RosettaCommons / RosettaCommons/RFdiffusion
<class 'IndexError'> in side chain generations step
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Description
Hi all,
I am setting up a new GPU box and could successfully generate binder scaffolds using Rfdiffusion in SE3nv env but I am facing this error:
"Struct with tag /test_0.pdb failed in 0 seconds with error: <class 'IndexError'>"
when trying to model side chains using proteinmpnn. Any ideas how to fix this? The pdb scaffolds generated are legit and are opened by pymol.
I should note that scaffolds generated on my other system can be successfully read by proteinmpnn in new machine, but not vise versa. so there might be something wrong in diffusion step.
Thanks in advance.
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Research direction
Start with the RFdiffusion side-chain generation step that produces /test_0.pdb, then compare that output and the environments on the two systems where ProteinMPNN behaves differently. Capture the complete IndexError traceback and verify whether the generated scaffold is accepted by ProteinMPNN; done means the failing PDB can be processed successfully.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100