[Chimera-users] Two-letter ID of polypeptide in Chimera

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 16 07:43:49 PDT 2019

Hi Pu Qian,
PDB format only has one column for chain ID, so if you put in a 2-character chain ID it is no longer the correct format.  Chimera only reads and understands the correct PDB format, not modified formats (except “pqr”), so I believe you would need to convert to mmCIF.

See PDB format documentation, chain ID is column 22 only:

Please use the address chimera-users at cgl.ucsf.edu (CC’d here) for Chimera questions unless you are including private data.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 16, 2019, at 3:29 AM, Pu Qian <p.qian at sheffield.ac.uk> wrote:
> Hi Meng anf Tom,
> I used two-letter (for example, AA, AB etc.) to ID polypeptide in DPB file. The protein can be displayed using chimera, however, chains of ID, name of ligands cannot be recognised by the chimera. Is there any way I can see them in the Chimera, or I have to convert it to .cif first?
> Best regards
> Pu Qian

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