Hello, You could simply text-edit the PDB file (plain text) to add a chain ID character in column 22 of the HETATM rows that have the atomic coordinates of the ligand.

See "intro to PDB format" specifically the format of the atomic coordinates rows, ATOM and HETATM https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#coords

Although Chimera has a "Change Chain IDs" tool, it only changes one ID to another, but may not be useful in the case of no ID.

If you don't want to edit the PDB file directly, you should try ChimeraX instead of Chimera. In ChimeraX you can simply use the "setattr" command to assign the chain ID, for example to assign ligand residues as chain B:

setattr ligand residues chain_id B

https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html

(Chimera has a setattr command but chain ID is handled differently, so the above would not work in Chimera.)

ChimeraX website and download https://www.rbvi.ucsf.edu/chimerax/index.html https://www.rbvi.ucsf.edu/chimerax/download.html

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 Apr 24, 2024, at 7:02 AM, kalabamelisa--- via Chimera-users chimera-users@cgl.ucsf.edu wrote:

Hello. I want to use PRODIGY web server to predict the binding affinity of my docked complexes, and the server requires a single PDB file containing both the docked ligand and the protein. I open the .pdbqt file containing the docking results using ViewDock and then I open my receptor file in .pdb format. I combine the two (receptor and the best ligand) and then save the complex as a PDB file. The server requires the ligand's name and what chain it's on, but when I open the complex in Chimera the ligand has no chain ID, it just shows up as "het". How do I assign a chain ID to my ligand in this situation?