Hey, I am pulling my hair out over this. I am trying to convert all residues in a protein to poly-Gly/Ala (for example 1ae1.pdb) but cannot find the Rosetta function to do so. I am replicating a paper where they included code and output, the output appears to be typical Rosetta output (the .pdbs are like 3tzc___1.pdb) which I am assuming were generated with a Rosetta function.
I have looked in Rosetta/tools/protein_tools/ and other folders within Rosetta/demos/public/ and /tutorials/ but cannot for the life of me find out how to convert a PDB to all Gly or Ala.
I have been looking at `phenix.pdbtools` too but that only truncates (i.e. doesn't change the res names to GLY or ALA in the PDB). The author of the paper used both Phenix and Rosetta so I am assuming it is in Rosetta this function occurs.
Does anyone know the Rosetta function to convert a given structure to poly-Gly/Ala please or what function/programme does so? I am not far from programming something myself in Python as it is frustrating, thank you.