The last time I tried to do something similar, I found HOLLOW (
http://hollow.sourceforge.net/) to be very useful. There's a nice tutorial
for showing a binding site, rather than an interior cavity, here:
http://hollow.sourceforge.net/binding.html .
Cheers,
-Michael
On Fri, May 20, 2011 at 7:11 PM, Ben Roberts <b...@roberts.geek.nz> wrote:
> Hi list,
>
> I'm trying to use PyMOL to construct an image of the total contiguous
> contact
> surface that starts at a particular place on the surface of a protein,
> without
> all the visual distraction and clutter that comes from other regions of the
> protein surface (not to mention internal cavities).
>
> I started by rendering up the whole protein as "Contact surface" with
> "Cavities and pockets only" shown. Unfortunately, this displays a large
> number
> of bubbles, some of which, despite being far away in space from the region
> of
> interest, manage to effectively obscure bits and pieces of it.
>
> So my next thought was to try removing the extraneous bits, however, I
> can't
> seem to select atoms in surface view; I have to display everything as lines
> or
> similar. Removing things that way gets very unwieldy, not least because of
> all
> the atoms that don't contribute anything to the surface but appear in front
> of, behind, or otherwise near to the atoms that do so.
>
> A third option I tried was to build the surface up, starting from the known
> points of interest, but this too is painstaking because of the need to
> guess
> where I should next expand the selection to in order to fill in the gaps.
>
> A remaining method of getting only the cavity of interest would, I guess,
> be
> to create a selection consisting only of those atoms that contribute
> something
> to the currently rendered surface (in this case, cavities and voids). I
> could
> then render those as spheres or something and hide unwanted contributors.
> Is
> there a way of specifying such a selection? Alternatively, is there some
> other
> smart way to achieve what I want (and by smart, I mean a way that isn't
> time-
> consuming and unusually error-prone)? I've already tried Googling, to no
> avail; I got, mostly, instructions about how to display surfaces in
> general.
>
> I should mention that I'm using a recent version of MacPyMol, on Mac OS X
> 10.6.7.
>
> Any tips are welcome. Thanks!
>
> Best regards,
> Ben
> --
> For greater security, I support S/MIME encryption.
>
>
>
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--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
------------------------------------------------------------------------------
What Every C/C++ and Fortran developer Should Know!
Read this article and learn how Intel has extended the reach of its
next-generation tools to help Windows* and Linux* C/C++ and Fortran
developers boost performance applications - including clusters.
http://p.sf.net/sfu/intel-dev2devmay
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