Hi Sid - 

I don’t think there is a way to accomplish this directly in PyMOL, but you can get partway there using the `ray_trace_mode` setting and named selections for the various regions you wish to depict.  http://pymolwiki.org/index.php/Ray#Modes

Ultimately, you’ll need to create a composite image.  So, first generate your figure the way you want it to look without the outlines, then ray trace and save the png.

Then (without changing the camera position) do something like:

hide everything
show surface, sel1
set ray_opaque_background, 0  # transparent background for ray-traced images
set ray_trace_mode, 2  # draws a black outline only
set ray_trace_color, red  # change the outline color as you like
png, sel1_outline.png, ray=1

Repeat this for as many selections as you like.  You can then layer the outlines on top of the original in an image editor, e.g. GIMP/Photoshop, and also clean up any unwanted “texture” lines.

You may also want to play with surface_quality, probe_radius, and surface_solvent settings to adjust the outline. You could also check out these ways to generate a “blob” surface if you want smoother outlines. http://pymolwiki.org/index.php/Surface#Smooth_surface_quick_.28blob.29

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Apr 8, 2014, at 9:47 AM, Sridharan, Sudharsan <sridharans@MedImmune.com> wrote:

Hi all,
 
I’d like to colour different regions on the same protein surface but also draw the outlines/boundaries of these regions as well to show where they overlap (I guess I could colour the common residues in a different colour but I don’t want to do that!). Can someone please let me know how to do this in Pymol (v 1.7)?
 
Many thanks.
 
Kind regards,
Sid.
 
 
<image002.png>
 
Sudharsan (Sid) Sridharan, Ph.D.
Scientist I, Protein Sciences, Department of Antibody Discovery and Protein Engineering
 
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