We added small molecule cif support in ChimeraX 1.6.  So you need to update your version of ChimeraX.   If a .cif file isn't a mmCIF, it will try to open it as a small molecule cif file.  And, in your case, you can open the CIR ligand without downloading it first with:

    open cir from ccd

or:

    open ccd:cir

ccd stands for the PDB's Chemical Component Dictionary that has all of the PDB's residue information, including the ligands.

    -- Greg

Sorry, this was the original error message:

 

From: "Jaremko, Matt Joseph" <matt.jaremko@merck.com>
Date: Monday, October 16, 2023 at 11:45 AM
To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: Open small molecule cif

 

Hello,

 

How do you open cifs for ligands? I’ve downloaded citrulline from the PDB database (attached), but I can’t open in ChimeraX:

 

Thank you,

Matt

 

Matt J. Jaremko, Ph.D. (He|Him)

Senior Scientist | Protein & Structural Chemistry

Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033

Office:  908.740.5613 | Cell:  808.741.6277 | Email:  matt.jaremko@merck.com

 

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