Re: [Jmol-users] Odd result from cavity command??

[Frieda R. <fr...@ns...>]

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 <ha...@st...>  
> 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
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>
>
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