Dear John, The PAE plot window has a context menu (shown by right-click, or if Mac trackpad or single-button mouse, Ctrl-click) with the choice to "Color plot green". This tool and its context menu are described in the help page shown by clicking the Help button, or you can view the copy at our website here: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#pae> Please note also that ChimeraX usage for commercial purposes requires getting a commercial license, if you haven't already done so: https://www.rbvi.ucsf.edu/chimera/commercial_license.html> Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On May 9, 2023, at 4:10 AM, John Maximos [Pharma] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Chimerax Team,

I have a problem that the pae plot color is not adjusted like the green one. How to solve this problem? I attached here a screenshot from my laptop.

Best Regards, John Maximos <image003.png> www.evapharma.com

<pae plot.png>