So, if I'm in ray_trace_mode=1 , bg_color affects the outline on the pictures that are made. When a pse is saved, the background color is saved, but this impact on the outlines is not saved. I have two pmls attached, where you can run:
pymol -qkc test.pml
pymol -qkc test2.pml
And it should produce 3 pictures like the ones attached. You'll notice 2.png has the wrong outlines around the protein.
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