Hi Thomas,
cavity3 is the object ID in this case, just a name Karl is giving the
isosurface so as to be able to refer to it in later commands...
isosurface [object id] [construction/mapping parameters] [surface
object]...etc.
Frieda
//////////////////////////////////////
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
413-253-2405
//////////////////////////////////////
On May 20, 2008, at 4:34 PM, Thomas Stout wrote:
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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