Dear Elaine, Thank you for your swift response, as always! The issue Ibm facing is that I have around 200 sequences, and as far as I know, mmaker only works pairwise. While in theory I could align each structure against the same reference, this would result in an unmanageable number of pairwise alignments. I also considered loading a multiple sequence alignment and using sel expand based on that, but that approach isnbt ideal eitherbit still includes gaps and depends heavily on the quality of the alignment. Let me know if Ibm missing a better strategy within ChimeraX for dealing with this sort of challenge. cheers, -- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118