Hi David, First color the structure with "Color PAE Domains." Then use the context menu on the plot and choose "Color plot from structure" See the AlphaFold Error Plot help for explanation of context menu choices: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#pae> For ChimeraX context menus in general, you show them by clicking on some tool with right-click (or if Mac trackpad or single-button mouse, control-click). <https://rbvi.ucsf.edu/chimerax/docs/user/window.html#context-menu> 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 Aug 4, 2024, at 3:36 PM, David S. Fay via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi All,

Was trying to get the ChimeraX 2D PAE plot to display the colored PAE domains consistent with the ribbon diagram. The button “Color PAE Domains” colors the ribbon diagram by coherent domains, but the 2D plot is still colored by PAE (error). The Meng et al., 2023 has nice examples of this (e.g., 1f) coloring.

Thanks in advance!

David