Protein domain structures are categorized hierarchically in the Structural Classification of Proteins (SCOP) database. Given a SCOP domain identifier, Chimera will try to retrieve the domain coordinate file from the ASTRAL Compendium. This input type can be indicated in the Fetch by ID dialog or by specifying the file as scop:sid, where sid is the SCOP domain identifier.
The 7-character sid consists of "d" + the 4-character PDB ID of the file of origin + the PDB chain ID ("_" if none, "." if multiple) + a single-digit integer if needed to specify the domain uniquely ("_" if not). For details and examples, see the SCOP release notes (sid is the "old scop identifier").
The SCOP domain files are in PDB format, but are distinguished from other PDB files by how they are specified and from where they are obtained.