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.Sampson@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




On Mar 4, 2013, at 2:37 PM, Yarrow Madrona <amadrona@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
------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net


--
Yarrow Madrona

Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697

<screenshot.png>------------------------------------------------------------------------------

Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net


------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net



--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120