When transform_to_assembly is called on structure of 1b11, the covalent linkage between C2 atoms of the symmetric ligand 3TL is lost. The complete ligand 3TL is only present in the assembly and the link is defined between different asymmetric units.

Outputs

Before generating assembly

st.connections
gemmi.ConnectionList([<gemmi.Connection covale1 A/3TL 201/C2 - A/3TL 201/C2>])

After generating assembly

st.connections
gemmi.ConnectionList([])

import gemmi
entry_id = '1b11'
st = gemmi.fetch.read_structure_with_code(entry_id, pdb_site='E')
how = gemmi.HowToNameCopiedChain.AddNumber
st.transform_to_assembly(assembly_name='1', how=how)
st.connections

gemmi version - 0.7.5