# Renumbering PDB

3 posts / 0 new
Renumbering PDB
#1

Hello,

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/pdb_renumber.py \--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/pdb_renumber.py", line 53, in <module>
residue.id=(' ',residue_id,' ')
File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Entity.py", 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?

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Wed, 2022-07-27 13:37
jgustat

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 https://github.com/biopython/biopython/issues/1551)

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
rmoretti

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
jgustat