Issues

• [BUG] RFD3 and RF3 hydra configs path search doesn't match distribution

  bug
  RosettaCommons/foundry#403 · Filter by author brianosmith opened on Oct 14, 2026

• [BUG] Atomworks dependency too lax

  bug
  RosettaCommons/foundry#402 · Filter by author brianosmith opened on Oct 14, 2026
  1

  

• [QUEST]Consistency between RFOptimization and gradient-based optimization

  question
  RosettaCommons/foundry#398 · Filter by author linjing-lab opened on Oct 11, 2026

• [BUG] Contiguous input fragments are broken apart during unindexed motif scaffolding

  bug
  RosettaCommons/foundry#395 · Filter by author TecnomaLaser opened on Oct 7, 2026
  1

• [FEAT]Add githash in output files for all models

  enhancement
  RosettaCommons/foundry#386 · Filter by author rclune opened on Sep 30, 2026

• MAX_TRANSFORMS symmetry variable capped at 10

  question
  RosettaCommons/foundry#382 · Filter by author jlmoraleshellin opened on Sep 23, 2026
  

• RF3 training cutoff uses PDB deposition date — implications for temporal benchmark leakage

  RosettaCommons/foundry#381 · Filter by author SanggeunParrk opened on Sep 18, 2026
  

• [Bug] RF3 validation step in end-to-end notebook uses undesigned RFD3 backbone instead of MPNN-designed structure, causing abnormally high RMSD

  bug
  RosettaCommons/foundry#380 · Filter by author staryGe opened on Sep 10, 2026

• [BUG] Hydrogen Bond Metrics Not Getting Calculated

  bug
  Bug

  RosettaCommons/foundry#374 · Filter by author rclune opened on Aug 14, 2026

• [BUG] RFdiffusion3 not respecting positions of fixed atoms in unindexed residues

  bug
  RosettaCommons/foundry#372 · Filter by author fakesemechki opened on Aug 12, 2026
  1

• sheet_fraction and helix_fraction

  question
  RosettaCommons/foundry#370 · Filter by author zhulinyu0527-eng opened on Jul 30, 2026
  2

• [QUEST] Inpainting residues with RFD3 only gives glycines

  question
  RosettaCommons/foundry#366 · Filter by author CamillaLeogrande opened on Jul 22, 2026
  4

• [Bug]int() parsing failure when component contains P suffix during RFD3 input parsing

  bug
  RosettaCommons/foundry#362 · Filter by author seacid opened on Jul 8, 2026

• [QUEST]multiple GPUs

  question
  RosettaCommons/foundry#336 · Filter by author zhulinyu0527-eng opened on Jun 30, 2026
  6

• [BUG] Denoised and noisy trajectories are accidentally swapped during reshaping in inference engine

  RosettaCommons/foundry#335 · Filter by author amorehead opened on Jun 29, 2026
  

• [BUG] RFD3 unindexed motif loss uses an atom-level mask as a token-level mask

  bug
  RosettaCommons/foundry#330 · Filter by author zwmjohn-cool opened on Jun 22, 2026
  

• sugar chains

  question
  RosettaCommons/foundry#328 · Filter by author zhulinyu0527-eng opened on Jun 21, 2026
  2

• [QUEST]

  question
  RosettaCommons/foundry#291 · Filter by author lucatondini opened on Jun 2, 2026
  3

• Strategies for retaining the hydrogen-bond donor/acceptor architecture defined in the RFD3 active-site model during LigandMPNN sequence optimization

  RosettaCommons/foundry#289 · Filter by author abinge668 opened on Jun 2, 2026
  1

• Ambiguous inter-chain attention indices definition

  RosettaCommons/foundry#280 · Filter by author amorehead opened on May 16, 2026
  

• [BUG] RFD3 symmetry fails for odd dihedral groups D3/D5

  bug
  RosettaCommons/foundry#278 · Filter by author runrah opened on May 13, 2026
  

• [BUG] RFD3 is missing training data artifacts

  bug
  RosettaCommons/foundry#276 · Filter by author amorehead opened on May 8, 2026
  

• Diffusion of unindexed fixed residues islands with unindexed unfixed island

  enhancement
  RosettaCommons/foundry#274 · Filter by author greenisvuwalphafold-lang opened on May 4, 2026
  3

• Missing ligand at zero occupancy

  bug
  RosettaCommons/foundry#271 · Filter by author mabr3112 opened on Apr 20, 2026
  

• [BUG]

  bug
  RosettaCommons/foundry#266 · Filter by author pekingb opened on Apr 7, 2026