I'd go with the atom property surfaceDistance. For example:
select water and surfaceDistance > 3.0
This actually calculates the distance of an atom from the "surface" of the
model. I'd have to look exactly how "surface" is defined. But it's basically
what you are talking about.
Bob
On Thu, Sep 15, 2011 at 12:03 PM, Eric Martz <[email protected]>wrote:
> Can anyone suggest how best to select residues (or specified sets of
> atoms) that are buried? In a simple sense buried might mean "all
> atoms beneath the surface of the protein". Ideally, one would like to
> exclude pockets that connect with a water-permeable channel to the
> surface, but that is a refinement.
>
> I am specifically interested in locating buried waters in 1w4y.
>
> In Jmol, the term "buried" is equivalent to the set of amino acids
> "ALA CYS ILE LEU MET PHE TRP VAL". That is not what I want.
>
> Thanks, Eric
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Doing More with Less: The Next Generation Virtual Desktop
What are the key obstacles that have prevented many mid-market businesses
from deploying virtual desktops? How do next-generation virtual desktops
provide companies an easier-to-deploy, easier-to-manage and more affordable
virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/
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