parse_PDB returns shorter sequence than pdb file about proteinmpnn

[dauparas]

Sounds good! Thanks for reaching out!

[adrienchaton]

I tried with a pdb generated with colabfold given the full sequence of 297 residues.
When parsing this pdb your codes return a sequence of the correct length, so I guess that pdb I had has some unusual formatting ...

[dauparas]

Hello!

Are any of the atoms (N, CA, C, or O) missing in the PDB file for the first residue? You could try running with --ca_only True and see if that returns the correct length of the sequence.

[adrienchaton]

Thanks ! That's indeed an issue with the pdb file I had, sorry.
I opened both the experimental one and that of the colabfold prediction, some atoms are missing in the first residue.
Using the colabfold pdb, your codes run without issue : )