Dear ChimeraX staff, I am trying to make a representation to display the conservation using a color scale similar to this tutorial: https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-c... I have downloaded ~500 target proteins using blast, downloaded the results, and aligned them in clusta omega, which gave me this file: [image: image.png] However everytime I try to open it in chimeraX I get this matrix-like window: [image: image.png] Which is different to what I would expect based on the tutorial. In fact, if I download the .ali from the tutorial, I see the correct alignment window. I have tried different alignment formats without success, and I still get the "matrix window". What software and format do you recommend using in Chimerax? Best Victor
