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Thanks for reporting. It seems that biojava outputs the residue number to both label_seq_id and auth_seq_id. In principle there's nothing wrong with that, but it is true that traditionally the PDB has not used label_seq_id for non-polymers. I had a quick look and it seems that we could make that the default behaviour with a patch. I'll submit a PR.
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josemduarte commentedon Nov 8, 2025
Thanks for reporting. It seems that biojava outputs the residue number to both
label_seq_idandauth_seq_id. In principle there's nothing wrong with that, but it is true that traditionally the PDB has not usedlabel_seq_idfor non-polymers. I had a quick look and it seems that we could make that the default behaviour with a patch. I'll submit a PR.Fix for #1116
josemduarte commentedon Nov 13, 2025
The fix is now released in BioJava 7.2.3
Adding safeguard, bug introduced in #1116 and reported in Biojava-l