In 1mbo the molecular oxygen is part of the heme structure and is therefore
ignored along with the heme.
>>> Bob Hanson <[EMAIL PROTECTED]> 5/20/2008 2:29 PM >>>
Oh, also, you might want to add OXY ot that list and also try
experimenting with the probe radius after the CAVITY parameter.
Something like:
isosurface cavity3 minset 500 pocket ignore (hem,solvent,oxy) color
yellow cavity 1.0 translucent
Karl Oberholser wrote:
> Hi All,
> When I use these two commands, select protein; isosurface cavity3
> minset 500 pocket color yellow cavity translucent, with myoglobin
> (1mbo), I obtain two cavities. If I add ignore hem to give isosurface
> cavity3 minset 500 pocket ignore hem color yellow cavity translucent,
> I just obtain the cavity that is binding the heme. I would have
> expected to get the two other cavities along with the heme binding
> cavity. Am I missing something?
>
> Karl
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
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