Openfold3

Hey everyone, I installed OpenFold3 on Gimel and tested it on epyc-A40. This command should work to activate the environment source /mnt/nfs/home/ak87/miniconda3/envs/openfold /mnt/nfs/home/ak87/miniconda3/envs/openfold then run

run_openfold predict --query_json=test.json --use_templates false

The json format is identical to AlphaFold’s. You can find the manual here: https://openfold-3.readthedocs.io/en/latest/Inference.html I’ve got an IndexError error without --use_templates false . I’m unsure why it is happening. If you find the fix, please LMK The prediction took ~20 min. ChimeraX couldn’t color the structure by the confidence metrics. If you want to set your own environment, here are the commands I used to do it

mamba create --name openfold python=3.11
mamba activate openfold
mamba install -c nvidia -c conda-forge cuda-toolkit=12.8 cuda-nvcc=12.8 -y
pip install openfold3
pip install pytest # for integration tests
setup_openfold
mamba install -c bioconda kalign3 -y

thanks to Andrii