transform_to_assembly and connectivity for pdb vs cif

[rimmartin]

Hi,
when applying transform_to_assembly
the resulting Structure sent to write_pdb doesn't get CONECT's for the transformed chains but

            gemmi::cif::Document mmcifDoc=gemmi::make_mmcif_document(structure);
            gemmi::cif::write_cif_to_stream(buf, mmcifDoc);

gets connectivity that displays in pymol.

Should I be writing pdb's by another set of steps/methods?

[wojdyr]

transform_to_assembly calls finalize_expansion to copy various annotations (secondary structrure, links, CISPEPs), but CONECT records are not copied for new chains. mmCIF doesn't use CONECT-like records, so connectivity is determined in another way. Perhaps removing CONECT's altogether would help PyMOL?