Hi Sepid, There is nothing to map genetic coordinates onto a structure. However, you can show the sequence that goes with your structure (if this is a protein, the amino acid sequence, NOT the DNA) in a separate window and choose residue(s) from there. How do you get the amino acid sequence? Well, you could fetch the corresponding UniProt ID, if you know what it is (e.g. go to uniprot.org <http://uniprot.org/> and search to find it), e.g. command open uniprot:LDLR_HUMAN ... or you can simply show the amino acid sequence directly taken from the structure, e.g. if it is chain B in your structure, command sequence chain /B See the Sequence Viewer documentation for how the sequence and associated structure interact. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.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 Sep 9, 2025, at 3:15 PM, Mazrouee, Sepideh (NIH/OD) [E] <sepid.mazrouee@nih.gov> wrote:
Hi Elaine,
Thank you for your suggestions. While arbitrary labels could be a workaround, I need a more precise solution.
I have a list of genetic coordinates for several protein domains generated by another program. Is there a way to map these coordinates onto the ChimeraX GUI? maybe via the “Nucleotide,” “Sequence,” or a related menu option? If I can locate the residues in the structure, I can then apply custom labels you suggested to highlight them.
I would appreciate your help!
Best, Sepid