Hi Amar, mmCIF files handle arbitrary length chain identifiers. For working with large structures with many atoms or many chains it is nothing but trouble using the old PDB format (.pdb). If the software you use handles mmCIF you should use that file format. Tom
On Jun 10, 2026, at 10:08 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
If you are reading in a PDB file, there is technically only one column for chain IDs, although ChimeraX will also accept using two columns, but not three. <https://rbvi.ucsf.edu/chimerax/docs/user/formats/pdbintro.html#coords>
It may be possible to put 3-character chain IDs in mmCIF (I'm not sure), but it's probably easier to keep using PDB but limit yourself to two characters.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 10, 2026, at 9:43 AM, Parvate, Amar D via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi My name is Amar and I am working on the structure of a phage tail complex. I have multiple dodecameric assemblies within the tail complex. Is there a way to change/name chain IDs from say P1 to P12 in chimeraX so that they are all read and rendered? Can I make ChimeraX read chains beyond P9 when I have numbered them from say P1 to P12? Coot reads it fine but ChimeraX gets confused after P9 (image attached). I cannot select chain “P12” or any residue/sidechain in it<image001.png> Best Amar
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