Greetings,
Please also investigate the following settings:
# needs a real atom selection
surface_carve_selection
# distance from the above selection to cull surfaces
surface_carve_cutoff
I looked at your data and there is a small problem. You have a few points
where one atom is mapped to multiple surface points. Thus, when you show it
as surface two pocket fragments show up. When you hide it they both hide.
Also of interest is PyMOL's ability to render pockets and cavities on its
own (Settings > Surface > Cavities & Pockets).
Cheers,
-- Jason
On Mon, Mar 4, 2013 at 2:15 PM, Sampson, Jared <jared.samp...@nyumc.org>wrote:
> Hi Yarrow -
>
> If you add "br. " to the show surface command, you will get more
> continuous surfaces, as the selection will be made by residue instead of by
> atom.
>
> show surface, br. protein within 0.5 of pocket_selection
>
>
> If you don't want to show the surface from a particular residue (e.g. if
> it's masking something else you want to show), you can hide surface for a
> selection.
>
> hide surface, resi 225+347
>
>
> Cheers,
> Jared
>
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> Old Public Health Building, Room 610
> 341 East 25th Street
> New York, NY 10016
> 212-263-7898
> http://kong.med.nyu.edu/
>
>
>
>
> On Mar 4, 2013, at 2:37 PM, Yarrow Madrona <amadr...@uci.edu> wrote:
>
> Thank you for your help Thomas,
>
> Using your settings I get a lot of "partial surfaces"
>
> Showing the surface around the Pocket selection like this:
>
> show surface, protein within 0.5 of pocket_selection
>
> worked well but I still see a piece of surface that I really don't want to
> show up. I guess I can take it out in photoshop but that just seems wrong.
> I have attached it.
>
> -Yarrow
>
>
>
> Hi Yarrow,
> should be as simple as:
> PyMOL> hide surface
> PyMOL> show surface, (organic around 8.0)
> PyMOL> set transparency, 0.3
> PyMOL> set two_sided_lighting
> See also:
> http://pymolwiki.org/index.php/Selection_Algebra
> Hope that helps.
> Cheers,
> Thomas
> Yarrow Madrona wrote, On 03/03/13 18:34:
>
> Hello,
> Does anyone know how to visualize a surface within a given radius from
>
> a
>
> ligand binding site? In chimera you can limit the display surface
>
> within
>
> 0-X angstrom of a ligand. This allows you to see the surface
>
> surrounding
>
> the ligand without the rest of the protein.
> I guess you could create a new selection of residues around a ligand
>
> and
>
> show this surface but I wondered if there are any other ways of doing
>
> this.
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
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> Yarrow Madrona
>
> Graduate Student
> Molecular Biology and Biochemistry Dept.
> University of California, Irvine
> Natural Sciences I, Rm 2403
> Irvine, CA 92697
>
> <screenshot.png>
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--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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