http://wiki.docking.org/index.php?action=history&feed=atom&title=Openfold3 2026-04-06T21:38:00Z Revision history for this page on the wiki MediaWiki 1.39.1 http://wiki.docking.org/index.php?title=Openfold3&diff=16999&oldid=prev 2025-11-25T17:30:03Z

<p>openfold3</p> <p><b>New page</b></p><div>Hey everyone, I installed OpenFold3 on Gimel and tested it on epyc-A40. This command should work to activate the environment<br /> source /mnt/nfs/home/ak87/miniconda3/envs/openfold /mnt/nfs/home/ak87/miniconda3/envs/openfold<br /> then run<br /> run_openfold predict --query_json=test.json --use_templates false<br /> The json format is identical to AlphaFold’s. You can find the manual here:<br /> https://openfold-3.readthedocs.io/en/latest/Inference.html<br /> I’ve got an IndexError error without --use_templates false . I’m unsure why it is happening. If you find the fix, please LMK<br /> The prediction took ~20 min.<br /> ChimeraX couldn’t color the structure by the confidence metrics.<br /> If you want to set your own environment, here are the commands I used to do it<br /> mamba create --name openfold python=3.11<br /> mamba activate openfold<br /> mamba install -c nvidia -c conda-forge cuda-toolkit=12.8 cuda-nvcc=12.8 -y<br /> pip install openfold3<br /> pip install pytest # for integration tests<br /> setup_openfold<br /> mamba install -c bioconda kalign3 -y<br /> <br /> thanks to Andrii</div>

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