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
<sridhar...@medimmune.com<mailto:sridhar...@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
Aaron Klug Building, Granta Park,
Cambridge, CB21 6GH, UK.
P: +44(0)1223 898195 F: +44(0)1223 471472
sridhar...@medimmune.com<mailto:sridhar...@medimmune.com>
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