Hi Alex, Command "sequence expandsel" expands a selection to all residues associated with the same column in a sequence alignment as the current selection: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#expandsel> So you would need to use the "show true" option of Matchmaker to show the corresponding pairwise sequence alignment in the Sequence Viewer, then after making the selection in one structure, use the above command to also select the sequence-aligned residue(s) in the other. This can also be done using the Sequence Viewer context menu: Structure... Expand Selection to Columns <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context> 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 22, 2025, at 3:02 PM, Alexander Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello ChimeraX community,

I have 2 pdb models of the same protein, but they don't have the same sequence numbering and length. After doing matchmaker, is there a command to select a selected residue's corresponding residue in the other model?

Ex: After doing matchmaker, I selected #1/A:100 (HIS). I want a command to select #2 (HIS) in the same part of the sequence. That residue may be > 2 Angstroms from #1:100, but it's in the same position sequentially. Is there a way to do this preferably via command line?

Regards, Alex