RFdiffusion3

5-30 minutesPaperCodeNeed >5GB

All atom protein design with atom-level and residue-level motif scaffolding

Job Name

EXAMPLES

Task *PDB/CIF File *Target ChainsHotspotsLigands

Binder Length minBinder Length maxNumber of DesignsScaffolding ModeAtoms to fix in motifMotif Atoms to FixInterface ChainInterface ResiduesDesigned LengthsOri TokenLigand Atom Conditions

JSON Input TypeRFD3 Config JSON FileRFD3 Config JSON StringInput Structure Files

Non-loopy conditioning Classfier-free guidanceunindexStep ScaleGamma 0

Readiness

Readiness: Need >5GB
Smoke: passed
Artifacts: passed
Production: need_gt5gb_foundry_slim_sif_checkpoint_pending
Storage: 5-20GB
Strategy: Use official Foundry container/image or build a Foundry-specific SIF; cache RFD3 checkpoints under shared Foundry checkpoint directory.
Next: Pull Foundry slim SIF, run foundry install rfd3 into /media/nik/seagate_nik/bio_server/cache/foundry/checkpoints, validate demo design, then wire rfdiffusion3 adapter.

generative structure/design model weights likely >5GB 2026-07-17T01:18:00+08:00 SOP Need >5GB next-10 audit: remains Need >5GB. Local registry maps to rfdiffusion3-smoke and cluster_tools routes it to generic genie_backbone_smoke; backend shared storage had no RFdiffusion3/foundry source, checkpoint, SIF, or model assets under /media/nik/seagate_nik/bio_server or /home/nik. Real runtime/checkpoints must be staged before adapter work. 2026-07-18T21:37:01+08:00 SOP Need >5GB batch source-staging: Official Foundry repo cloned to backend /media/nik/seagate_nik/bio_server/repos/foundry at 551a901 (311MB). Agent audit confirmed public Foundry docs and `foundry install rfd3 --checkpoint-dir` path; no Foundry image/checkpoint cache/SIF yet. 2026-07-18T22:34:12+08:00 SOP Need >5GB continuation batch: No new runtime build completed in this continuation. Foundry source remains staged; next production step remains official Foundry image/SIF plus RFD3 checkpoint install and sample design. 2026-07-19T23:00:00+08:00 SOP Need >5GB active install continuation: Foundry/RFD3 should stay separate from classic RFdiffusion. Use rosettacommons/foundry:slim plus RFD3 checkpoint; avoid foundry:latest because its compressed size is ~19.4GB and likely becomes Need >20GB after SIF conversion/cache. No Foundry SIF/checkpoint was started in this pass due concurrent RF/ADP/DiffDock installs and 31GB remaining disk.