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There is currently (as of PyMOL v.1.7) no way to outline a selection directly within PyMOL. However, it can be accomplished indirectly with a composite image.

Relevant Settings


The following script was used to generate the first two images from PyMOL.

bg_color white

fetch 3cyt, async=0

as surface
color marine

select outline, br. chain I and resi 85 around 2

set_view (\
     0.061975956,   -0.950684488,    0.303902954,\
     0.703773856,    0.257531703,    0.662103057,\
    -0.707715809,    0.172843516,    0.685028315,\
     0.000000000,    0.000000000, -152.244812012,\
    25.274658203,    8.288025856,    9.110867500,\
    51.143974304,  253.345642090,  -20.000000000 )

png base.png, ray=1

hide everything
as surface, outline
set ray_trace_mode, 2
set ray_trace_color, yellow
set ray_opaque_background, 0

png overlay.png, ray=1

In an image editing program, position overlay.png in a layer exactly overlapping base.png. The extra outline lines can also (optionally) be cleaned up by carefully erasing them using the graphics program's eraser tool.