First, to all, see also the main thread & comments section of this related post: How to keep the same view for different AlphaFold 3 simulations in ChimeraX?.

Hi Picasa

Try this:

import os
import sys

def run(session, pdb_path, pae_path, output_path):
    from chimerax.core.commands import run as cxrun
    from chimerax.alphafold import show_pae_plot

    cxrun(session, f'open {pdb_path}')
    cxrun(session, f'alphafold pae #1 {pae_path}')

    pae_tool = show_pae_plot(session)
    pae_tool.save_image(output_path)

def run_script(session):
    # Entry point for ChimeraX
    # This function is called when using `chimerax --script save_pae_only.py ...`
    import sys
    args = sys.argv[-3:]  # expects last 3 args to be: pdb, pae, output
    run(session, *args)


if __name__ == "__main__":
    # Entry point for regular Python execution (optional but for completeness)
    pdb_path = sys.argv[1]
    pae_path = sys.argv[2]
    output_path = sys.argv[3]

    os.system(f'chimerax --nogui --script "save_pae_only.py {pdb_path} {pae_path} {output_path}"')

This implementation enables you to call it directly with python via:

python save_pae_only.py model1.pdb pae1.json output1.png

or you could also use chimerax like so:

chimerax --nogui save_pae_only.py model1.pdb pae1.json output1.png

If it doesnt work please let me know