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Renumbering PDB

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Renumbering PDB


I have been running this command other pdbs:

python2.7 /mnt/c/Users/No\ LOL/Desktop/Rosetta-jgustat/rosetta_bin_linux_2020.08.61146_bundle/main/tools/protein_tools/scripts/ \--norestart HER2_C_G3_A_full.pdb HER2_C_G3_A_full.pdb

and it has worked. Yet when I run it for my current pdb, it produces this error:

Traceback (most recent call last):
  File "/mnt/c/Users/No LOL/Desktop/Rosetta-jgustat/rosetta_bin_linux_2020.08.61146_bundle/main/tools/protein_tools/scripts/", line 53, in <module>' ',residue_id,' ')
  File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/", line 176, in id
    "for a sibling of this entity.".format(self._id, value, value)
ValueError: Cannot change id from `(' ', 1, ' ')` to `(' ', 125, ' ')`. The id `(' ', 125, ' ')` is already used for a sibling of this entity.


What should I do? 

Post Situation: 
Wed, 2022-07-27 13:37

This is an issue with Biopython -- they changed how they handled renumbering of residues, which caused some of the scripts to no longer work properly. (See

If you can try a different Biopython version, that might help. I think v1.64 is before the change and should work. I think v1.76 is after a fix which makes it work again, but I haven't done an extensive test, and I might be off a bit.

Wed, 2022-07-27 15:22

I switched my Biopython version from v1.76 to v1.68 and v1.64 and I got the same error. Should I continue switching Biopython versions or would you suggest a different approac?

Thu, 2022-07-28 10:00