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Known Issues

Numerical performance for CUDA Capability 7.x GPUs

All CUDA Capability 7.x GPUs (e.g. V100) produce obviously bad output, with lots of clashing residues (the clashes cause a ranking score of -99 or lower), unless the environment variable XLA_FLAGS is set to include --xla_disable_hlo_passes=custom-kernel-fusion-rewriter.

Incorrect handling of two-letter atoms in SMILES ligands

Between commits https://github.com/google-deepmind/alphafold3/commit/f8df1c7 and https://github.com/google-deepmind/alphafold3/commit/4e4023c, AlphaFold 3 handled incorrectly any two-letter atoms (e.g. Cl, Br) in ligands defined using SMILES strings.