[chimerax-users] Re: How to save the PAE plot as an image in ChimeraX using command line ?

Hi, As far as I know there is no command. There is an option to "Save image" (PNG format) in the context menu of the PAE plot. To get the context menu, you have to right-click on the Plot (or on Mac, may be Ctrl-click instead). The choices in the context menu are described inthe help;: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#pae> 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 Apr 11, 2025, at 9:35 AM, picasa1983--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

I am using ChimeraX to visualize AlphaFold models and display the PAE plot with:

alphafold pae #1 /path/to/confidences.json

I would like to save only the PAE plot (not the 3D structure view) as a .png or .pdf file.

What is the correct command to save the PAE plot image in ChimeraX?

Thanks a lot!