It seems to me that is what the standard SLAB command is for. Right?
If you use
slab on
slab 60 # or whatever
set slabByAtom
it might be very close to what you are talking about.
Bob
On Fri, Sep 3, 2010 at 9:36 AM, Alexander Rose
<[email protected]>wrote:
> Hi Bob,
>
> I set up a web page to clarify what I mean:
> http://weirdbyte.de/jmol-test/html/nav.html
>
> There are three applet, showing a protein in the same orientation. The
> first applet shows the protein in the normal - non navigation - mode and has
> some atom obscuring most of the rest. The second applet is in navigation
> mode and has the default visualRange = 5 setting. According to the
> documentation this results in "any object in a plane that is less than 5.0
> Angstroms across will be clipped automatically". And it works, giving a
> beautiful clear view, this is what I would like for the non navigation mode,
> too!. Applet 3 then is also in navigation mode but with visualRange set to 1
> so that the notorious atom is not clipped automatically and obscures the
> view again, the reflection is nice though. I hope this makes my intention
> clear.
>
>
> Best
> Alexander
>
>
> ps: congrats for your jmol related publication!
>
> ----- Ursprüngliche Mail -----
> > Von: "Robert Hanson" <[email protected]>
> > An: [email protected]
> > Gesendet: Mittwoch, 25. August 2010 15:58:20
> > Betreff: Re: [Jmol-users] camera dependent slab setting
> > I thought that was what you meant -- the equivalent of visualRange but
> > for standard mode.
> >
> >
> > On Wed, Aug 25, 2010 at 7:57 AM, Alexander Rose <
> > [email protected] > wrote:
> >
> >
> > Hi,
> >
> > I tried rotationRadius, but it has not the effect visualRange has. In
> > fact I do not really understand the effect, apart from somehow setting
> > the zoom and the possible zoom range. That is with 12.0.8.
> >
> >
> > Alex
> >
> >
> > ----- Ursprüngliche Mail -----
> > > Von: "Robert Hanson" < [email protected] >
> > > An: [email protected]
> > > Gesendet: Dienstag, 24. August 2010 22:24:17
> >
> > > Betreff: Re: [Jmol-users] camera dependent slab setting
> >
> >
> >
> > > Indeed!
> > >
> > > set rotationRadius (Angstroms)
> > >
> > >
> > >
> > > Sets the nominal rotation radius for the model effectively setting
> > > the
> > > size of the model at zoom 100 . Normally set to the radius that will
> > > contain within the screen the entire model when rotated relative to
> > > the default rotation center.
> > >
> > >
> > >
> > > :)
> > >
> > > Bob
> > >
> > >
> > >
> > > On Mon, Aug 23, 2010 at 5:16 AM, Alexander Rose <
> > > [email protected] > wrote:
> > >
> > >
> > >
> > > Because its such a different experience I came to think that
> > > something
> > > like visualRange would be useful for the non nav mode?!
> > >
> > >
> > > Best
> > > Alexander
> > >
> > >
> > >
> > >
> > >
> > >
> > > --
> > > Robert M. Hanson
> > > Professor of Chemistry
> > > St. Olaf College
> > > 1520 St. Olaf Ave.
> > > Northfield, MN 55057
> > > http://www.stolaf.edu/people/hansonr
> > > phone: 507-786-3107
> > >
> > >
> > > 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
> > >
> > >
> ------------------------------------------------------------------------------
> > > Sell apps to millions through the Intel(R) Atom(Tm) Developer
> > > Program
> > > Be part of this innovative community and reach millions of netbook
> > > users
> > > worldwide. Take advantage of special opportunities to increase
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> > > and
> > > speed time-to-market. Join now, and jumpstart your future.
> > > http://p.sf.net/sfu/intel-atom-d2d
> >
> > > _______________________________________________
> > > Jmol-users mailing list
> > > [email protected]
> > > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
> ------------------------------------------------------------------------------
> > Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> > Be part of this innovative community and reach millions of netbook
> > users
> > worldwide. Take advantage of special opportunities to increase revenue
> > and
> > speed time-to-market. Join now, and jumpstart your future.
> > http://p.sf.net/sfu/intel-atom-d2d
> >
> >
> >
> > _______________________________________________
> > Jmol-users mailing list
> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
> >
> > --
> > Robert M. Hanson
> > Professor of Chemistry
> > St. Olaf College
> > 1520 St. Olaf Ave.
> > Northfield, MN 55057
> > http://www.stolaf.edu/people/hansonr
> > phone: 507-786-3107
> >
> >
> > 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
> >
> >
> ------------------------------------------------------------------------------
> > Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> > Be part of this innovative community and reach millions of netbook
> > users
> > worldwide. Take advantage of special opportunities to increase revenue
> > and
> > speed time-to-market. Join now, and jumpstart your future.
> > http://p.sf.net/sfu/intel-atom-d2d
> > _______________________________________________
> > Jmol-users mailing list
> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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