So what you are seeing is not a bond, it is a cartoon connecting the disjoint parts of a single Intron. According to the mmCIF file's metadata, those two fragments are next to each other. That a bug in the mmCIF file. And ChimeraX faithfully reproduces buggy data, otherwise, you'd never know. The PDB should have caught that error on deposition. It might be a bug in software used to refine the structure. Please continue to report problems like this. mmCIF files are relatively new, and we are still learning about how Analysis: The entity_poly table says that Intron entities have 122 nucleotides. The atom_site table's label_asym_id and label_seq_id values indicate that there is one instance of the Intron entity with its first 61 residues present. Adjacent nuceotides are implicitly connected. Gaps are indicated by gaps in the label_seq_id values, and there are none. As you observed, from the disjoint fragments in 3D, that information is not correct. Another clue is the auth_seq_values that range from 1 to 24 and 136 to 154. Since the 136 is more that 122, maybe it should really be two separate chains instead of one chain? Or maybe the numbering is wrong. Can't tell. Bad data. I'd recommend contacting the author and/or the PDB to get it fixed. HTH, Greg On 8/25/2026 4:34 AM, Vorländer,Matthias Kopano via ChimeraX-users wrote:
Dear ChimeraX staff,
For some mmCIFs, ChimeraX displays bonds that are physically unrealistic. For example, if you take PDB 9S2E ChimeraX draws a bond between residue /IN:52 and and /IN:154 (see screenshot). The PDB mol viewer (https://www.rcsb.org/3d-view/9S2E) does not display this bond.
I noticed that structures in PDB format don’t show these bonds, so this is probably due to some connectivity records in cif format. I also have only observed this in nucleic acids, not proteins.
Is this a bug that could be addressed?
Thanks a lot and best wishes, Matthias
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