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Fixed Segments in Generated PDB Files Don't Match Reference PDB File #265
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I'm unsure how well RFdiffusion works with insertion codes. You can try explicitly including things in the contig (something like *) Automated methods exist. I'd personally use Rosetta to do it, because that's what I'm familiar with. Other programs will also do it, though. |
After further investigation, I identified the cause of the behavior I described. When RFdiffusion parses the PDB files using the To address this, I have opted to renumber my files without insertion codes. |
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.
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