The atom in the plane is returned by within(0, ....) I believe.
On Tue, Oct 26, 2010 at 3:57 AM, P.Canepa <[email protected]> wrote:
> I am sorry, it just works great! I was wondering if I want to leave atom in
> the plane and remove only the atom above or below. it's there any way to
> exclude them ?
>
> Secondly, I have also introduce in J-ICE an option to remove atoms around
> an atom, something like: select within( distance, { x y z}); remove selected
> or hide selected. I'd like to draw a sphere of radius distance around the
> point. Is it possible ?
>
draw sphere1 width 3.5 {0 0 0} translucent
draws a sphere with id $sphere1 of diameter 3.5 Angstroms centered at {0 0
0}
don't forget to exclude the point itself. Note that an atom's xyz
coordinates or the atom itself can be used:
draw sphere1 width 3.5 {atomno=30} translucent
and same goes for WITHIN:
select within(3.5, {atomno=30}) and not atomno=30
for example.
> I know there is an option for isosurface, can I use it ? Can also the user
> decide to remove outside the distance? It would be nice!
>
> Thanks, Piero
> --
> Please consider the environment before printing this e-mail.
>
> Pieremanuele Canepa
> Room 104
> Functional Material Group
> School of Physical Sciences, Ingram Building,
> University of Kent, Canterbury, Kent,
> CT2 7NH
> United Kingdom
>
> e-mail: [email protected]
> mobile: +44 (0) 7772-9756456
> -----------------------------------------------------------
> ________________________________________
> From: Robert Hanson [[email protected]]
> Sent: Monday, October 25, 2010 5:36 PM
> To: [email protected]
> Subject: Re: [Jmol-users] Several questions
>
> I tried:
>
> isosurface plane {0.5, 0, 0, -0.5}
> select within(2.0, plane, {0.5, 0, 0, -0.5})
> selectionhalos on
> select within(-2.0, plane, {0.5, 0, 0, -0.5})
> isosurface hkl {2 0 0}
> select within(-2.0, hkl, {2 0 0})
> select within(2.0, hkl, {2 0 0})
>
> with a polymer example (polymer.out), and it worked just fine.
>
> Can you show me a concrete example that doesn't work for you, Piero?
>
>
>
> On Mon, Oct 25, 2010 at 10:58 AM, P.Canepa <[email protected]<mailto:
> [email protected]>> wrote:
> I tried select WITHIN(distance,planeType, planeDesignation) with slab and
> polymer. This doesn't make difference between negative and positive numbers
> in slab and polymer once defined the plane.
>
> Thanks, Piero
> --
> Please consider the environment before printing this e-mail.
>
> Pieremanuele Canepa
> Room 104
> Functional Material Group
> School of Physical Sciences, Ingram Building,
> University of Kent, Canterbury, Kent,
> CT2 7NH
> United Kingdom
>
> e-mail: [email protected]<mailto:[email protected]>
> mobile: +44 (0) 7772-9756456
> -----------------------------------------------------------
> ________________________________________
> From: Robert Hanson [[email protected]<mailto:[email protected]>]
> Sent: Monday, October 25, 2010 12:02 PM
> To: [email protected]<mailto:
> [email protected]>
> Subject: Re: [Jmol-users] Several questions
>
> On Sun, Oct 24, 2010 at 7:05 PM, P.Canepa <[email protected]<mailto:
> [email protected]><mailto:[email protected]<mailto:[email protected]>>>
> wrote:
>
> Dear all,
>
> I got several questions to ask
>
> 1) I was wondering whether is possible or not to re-set the origin of the
> unitcell. The command set unitcell {1/2 1/2 1/2 } do that. Apparently is
> just a graphical nice feature.In fact, I noticed that whenever I operate an
> expansion of the cell with the command load '' { 2 1 1 } the cell origin is
> always set to 0 0 0. How come ? Is it possible to fix the origin of the
> cell. This becomes particularly useful when user want to change periodical
> properties of crystals.
>
> Because the symmetry operators are based on the unit cell having a specific
> origin. Obviously if you have P1 symmetry it doesn't matter, but that's a
> special case. Changing the unit cell using the UNITCELL command is not just
> for looks. It changes the calculation of atom properties uxyz, ux, uy, and
> uz.
>
>
> 2) I also noticed a possible bug when I use PACKED on 2D slab periodic
> structure, the structure becomes flat loosing all the Z coordinates. I
> didn't try the case od polymer but I suspect is the same.
>
>
> ok, I'll get that fixed.
>
> 3) Is in Jmol any way to select many atoms in one shot ! It would be nice
> having a sort of 2D, 3D graphic selectors. The possibility of drawing line,
> circle and sphere into Jmol to select many atoms contemporaneously would be
> rather useful. This is especially true when the user want for instance
> remove atoms located in the same area or refine a structure before creating
> a snapshot. Secondly the numerical selection available in Jmol is only
> useful when atom are grouped forming sequence. This is not always the case.
>
>
> all this is possible. Check the documentation.
>
> 4) Bob the Z-matrix functions you kindly sent me doesn't work for crystals
> and surfaces. To be precise it works but
> loosing entirely the structure periodicity.Have a try
>
> Are you saying you want to add an atom in every unit cell using internal
> coordinates? Then I think that's up to you to write a specialized set of
> functions that does that. It should be possible. Just increment the final
> atom position by whatever unit cell coordinates you have, and it should
> work.
>
>
>
> Thanks a lot, Piero
> --
> Please consider the environment before printing this e-mail.
>
> Pieremanuele Canepa
> Room 104
> Functional Material Group
> School of Physical Sciences, Ingram Building,
> University of Kent, Canterbury, Kent,
> CT2 7NH
> United Kingdom
>
> e-mail: [email protected]<mailto:[email protected]><mailto:[email protected]
> <mailto:[email protected]>>
> mobile: +44 (0) 7772-9756456
> -----------------------------------------------------------
>
> ------------------------------------------------------------------------------
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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
>
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America
> contest
> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in
> marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> Jmol-users mailing list
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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
>
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America
> contest
> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in
> marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> 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
------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
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