Re: [PyMOL] Display 'outer' surface only

[Jason V. <jas...@sc...>]

Hugues,

Here's a tricky way to do it:

Download and run "findSurfacerResidues"
(http://pymolwiki.org/index.php/FindSurfaceResidues) and run it on
your protein.  The resultant selection contains surface residues.
Next, just set the "flag" on all those that are not returned and show
that as surface.

Example:

fetch 1hpv
run findSurfaceResidues.py
# this function returns a selection called "EXPOSED_XYZ" where XYZ is
some random integer
findSurfaceResidues (1phv), 0.5

flag ignore, not exposed_RESULT
as surface, 1hpv

Let me know if that works.  By the way, you might need to "rebuild"
after setting the flag.

Hope this helps,

-- Jason

On Tue, Jan 12, 2010 at 11:51 AM, Hugues Nury <hug...@gm...> wrote:
> Dear Pymolers,
>
> Do you know if there is a way to display only the outer surface of a
> protein without its buried pockets ? I've noticed that
> set surface_cavity_mode, 1
> does the opposite, ie display 'inner' surfaces only, but I haven't
> found the setting for the other way round.
>
> Thanks for you help,
> Hugues
>
> --
> Hugues Nury
> Postdoctoral fellow, Dynamique Structurale des Macromolécules
> Institut Pasteur, Paris, France
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120