Issue with IMGT renumbering of PDB structures

[victorlr1992]

Hi,

I cannot seem to run the IMGT renumbering for some TCR pdb structures.

(base) python Example_scripts_and_sequences/ImmunoPDB.py -i 999-coot-1.pdb -o test4_999.pdb -s imgt --receptor tr
/scratch/victor.rangel/ANARCI_conda/ANARCI/Example_scripts_and_sequences/ImmunoPDB.py:11: SyntaxWarning: invalid escape sequence '\ '
description='''
999-coot-1.pdb could not be parsed: Cannot change id from (' ', 1, ' ') to (' ', 2, ' '). The id (' ', 2, ' ') is already used for a sibling of this entity.

Can you please help?

[ALGW71]

Hi,

Can you strip your pdb file down to only have chains which are TCRs and try again please?

Make sure there are no other objects in the file other than TCR chains and let us know if that works.

BW,
Alex

[victorlr1992]

Hi Alex, thank you for your quick reply. I've done it, I now have only the TCR alpha and beta chains, but still have the same issue. I believe this has something to do with some changes made to the biopython library which now does not allow 2 residues to have the same number. I believe this happens momentarily when the program runs. I also had to modify the ImmunoPDB.py to comment the Bio.Alphabet import line and change the Bio.Data.SCOPData, which means I might be using a wrong version of the libraries. Can you confirm which versions of bio libraries the program is using? Many thanks and best wishes, Victor

…

On Tue, 9 Apr 2024, 15:57 AlexGW, ***@***.***> wrote: Hi, Can you strip your pdb file down to only have chains which are TCRs and try again please? Make sure there are no other objects in the file other than TCR chains and let us know if that works. BW, Alex — Reply to this email directly, view it on GitHub <#87 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APWZCANR6DJA6U6IVF7H6ETY4P6WPAVCNFSM6AAAAABF6XO4N6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBVGM4TGNJRGE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[ALGW71]

This is the issue:
biopython/biopython#4623

I have asked them what is happening - it should be solved, but it clearly isn't in version 1.83.

I am trying the dev version - will let you know :)

[ALGW71]

@victorlr1992 If you install the dev version of biopython (version 1.84) - then it works!

Let me know and I will close the issue.

I need you to confirm that you changed the import line to this:

from Bio.PDB import *
from Bio.File import as_handle
# from Bio.Alphabet import generic_protein
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.SCOP.Raf import protein_letters_3to1_extended as protein_letters_3to1
from Bio.SeqUtils import seq1

[victorlr1992]

Indeed this worked! Well done and many thanks for looking into this. Best wishes, Victor

…

On Wed, 10 Apr 2024, 15:49 AlexGW, ***@***.***> wrote: @victorlr1992 <https://github.com/victorlr1992> If you install the dev version of biopython (version 1.84) - then it works! Let me know and I will close the issue. I need you to confirm that you changed the import line to this: from Bio.PDB import * from Bio.File import as_handle # from Bio.Alphabet import generic_protein from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from Bio.SCOP.Raf import protein_letters_3to1_extended as protein_letters_3to1 from Bio.SeqUtils import seq1 — Reply to this email directly, view it on GitHub <#87 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APWZCAJPTO25S5FNCFICWWLY4VGPDAVCNFSM6AAAAABF6XO4N6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBXG43DGNRRGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[ALGW71]

#89

[alba-ug]

Hello @ALGW71, I can't seem to find biopython 1.84. Could you guide me on how to install it please? Thank you.

Best regards

[ALGW71]

Hi @alba-ug

Go to this repo:
https://github.com/biopython/biopython

You will have to clone the repo and install it using their user guide.