Sorry to burst in on this thread, but I found it interesting and then the specification caught my eye:

what does "cavity3" mean?  I don't find that in the documentation for the isosurface command (http://chemapps.stolaf.edu/jmol/docs/?ver=11.6#isosurface).   According to this, "cavity" should take two arguments, "cr" and "en", and so should look like: "cavity 1.2 10" (using the defaults).   Is "cavity3" shorthand for "cavity 3.0 10" ?

Thanks!
-Tom


On Tue, May 20, 2008 at 11:29 AM, Bob Hanson <hansonr@stolaf.edu> wrote:
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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