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