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 <[EMAIL PROTECTED]> 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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