OK, it's
set slabRange 5.0
-- As long as slabRange > 1, Jmol will use it instead of the slab setting.
-- Setting slab the usual way automatically sets slabRange to 0, turning it
off
-- Still requires slab ON
It's a little odd.... but it might be interesting.
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
Bob
On Sat, Sep 4, 2010 at 9:24 AM, Alexander Rose
<alexander.r...@weirdbyte.de>wrote:
> Hi,
>
> Am 03.09.2010 um 18:49 schrieb Robert Hanson:
>
> So I think we could set some slab option to be dependent upon zoom. For
> example:
>
> slab 5.0
>
> a decimal here would indicate that at whatever zoom level you are at, the
> slab would be set to be wherever the visual range is 5.0 Angstroms.
>
> Something like that?
>
>
> that sounds great!
>
>
> On Fri, Sep 3, 2010 at 11:10 AM, Alexander Rose <
> alexander.r...@weirdbyte.de> wrote:
>
>> Hi,
>>
>> ----- Ursprüngliche Mail -----
>> > Von: "Robert Hanson" <hans...@stolaf.edu>
>> > An: jmol-users@lists.sourceforge.net
>> > Gesendet: Freitag, 3. September 2010 16:46:50
>> > Betreff: Re: [Jmol-users] camera dependent slab setting
>> > It seems to me that is what the standard SLAB command is for. Right?
>> >
>>
>> In a way, but it's static, the slab is not dependent on the zoom. So when
>> I zoom in more deeply, I would have to adjust the slab setting to show less,
>> and when I zoom out to show more again. This fine when creating images or
>> focusing on one area, but when exploring a larger part of a protein it
>> becomes annoying and I miss such a feature as it is available in other
>> viewers.
>>
>>
>> Best
>> Alexander
>>
>> > 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 <
>> > alexander.r...@weirdbyte.de > 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" < hans...@stolaf.edu >
>> > > An: jmol-users@lists.sourceforge.net
>> > > 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 <
>> > > alexander.r...@weirdbyte.de > 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" < hans...@stolaf.edu >
>> > > > An: jmol-users@lists.sourceforge.net
>> > > > 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 <
>> > > > alexander.r...@weirdbyte.de > 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
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>> > > 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.
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>> > > _______________________________________________
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>> > > 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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>>
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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
>
> ------------------------------------------------------------------------------
> This SF.net Dev2Dev email is sponsored by:
>
> Show off your parallel programming skills.
> Enter the Intel(R) Threading Challenge 2010.
>
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>
>
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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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