Hi everyone, I'm trying to use the match command (not matchmaker) to align the ring atoms of a ligand. The command gives "No matrix compatible with both reference structure and all match structure" and translates the match command to matchmaker in the reply log. However, in Chimera I'm able to align jjst those ring atoms with the match command. Of course, using matchmaker on just those atoms in Chimera gives "No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix" tl;dr. Trying to align ring atoms of a ligand instead of protein chain Chimerax mask 1 = #1:203@C19,C20,C21,C16,C17,O18 mask 2 = #2:125@C2,C3,C4,C5,C6,O6 matchmaker: No matrix compatible with both reference structure and all match structures match: Same as above. In reply log, match is extended to matchmaker Chimera mask 1 = #0:203@C19,C20,C21,C16,C17,O18 mask 2 = #1:125@C2,C3,C4,C5,C6,O6 matchmaker: No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix match: Gives me RMSD ** I need this atom match functionality in ChimeraX Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010@uga.edu Mobile: (470) 641-3884