Re: [PyMOL] boundaries/outlines of overlapping regions on surface

[Sridharan, S. <sri...@Me...>]

Hi Carsten and Jared,

Thanks very much for the tips.

Jared's method seems to be the solution. I just had to be careful with the step of cleaning up the unwanted lines in GIMP!

Many thanks again both!

Kind regards,
Sid.

From: Sampson, Jared [mailto:Jar...@ny...]
Sent: 08 April 2014 18:50
To: Sridharan, Sudharsan
Cc: pym...@li...
Subject: Re: [PyMOL] boundaries/outlines of overlapping regions on surface

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/






Sid,

I'm guessing here, but may be coloring by properties (new in 1.7) may be the way to go. Usually I would color the residues and if you want to show the underlying residues I would just make another object for those.

HTH,

                Carsten



On Apr 8, 2014, at 9:47 AM, Sridharan, Sudharsan <sri...@Me...<mailto:sri...@Me...>> 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


sri...@me...<mailto:sri...@me...>
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