--- name: xuzhougeng/openfold3 source: https://app.decimal.ai/s/xuzhougeng-openfold3@1/SKILL.md source_sha256: 4cc3d44f8a52 --- # OpenFold3 Structure Prediction ## Prerequisites | Requirement | Minimum | Recommended | | ----------- | ------- | ----------- | | Python | 3.10+ | 3.11 | | CUDA | 12.1+ | 12.4+ | | GPU VRAM | 24GB | 80GB (H100) | | RAM | 32GB | 64GB | | Disk (weights) | 3GB | - | ## How to run ### Installation ```bash pip install 'openfold3[cuequivariance]==0.4.1' ``` The default attention kernel is DeepSpeed `DS4Sci_EvoformerAttention`. If DeepSpeed is unavailable, switch to the cuEquivariance triangle kernels (no build-from-source) by overriding the eval memory settings in `model_config.py` (`use_deepspeed_evo_attention: False`, `use_cueq_triangle_kernels: True`). Some pre-built environments already ship this override; check before re-patching. ### Weights Apache-2.0, ~2.3 GB from HF `OpenFold/OpenFold3`. The repo is **gated** (auto-approval) — accept the access form on the HF model page and authenticate (`huggingface-cli login` or `HF_TOKEN`) before downloading: ```bash export OPENFOLD_CACHE=~/.openfold3 huggingface-cli download OpenFold/OpenFold3 checkpoints/of3-p2-155k.pt \ --local-dir "$OPENFOLD_CACHE" ``` `run_openfold` will also auto-download to `$OPENFOLD_CACHE` on first run if egress is open and HF credentials are available (either `HF_TOKEN` or a prior `huggingface-cli login`) with repo access granted. The interactive `setup_openfold` helper exists but prompts on stdin; prefer the explicit download above for non-interactive runs. ### Running ```bash export OPENFOLD_CACHE=/path/to/cache run_openfold predict \ --query_json=queries.json \ --output-dir out/ \ --use-msa-server false \ --use-templates false ``` `run_openfold` discovers the checkpoint under `$OPENFOLD_CACHE` automatically. Only pass `--inference-ckpt-path ` if you have a non-standard layout or multiple checkpoints and need to pin one explicitly. For MSA + templates (slower, higher accuracy), drop the two `false` flags. The MSA server is `api.colabfold.com`; template chain-ID remap hits `data.rcsb.org` (GraphQL) — both must be reachable. ## Query JSON format OpenFold3 does **not** read FASTA. Queries are a JSON object validated by `InferenceQuerySet` (pydantic, `extra: forbid` — unknown keys reject): ```json { "queries": { "my_complex": { "chains": [ {"molecule_type": "protein", "chain_ids": ["A"], "sequence": "MQIFVK…"}, {"molecule_type": "protein", "chain_ids": ["B", "C"], "sequence": "MVLSPA…"}, {"molecule_type": "ligand", "chain_ids": ["L"], "smiles": "CC(=O)Oc1ccccc1C(=O)O"} ], "use_msas": true } }, "seeds": [42] } ``` | `molecule_type` | required field | | -------- | ---- | | `protein` / `dna` / `rna` | `sequence` | | `ligand` | `smiles` **or** `ccd_codes: ["HEM"]` | `chain_ids` is a list — repeat the same sequence across multiple chain IDs for homo-oligomers. Per-chain `paired_msa_file_paths` / `main_msa_file_paths` let you supply your own a3m instead of the server. ## Key parameters | Flag | Default | Description | | ---- | ------- | ----------- | | `--num-diffusion-samples` | 5 | Structures per (query, seed) | | `--num-model-seeds` | 1 | Number of model seeds per query (multiplies output count alongside JSON `seeds` and diffusion samples) | | `--use-msa-server` | true | ColabFold MMseqs2 server for MSA | | `--use-templates` | true | ColabFold template search + RCSB remap | | `--inference-ckpt-path` | auto-discovered under `$OPENFOLD_CACHE` | Override only — for non-standard layouts or to pin a specific checkpoint file | ## Wisp execution Use `python` only for bounded interactive checks. For a long or GPU-backed workload, require a selected and probed `ssh:` context and load `remote-compute-ssh`. Put the documented invocation in a self-contained project script, activate the remote environment explicitly, stage only small files with `input_paths`, and make the command write to a known absolute remote result path. Submit it with `run_in_context` and register that exact `ssh://` path in `output_specs`. Call `monitor_run` once when waiting is needed, `get_run` once for a snapshot, or `cancel_run` to stop. Do not send a scheduler submission through the SSH-direct runner. ## Output format ``` out/ ├── summary.txt ├── model_config.json / experiment_config.json ├── inference_query_set.json └── /seed_/ ├── _seed__sample__model.cif ├── _seed__sample__confidences.json # full PAE/pLDDT ├── _seed__sample__confidences_aggregated.json └── timing.json ``` `*_confidences_aggregated.json` is the small one to read first: ```json { "avg_plddt": 78.96, "ptm": 0.667, "iptm": 0.0, "gpde": 0.73, "has_clash": 0.0, "sample_ranking_score": 0.133, "chain_ptm": {"A": 0.667}, "chain_pair_iptm": {} } ``` ## What good output looks like - `summary.txt` shows `Successful Queries: N` matching your input count - avg_plddt > 70 (single-seq) / > 80 (with MSA) - ptm > 0.6; for complexes, iptm > 0.5 - `has_clash: 0.0` - `.cif` ~50-150 KB per sample for a small protein ## Verify ```bash grep -E 'Successful|Failed' out/summary.txt find out -name '*_model.cif' | wc -l # = queries x json_seeds x num-model-seeds x num-diffusion-samples ``` --- ## Troubleshooting | Error | Cause | Fix | | ----- | ----- | --- | | `_deepspeed_evo_attn requires that DeepSpeed be installed` | default eval kernel is DS4Sci on CUDA | install `deepspeed` (needs nvcc + CUTLASS), **or** in `model_config.py` eval block set `use_deepspeed_evo_attention: False` + `use_cueq_triangle_kernels: True` (cuEq path; no build) | | `CUTLASS_PATH ... not set ... cutlass_library is not installed` | cuEq path still needs the python `cutlass_library` shim | `pip install nvidia-cutlass` | | `libXrender.so.1: cannot open shared object file` | rdkit (via pdbeccdutils) needs X11 render libs | `apt-get install libxrender1 libxext6 libsm6` | | `ModuleNotFoundError: boto3` (or `awscrt`) | `openfold3.core.data.io.s3` is eager-imported even when weights are local | `pip install boto3 awscrt` | | `ValidationError: queries / Field required` or `Input should be an object` | wrong JSON shape | top-level is `{"queries": {"": {...}}}` (a dict, not a list) | | `ValidationError ... settings / Extra inputs are not permitted` | tried to override model config via `--runner-yaml` | `--runner-yaml` is `InferenceExperimentConfig` only; kernel/memory settings live in `model_config.py` | | `Failed to fetch chain ID mappings from RCSB for N entries` | `data.rcsb.org` unreachable (allowlist/offline) | run with `--use-templates false`, or open egress to `data.rcsb.org` | | `CUDA out of memory` | large complex / many samples | reduce `--num-diffusion-samples`; the `low_mem` preset (`model_setting_presets.yml`) offloads more aggressively |