I talked to the PDB about this error. The PDB's OneDep deposition system generates the entity_poly.pdbx_strand_id data item if there is associated entity_poly data in the file or if the full sequence is given as part of the deposition process. So I suspect that the real bug is that there is missing sequence information for some/all of the chains in your molecule. And, by default, ChimeraX does not save the entity_poly table for chains if it wasn't read in. Which can lead to the error. If this is not the case, then please share with me one of the problematic mmCIF files, so I can reproduce the exact problem. Or you could work with the PDB directly. There are several ways to get the sequence information into the mmCIF output: (A) If you are using phenix, using the full sequence, you post-process the mmCIF file with phenix's pdb_extract tool. (B) If you are using ChimeraX 1.9 (currently the daily build), after you open the full sequence, you can use the "sequence update" command or the use the context menu in the Sequence Viewer and the Structure / Update Chain Sequence dialog. (C) If the sequence of the molecule is the full sequence, then you can use "save model.cif bestGuess true". bestGuess can't tell how big gaps are, nor fill in the missing head or tail residues, so you're better off with A or B. Consequently, at this time, there are no plans to add the entity_poly.pdbx_strand_id data item to ChimeraX's mmCIF output. HTH, Greg