Download skills/bionemo-rfdiffusion-nim/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does rfdiffusion-nim live?
The publisher keeps it at https://github.com/NVIDIA/skills.
Which agents can use rfdiffusion-nim?
Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.
>
name: rfdiffusion-nim
description: >
Run RFDiffusion protein backbone design via NVIDIA NIM. Use for de novo protein backbones, motif scaffolding, binder design, hotspot residues, contigs syntax, diffusion steps, hosted NVIDIA API calls, local Docker deployment, and PDB backbone outputs for ProteinMPNN sequence design.
license: Apache-2.0 AND CC-BY-4.0
compatibility: "requests>=2.28"
allowed-tools: Bash, Read, Write, AskUserQuestion
RFDiffusion NIM
Design protein backbone PDBs for de novo proteins, motif scaffolds, and binders.
Use this guide for first-pass hosted/local usage; load supplemental files
only when needed:
Local inference paths do not include /v1/. Hosted requests use Authorization: Bearer $NGC_API_KEY. Supported local Docker
startup uses NGC_API_KEY (or NVIDIA_API_KEY via the preflight) for
registry login, entitlement checks, and first-run model downloads; pass it
into the container with -e NGC_API_KEY. Local inference requests use no
auth header after readiness. Warm-cache key-free startup varies by
image/version and should not be assumed.
Local Docker
For local setup answers, copy the preflight below exactly before docker login,
docker run, readiness, and the no-auth local request. Do not replace it with a
simple : "${NGC_API_KEY:?Set NGC_API_KEY}" check, do not invent a cache
default, and do not drop the NVIDIA_API_KEY fallback. Default setup is single
GPU device=0.
set -a
[ -f .env ] && . ./.env
set +a
if [ -z "${NGC_API_KEY:-}" ] && [ -n "${NVIDIA_API_KEY:-}" ]; then
export NGC_API_KEY="$NVIDIA_API_KEY"
fi
: "${NGC_API_KEY:?Set NGC_API_KEY or NVIDIA_API_KEY}"
: "${LOCAL_NIM_CACHE:?Set LOCAL_NIM_CACHE}"
echo "$NGC_API_KEY" | docker login nvcr.io --username '$oauthtoken' --password-stdin
mkdir -p "${LOCAL_NIM_CACHE}"
chmod 755 "${LOCAL_NIM_CACHE}"
docker run -it \
--runtime=nvidia \
--gpus "device=0" \
-e NGC_API_KEY \
-v "${LOCAL_NIM_CACHE}:/opt/nim/.cache" \
-p 8000:8000 \
nvcr.io/nim/ipd/rfdiffusion:2
Readiness:
until curl -sf http://localhost:8000/v1/health/ready; do sleep 5; done
Contigs DSL
contigs defines what to keep and what to generate. For the full pattern
syntax (fixed length, ranges, kept chain segments, chain breaks), see
references/api.md under Contigs Language Reference.
Design modes:
De novo: contigs="80-120"; live hosted validation requires a non-empty
input_pdb or input_pdb_asset, so inline requests should include the dummy
PDB below.
Motif scaffolding: read target.pdb, pass input_pdb, use a contig like
"A25-35/0 50-80".
Binder design: pass target input_pdb, contig with target and binder segment,
and hotspot_res=["A50", "A51", ...] in ChainResidue string format.
DUMMY_PDB = (
"CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1\n"
"ATOM 1 CA ALA A 1 0.000 0.000 0.000 1.00 0.00 C\n"
"END\n"
)
Save result["output_pdb"] as a PDB artifact and report elapsed_ms when
present. Generated backbones are not final proteins; feed them to ProteinMPNN
for sequence design, then validate sequences/structures with Boltz2 or
OpenFold3. For PDB and contig checks, read references/validation.md.
Limits And Troubleshooting
diffusion_steps: 1-50; 50 is maximum quality, fewer is faster.
Single GPU; minimum GPU VRAM is about 12 GB.
hotspot_res uses strings like "A50", not tuples.
422 usually means chain IDs in contigs/hotspot_res do not match
input_pdb, a malformed contig, or omitted input_pdb for hosted de novo.
Local URL 404 usually means an accidental /v1/ prefix.
How do I install rfdiffusion-nim?
Download skills/bionemo-rfdiffusion-nim/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does rfdiffusion-nim live?
The publisher keeps it at https://github.com/NVIDIA/skills.
Which agents can use rfdiffusion-nim?
Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.