Hi Victor, When the alignment contains a higher number of sequences it is automatically opened in the grid view (Profile Grid tool) because the standard view (Sequence Viewer tool) is less compact and may take much longer to draw. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#sequence> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/profilegrid.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html> However, which of those two tools shows the alignment does not matter for the conservation coloring; the Conservation header (and resulting attribute for coloring) is the same for either tool: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers> If your profile grid view does not show the Conservation header, turn it on using Profile Grid context menu: Headers... Conservation. Show a context menu by right-click in the tool (or Ctrl-click if using a Mac trackpad or single-button mouse). You can still do the tutorial but wherever it says Sequence Viewer you would mentally substitute Profile Grid. E.g. where it says to use Settings in the Sequence Viewer context menu, it would instead be Settings in the Profile Grid context menu. You can control which you get, e.g. with the open command "viewer" option, and/or size threshold in the Preferences category Sequences, although it may not be a good idea if your alignment is huge: open myalignment.ali viewer seqview Details of how to control it: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#viewer> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#sequences> Another issue with your alignment is that if it is very sparse (lots of gap characters in many columns) the conservation value may not be calculated in those columns and you will get a patchy coloring. What fraction of gaps is acceptible for calculating conservation is controlled in the conservation parameters. There is an example of changing that in the third part of that tutorial, bacterial outer-membrane protein. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Mar 25, 2026, at 3:26 PM, Victor Ruiz-Arroyo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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