Outline

Outline

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

• ray_opaque_background
• ray_trace_mode
• ray_trace_color
• ray_trace_gain
• surface_quality

Example

• 

  Structure of Cytochrome C (PDB 3cyt) shown in surface representation.

• 

  Outline of residues within 2Å of Lys85 on chain I. Notice the image background is transparent.

• 

  Composite of the previous 2 images.

• 

  The same composite image, cleaned up.

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.