/documents/2016/02/17/2016-03214/standards-of-ethical-conduct-for-employees-of-the-executive-branch-amendments-to-the-seeking-other<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.federalregister.gov_documents_2016_02_17_2016-2D03214_standards-2Dof-2Dethical-2Dconduct-2Dfor-2Demployees-2Dof-2Dthe-2Dexecutive-2Dbranch-2Damendments-2Dto-2Dthe-2Dseeking-2Dother&d=DwQGaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=l0C00BzgumWhrcADIiRNk0NykXTo-eQNBsvVQSn82eU&m=Xu3ShQxkydr5vec1aiRAJ-KIzr11BxQFoCW48t85Jxwrnj72v3rTB0i4MZ2Dpp4B&s=gIPjwBT-XXnjJoJcbjhVDoCMpDe7SVg_N-0OjPOkG5g&e=> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender’s own and not expressly made on behalf of the NIAID by one of its representatives.
Hi David, Thanks for reporting the problem. I have fixed ChimeraX AlphaFold prediction. The fix was in the Google Colab script which ChimeraX downloads when run so it does not require updating ChimeraX. The problem arose because Google Colab updated its Nvidia CUDA library version from 11 to 12, and that required an update in a library called jax used to run AlphaFold jobs on the GPU, and the newer jax library introduced this bug. I found the ColabFold developers had patched this bug and I used their patch. ColabFold is an optimized version of AlphaFold that ChimeraX uses for predictions and I updated it to the current November 1, 2023 Colabfold code on github. Tom
On Nov 8, 2023, at 7:41 AM, Margulies, David (NIH/NIAID) [E] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Beginning yesterday, I have had repeated failure of alphafold2_multimer running through chimerax to generate models of two protein complexes (Ab H cand L chains, for instance). Individual chains work fine. The error from Colab AI says:
The error is due to a bug in the ColabFold library. The kabsch function in the colabfold.py file is using the linalg.svd function to calculate the singular value decomposition of a matrix. However, the linalg.svd function is not guaranteed to converge, and in some cases it can fail to converge. This can cause the kabsch function to fail, and in turn cause the plot_protein_backbone function to fail.
The bug has been fixed in the latest version of the ColabFold library, which is available on GitHub. To fix the error, you can upgrade to the latest version of the library. You can do this by running the following command in the Colab notebook:
content_copy !pip install colabfold --upgrade Use code with caution <https://g.co/legal/generative-code> Once you have upgraded to the latest version of the library, you can run the code again and the error should be fixed.
Can you advise? Thanks for your help.
D
David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bldg. 10; Room 11D12 10 Center Drive Bethesda, MD 20892-1892
Email: dmargulies@niaid.nih.gov <mailto:dmargulies@niaid.nih.gov>, dhm@nih.gov <mailto:dhm@nih.gov> Ph: 301-496-6429 Fax: 301-480-7352 Web: https://www.niaid.nih.gov/research/david-margulies-md-phd
“Public service is a public trust, requiring employees to place loyalty to the Constitution, the laws, and ethical principles above private gain.” – executive order 12674, https://www.federalregister.gov/documents/2016/02/17/2016-03214/standards-of... <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.federalregister.gov...>
Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender’s own and not expressly made on behalf of the NIAID by one of its representatives.
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participants (2)
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Margulies, David (NIH/NIAID) [E] -
Tom Goddard