I believe this to be a bug with Avogadro
Avogadro version: 1.94
Operating system and version: Windows 10 64 21H1
Avogadro can read PDB file created with Avogadro 1.2.0
Especially PDB files with crystal structures created with 1.2.0 cannot be read with 1.94.
Error is “Failed to parse chain identifier”.
Other tools can read the PDB files, although they are a bit buggy - say use the same identifier for many atoms.
E.g. in 1.2.0
- File / Import / Crystal C -graphite
- Build / Supercell / 2x2x1
- Save as PDB
The resul cannot be read in 1.94.