I am trying to make a representation to display the conservation using a color scale similar to this tutorial:

I have downloaded ~500 target proteins using blast, downloaded the results, and aligned them in clusta omega, which gave me this file:

However everytime I try to open it in chimeraX I get this matrix-like window:

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