RosettaCommons / RosettaCommons/RFdiffusion
Fixed Segments in Generated PDB Files Don't Match Reference PDB File
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- Python
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Description
While performing motif scaffolding with RFdifussion, I have noticed that the fixed segments in the generated PDB files do not exactly match those in the reference PDB file. For example, I'm using the following contig [B1-94/14-20/B103-111] and I have a PDB file in which the sequence includes Gly, Ser, Ser at positions 52, 52A, 53. However, in the generated PDB files, only Gly and Ser are present at positions 52 and 53, with the insertion at 52A being discarded.
Questions:
- Is this behavior expected, or is it a bug?
- Does anyone know a fix or workaround to ensure that the fixed segments, including insertions, are accurately preserved in the generated PDB files?
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Research direction
No source file or test is identified in the issue. Reproduce the reported case with contig B1-94/14-20/B103-111 and the reference PDB containing the 52A insertion, then trace the PDB generation path to determine where insertion numbering is lost. Done means fixed segments, including residue 52A, are preserved in generated PDB files or the expected limitation is documented.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100