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




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
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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

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