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Use when working directly with the `esm` Python SDK, ESM3 or ESMC model IDs, Forge/Biohub inference clients, or ESMFold2 folding workflows.
Passed 24 of 24 test cases with the skill, and 13 of 24 without it.
and 13 more in the full report
11 fixed13 passed either way0 still failing0 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 11 test cases the skill fixed. Same model, same prompt, with and without the skill.
When calling structure export or selection methods on an ESM3 structure object, what is the default chain identifier selected if no explicit chain identifier is specified?
| Checked | Without skill | With skill |
|---|---|---|
| The response states that the default chain selection identifier is "all". | Missed | Passed |
The instructions your model reads when the skill loads.
Use for Biohub's esm SDK: ESM3 masked multimodal generation, ESMC sequence
representations, and ESMFold2 all-atom prediction. The former Forge platform
migrated to https://biohub.ai, including ESM3; SDK class names still contain
Forge. This skill targets the released esm 3.4.1.post1, verified against
its wheel and current official documentation.
fair-esm is Meta's separate, older ESM2/ESMFold/ESM-IF distribution. Both
packages import as esm; install them in separate environments. The legacy
esm.pretrained.esm2_* interface is not the Biohub ESMC interface. Hugging Face
Transformers' native ESMC implementation is another API: do not interchange its
version requirements or output types with this SDK.
uv venv --python 3.12 .venv-esm
uv pip install --python .venv-esm/bin/python "esm==3.4.1.post1"
The release declares Python >=3.12, Torch >=2.11,<2.12 and Transformers
=4.57.6,<5. Python 3.12, Torch 2.11.0 and Transformers 4.57.6 were tested on CPU. Linux x86_64 installs include GPU-specific dependencies; use a supported inference machine and budget disk space. Flash Attention is optional; it is unnecessary for the tiny CPU tests. Do not install this stack into a shared environment containing incompatible Transformers or Torch pins.
| Task | Local model/API | Hosted client/model |
|---|---|---|
| ESM3 sequence/structure/function generation | ESM3.from_pretrained("esm3-sm-open-v1") | client("esm3-medium-2024-08"); small/large IDs in the ESM3 reference |
| ESMC embeddings | EsmcForMaskedLM and EsmcTokenizer; biohub/ESMC-300M, biohub/ESMC-600M, biohub/ESMC-6B | esmc_client("esmc-600m-2024-12"); 300M/6B also documented |
| ESMFold2 all-atom structures | EsmFold2Model, ESMFold2InputBuilder; biohub/ESMFold2 | esmfold2_client("esmfold2-fast-2026-05") |
ESMC 6B weights are now available locally. Current Biohub model cards identify
MIT licensing, with ESMC cards also linking third-party notices; review the
exact selected artifact's card and access requirements.
The older ESMC class remains as a deprecated compatibility wrapper. Local
test cases passed, vs 13 / 24 without
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