symexp does weird things when symmetry annotation is missing

[chmnk]

Describe the bug

In some cryo structures in PDB, symmetry is not set correctly since it is unknown. For them, gemmi ignores symmetry mates reconstruction, while pymol produces overlayed and slightly displaced structures.

I am not sure if there is any convention, but some patterns of missing symmetries are quite common, e.g.

• _cell.length_a 1.0, which is the default cell fill value in such cases (e.g. in 9hfl) -- and the corresponding PDB CRYST1 1.000 1.000 1.000
• some of them additionally have _pdbx_struct_oper_list.symmetry_operation ? (e.g. in 8ghv)

To Reproduce

Steps to reproduce the behaviour:

fetch 8ghv
symexp sym, 8ghv, 8ghv, 5

Expected behavior

To me looks like the 1A cell expansion leads to that overlayed mates. So I'd expect no symmetry expansion at all for <=1A cell definitions, even though it looks like a workaround? Or a min cell size for expansion as a parameter that can be set through set?

Also no sym exp for a ?-filled _pdbx_struct_oper_list.symmetry_operation (not sure if it can be ? in other structures though)?

Screenshots

Environment

• PyMOL Version: 3.1.0
• PyMOL Source: conda pymol-open-source
• If you are using a conda environment, please supply your conda list: it is very long but I can create a toy env and supply it here if needed.