PyMOL parses the following record types in a PDB file:

• HEADER
• CRYST
• SYMMn
• HELIX & SHEET
• ATOM & HETATM
• TER
• END
• MODEL & ENDMDL
• CONECT
• USER

By default, PyMOL determines molecular structure connectivity in PDB files automatically using distance-based criteria. It is also possible possible to provide connectivity explicitly with CONECT records, which include not only bond information, but can encode bond valences as well.

PyMOL supports multimodel PDB files several different ways. Multiple standard PDB files containing a HEADER record can simply be concatenated together and loaded into PyMOL directly. The resulting objects will be labeled according to the PDB code in the HEADER (if present), or by the text in the HEADER, or failing that, with automatic numbering.

PyMOL can output the following records into a PDB file.

• ATOM & HETATM
• TER
• END
• MODEL & ENDMDL